===============================================================================
MANUAL FOR RUNNING THE ACCESSIBILITY PROGRAM OR PREPARING
AN INPUT FILE FOR THE VOLUME PROGRAM
The program is written in VAX-11 FORTRAN which is based on American
National Standard FORTRAN-77 (ANSI X3.9-1978).
It was modified for compilation on UNIX by P.J. Fleming in 1995
Original and earlier versions produced by: B. Lee, F.M. Richards,
T.J. Richmond and J.B. Matthew.
Copywrite (c) Yale University, March 1983
(Please note full copywrite statement in header to the
ACCESS source code. )
Present Version: 1995
Authors: Mark D. Handschumacher and F.M. Richards
References: For a general introduction to molecular areas and volumes
and the principles used in calculating these properties
see:
1) LEE, B. and RICHARDS, F.M., J. Mol. Biol. 55: 379-400 (1971)
The Interpretation of Protein Structures: Estimation of
Static Accessibility
2) RICHARDS, F.M. Ann. Rev. Biophys. Bioeng. 6:151-176 (1977)
Areas, Volumes, Packing and Protein Structure
3) RICHARDS, F.M. Methods in Enzymology 115: 440-464 (1985)
Calculation of Molecular Volumes and Areas for
Structures of known Geometry
For each atom in a list the program ACCESS is designed to
find the surface area in square Angstroms that is accessible to a
probe sphere of a radius specified by the user. The program requires
atom identification data and crystallographic coordinates from an
input file. The present version will accept: 1) the output file from
the Konnert-Hendrickson refinement program, 2) a file from the
Brookhaven Protein Data Bank, or 3) a file prodiced internally during
operation of this program. (The program can be easily modified to
accept other formats). Atom types are identified through residue and
atom names. Van der Waals radii are assigned to each atom on the basis
of atom type. The values are listed in the subroutine RADASN. The data
statements in that program can easily be changed by the user if a
different set of standard values are wanted. Any atoms that cannot be
identified by this subroutine are assigned a default radius of 1.80
angstroms. The radius of the spherical probe may be assigned any value
in the range 0.0 to 9.9. Adjustments to the source program must be
made to accomodate values outside of this range. A water molecule is
commonly assumed to have a radius of 1.40 Angstroms.
The output of the program is a file containing all of the input data
for each atom, the assigned Van der Waals radii, certain internal flags
indicating the atoms included in the calculation, the accessible area
and the contact area. The accessible area is the area in square
Angstroms units of the locus of the center of the probe. The contact
area is the area in square angstroms on the Van der Waals surface of
an atom that can be contacted by the probe.
A companion program, ACCFMT.FOR can be used to create area summaries
by residue type and sequence, including various totals and averages.
(This is not yet modified for UNIX).
[NOTE: The initial part of this program may be used to prepare an output
file to be used as input for the VOLUME program which is a separate
unit. Instructions for this purpose appear at the appropriate place.]
OPERATION:
----------
The user must first have access to a an appropriate input file of
atom and coordinate data. The accessibility program is then initiated
by the command:
access
A series of prompts for input data will then appear as follows:
(You may respond in either upper or lower case).
1) The program will ask you for the NAME of the OUTPUT
FILE. This file will contain information identifying the type of atom
in the list, the coordinates if the atom, the Van der Waals radii used
in the program during the accessibility calculations, and the contact
surface area and accessible surface area. Coordinates and Van der Waals
radii are in angstroms and the surface areas are in square angstroms.
Prompt:
PROGRAM: ACCESS
AUTHORS: MARK HANDSCHUMACHER AND F. M. RICHARDS
VERSION: MARCH 4, 1983
PURPOSE: CALCULATION OF THE ACCESSIBILITY OF THE VAN DER WAALS SURFACE
OF ATOMS TO A PROBE SPHERE OF THE GIVEN RADIUS SPECIFIED BY
THE USER. FOR FURTHER INFORMATION SEE THE MANUAL.
-----------------------------------------------------------------------
WHAT IS THE NAME OF THE OUTPUT FILE;===>--->
Enter: (X)n.XXX
2) You will be asked for the NUMBER of INPUT FILES. You may have
different coordinate files that you prefer to keep separate
except for the running this program. Currently you can specify a
maximum of two input files.
Prompt:
HOW MANY COORDINATE FILES DO YOU WANT TO READ :--->--->
Enter: 1 or 2
3) You will be asked for the NAME(S) of the INPUT FILE(S).
Prompt:
NAME OF COORDINATE FILE (1(or)2):===>--->
Enter: (Y)n.YYY
4) The absolute minimal data neccessary for the program to
function would be a list of three dimensional coordinates x, y, and z.
In this case the default radius would be assigned to all atoms and you
would need some means outside of this program for identifying a given
atom by the record number of the input list. The maximimum amount of
information potentially used in the current version of the program is:
a) chain number
b) sequence number
c) residue name
d) atom name
e) x, y, and z coordinates
f) preassigned Van der Waals radii
g) a flag value of 1, 0, or -1
h) the number of the input file - only useful when more than
one input file is declared.
You will be asked for the FORMAT of the INPUT FILE(S).
The current formats accepted by this program are Konnert - Hendrikson,
BNL PROTEIN DATA BANK, and our own 'Accessibility' format.
The later is a file that contains locations for all the data mentioned
in the above list. You do not need to have the complete
set of data expected by the particular format. It is absolutely
neccessary, however, to match all data that you will use to the
locations designated by the format chosen. An example would be that
you have a list of atoms, with the atom name, residue type, sequence
number and coordinates for each atom. You could write a small program
to place the information in the same columns used in Brookhaven format.
Since you don't have a chain number and you have no need for
temperature factors in any calculation, you can leave the columns that
are designated for that information blank. These two pieces of
information are part of the standard Brookhaven format. The temperature
factor is ignored by this program and while it is possible to
use the chain number to flag certain atoms, it is not required
information
Prompt:
WHAT IS THE FORMAT OF FILE - 1 ( or 2 )
AVAILABLE OPTIONS ARE:
1) "WAH"
2) "BNL"
3) "RAD"
Enter: selected option below
------
WAH
------
5) You will be presented with a sample of the expected format
based on the type you just entered. If all the data fits in the
appropriate columns you are ready to continue and should type "NEXT"
If not, you can type "CHANGE". This will send you back to the begining
at step 1). If it appears that none of the formats you have tried line
up with the sample formats you will have to write your own program to
perform this function. It should be mentioned that the decimal points
of your file do not have to line up with those of the sample.
Prompt:
EXPECTED FORMAT FOR FILE - 1 - IS "WAH"
EXPECTED FORMAT ON TOP LINE
READ FORMAT ON BOTTOM LINE
-------------------------------------------------------------------------------
1 ARG R143NEH1 23456.890 23456.890 23456.890 2345.7890 234.67890 1
1 THR T 1N 69.45647 49.84090 0.79071 29.31636 0.00000
-------------------------------------------------------------------------------
TYPE "CHANGE" IF YOU WANT TO CHANGE FORMAT ASSIGNMENTS
TYPE "NEXT" IF FORMAT IS OK
TYPE "STOP" IF YOU WANT TO EXIT FROM PROGRAM
Enter: command selection below
------
NEXT
------
6) After "NEXT" has been entered at step (5) the program reads
the input file(s), stores all the data into arrays and assigns the
Van der Waals radii. The number of atoms that have been read into the
arrays will be presented. If any atoms have not been found in the
radius assignment subroutine the data associated with that atom will be
displayed with an annotation as to whether the RESIDUE NAME or ATOM
NAME was not found. If you are concerned because atoms have been
assigned default radii you should determine why the atom names or the
residue names were not found and try to correct the problem. This may
mean editing the subroutine responsible for assigning radii to include
a new RESIDUE TYPE or ATOM NAME. It may also mean that the format of
your input file was not aligned with the expected format. Once again,
if everything is satisfactory, you should enter"NEXT" and this will
send you on to step (7).
Prompt:
THE NUMBER OF ATOMS FROM FILE - 1 - = 6612
NUMBER OF ATOMS READ INTO ARRAYS = 6612
NUMBER OF ATOMS ASSIGNED DEFAULT RADII = 0
TYPE "NEXT" IF YOU WANT TO MOVE TO NEXT BLOCK
TYPE "STOP" IF YOU WANT TO EXIT FROM THE PROGRAM
Enter: command selection
------
NEXT
------
7) You will be presented with three options that deal with
which atoms are to be included in the accessibility calculation.
The options "ALLATM" and "PRESET" are explained well enough in the
prompts. The "SUBSET" option is described in a separate section titled
"CREATION OF SUBSETS" (see below).
To allow flexibility and to reduce and eliminate unneccessary
repetition of calcuations a flag system is utilized. Every atom is
assigned an integer FLAG VALUE of -1, 0, or 1. When the flag has a
value of:
# -1, the atom is completely ignored during the accessibility
calculation. This would be the same as omitting the
particular atom from the input coordinate file.
# 0, the area is to be calculated for this atom. The surrounding
consists of all other atoms flagged either "0" or "+1".
# 1, the atom is considered part of the protein environment but no
area calculations will be performed on this atom.
The program will loop through the atoms until an atom has a
flag value 0.
The program then finds all those atoms with a value of 0 or 1 that
fall within the 'touching' distance of the atom whose calculation is
being performed. This distance will vary with the Van der Waals radii
and probe radius chosen.
FLAGS can be used for finding changes in the accessibility of the
protein upon the removal of SUBSTRATE(S) or upon deletion of a section
of the protein. They may also be used if you only have an interest in
the accessibility of certain RESIDUE types or ATOM types and do not
wish to waste time doing the calculation for all atoms in the
coordinate list.
The option "SUBSET" is designed to handle a few of the most logical
flag assignments. If you have something that cannot be handled by the
"SUBSET" flag setting subroutine you can then create your own file
and set the flags as you wish. The file should then be in the
"RAD" format and you should then enter "PRESET" in this step.
The output of this program is acceptable input for the "RAD" format
Van der Waals radii are asssigned and there is a column for the
FLAG VALUES described in this section in addition to the FLAG VALUES
used for the "SUBSET" option.
Prompt:
THERE ARE THREE BASIC OPERATIONS THAT CAN BE PERFORMED
1) ENTERING "ALLATM" WILL CALCULATE THE ACCESSIBLE
SURFACE OF ALL ATOMS READ INTO
THE DATA ARRAYS.
2) ENTERING "SUBSET" WILL ALLOW YOU TO DEFINE A SUBSET
OF ATOMS. IF YOU HAVE AN INTEREST
IN A PARTICULAR GROUP OF ATOMS
THEY CAN BE SPECIFIED RATHER THAN
PRODUCING LENGTHY OUTPUT FILES AND
TAKING UP UNNECCESSARY PROGRAM RUN
TIME. FURTHER INFORMATION WILL BE
PROVIDED IF THIS OPTION IS ENTERED.
3) ENTERING "PRESET" THIS OPTION IS AVAILABLE ONLY IF
THE INPUT FILE(S) WERE OF "RAD"
FORMAT. THIS WILL TAKE THE FLAG
VALUES FROM THIS FILE AND CREATE
THE INDICATED SUBSETS BASED ON THE
STANDARD FLAG VALUES.
Enter: command selection below
------
ALLATM
------
8) After all flags have been set in step (7) the total number
of flagged atoms will be broken down into the number of atoms with each
flag. You will also be presented with the current values for the
PROBE RADIUS and the STEP THICKNESS.
Prompt:
ALL ATOM FLAGS HAVE BEEN SET FOR THE ACCESSIBILITY RUN
------------------------------------------------------
THE NUMBER OF ATOMS TO BE OMMITED ENTIRELY = 0
THE NUMBER OF ATOMS TO BE INCLUDED = 0
THE NUMBER OF ATOMS TO BE CALCULATED = 6612
THE TOTAL NUMBER OF ATOMS = 6612
ENTER "NEXT " IF THIS IS ACCEPTABLE
ENTER "RESET " IF YOU WANT TO REDEFINE THE THE FLAGS
Enter: command selection below
------
NEXT
------
9) The PROBE RADIUS is the radius of the sphere for which the
Van der Waals surface of each atom flagged 0 will be tested. It is
ordinarily assumed that you will be testing for accessibility to water.
We use a standard radius of 1.40 Angstroms for water so this is the
default value. If you want to change the probe radius because you are
testing accessibility to something other than water or have a different
value for water this is where to make the change.
The ZSTEP value will determine the accuracy of the accessibility
calculation. The program finds a given atom whose accessibility is to
be calcuated. Then it finds all the neighboring atoms (rejecting or
including according to FLAG value), and sequentially slices through
the effective spheres of the set of atoms along the z axis. The circle
of intersection of the atom whose accessibility is being calculated is
analyzed to see what arc length of this circle is overlaped by the
intersecting circles of neighboring atoms. The arc distance that
remains is then considered to be accessible to the PROBE. The total
accessibility is calculated by simply summing the arc
distance for all the slices through the particular atom of interest
and multiplying by the distance between the slices. This distance is
designated by the variable ZSTEP. The smaller the ZSTEP the more slices
and the greater the accuracy (also the more computer time). Since
the smallest Van der Waals radii are on the order of 1.10 Angstroms
and the probe will usually be 1.40 Angstroms the diameter of the
smallest effective sphere = 2.0 x (1.40 + 1.10) = 5.0 Angstroms.
With a ZSTEP of 0.25 this would give 20 slices through the sphere.
This is acceptable for most of the conditions for which this program
will be utilized. We recommend that the ZSTEP value be no less than
0.10 and no greater than 0.50 for the reasons of program time and
diminished accuracy respectively.
=======================================================================
If the program "VOLUME" is to be entered, the area calculation need
not be carried out and can be skipped. The output file will have the
same format with or without the area calculation, but in one case it
will contain actual area data and in the other only dummy entries will
occur in the columns for area.
The output file for the normal area calculation contains data only
on those atoms whose area was calculated. When the area calculation is
skipped, the output file contains all of the atoms read from the input
file(s). The flags indicating OMIT, INCLUDE or CALCULATE remain intact.
Thus you may specify subsets of atoms to be used in the VOLUME
calculation just as you do for the AREA calculation.
=======================================================================
Prompt:
------------- ------- -------------------------------------
PROBE = 1.40 RADIUS OF PROBE SPHERE IN ANGSTROMS.
ZSTEP = 0.25 THICKNESS OF CROSSECTIONS THROUGH
ATOMS IN ANGSTROMS.
SKIP = NO = DO THE AREA CALCULATION
YES = DO NOT CALCULATE AREA, EXIT FOR
VOLUME CALCULATION.
(NOTE: use capital letters for YES and NO)
------------- ------- -------------------------------------
ENTER "PROBE " IF YOU WANT TO CHANGE THE PROBE RADIUS
ENTER "ZTEP " IF YOU WANT TO CHANGE THE STEP INCREMENT
ENTER "SKIP " IF YOU WANT TO CHANGE THE STATUS OF THE
SKIP VARIABLE.
ENTER "NEXT " WHEN YOU ARE DONE.
Enter: command selection below
------
NEXT
------
NOTE: The output file from the area calculation may also be used for
program VOLUME.
10) The area calculations are now being performed. During the
interim a few interesting bits of information may flash onto
the screen. This is to make you feel as though something is
actually happening. After every 100 atoms are processed a
message will appear indicating how many atoms have been
calculated. When this run on the SET or SUBSET you have
defined is finished, this will be indicated and you will then
be asked if you want to try another run. This option was implimented
to allow the user to calculate the accessibility of a number
of different SUBSET assignments within a given MAINSET coordinate
list.
XMIN = 24.07699 XMAX = 101.2750 DELTAX = 77.19798
YMIN = -9.452740 YMAX = 72.36063 DELTAY = 81.81337
ZMIN = -5.940830 ZMAX = 62.11293 DELTAZ = 68.05376
THE MAXIMUM RADIUS ASSIGNED TO AN ATOM = 3.400000
COMPLETED 100 ATOMS
COMPLETED 6600 ATOMS
TOTAL NUMBER OF ATOMS WHOSE AREA WAS CALCULATED = 6612
FINISHED WITH ACCESS SUBROUTINE
DO YOU WANT TO TRY ANOTHER CYCLE:("YES" OR "NO")--->
Enter: command selection below
------
NO
------
If you type "YES" you will be returned to STEP (7) otherwise
its been a pleasure, aurevoir, ciao, and I hope its been worth
while.
This program is the first version of an exportable package and
while considerable care has been taken to make running as 'user
friendly' as possible, there may be some problems that haven't
been debugged.
If you have any questions or problems you can contact
F. M. RICHARDS at YALE UNIVERSITY Dept of MOLECULAR BIOPHYSICS &
BIOCHEMISTRY. Try (203)-432-5620.
==============================================================================
ADDITIONAL NOTES:
1)WAH FORMATTED FILES - The format is the same as the standard output
file from KONNERT - HENDRICKSON REFINEMENT. It is assummed that no
header information or remarks are included in these files.
2)BNL FORMATTED FILES - These files usually have a number of lines of
header information dealing with references to papers, crystallographic
parameters, sequence information and other information realted to the
structure. This information is typed on the screen record by record
until a line begining with the word "ATOM " or "HETATM" is found.
The "ATOM" or "HETATM" line should match the sample BROOKHAVEN format.
When the program assigns Van der Waals radii to the atoms an
intermediate file is first created. This file contains only those lines
that have the "ATOM " or "HETATM" keyword in the first six columns
of that line. The program will then read the intermediate file line
by line assigning Van der Waals radii according to atom name and
residue type.
3)RAD FORMATTED FILES - These files are the standard output files of
this program. It is generally recommended that when you work on a given
molecular structure that the accessibility calculation first be
performed on the entire structure. This way you will have an output
file that can be used for a reference file when different subsets are
calculated. You can also use this standard output file as the input
file for future accessibility calculations on any SUBSET specified by
the flags. Since the Van der Waals radii have already been assigned and
are included in the file time can be save by skipping over the radius
assignment section. Also no intermediate file is needed as in the case
of BROOKHAVEN files. The time expended creating and reading from this
file is then eliminated. It is also useful as a reference when subsets
are calculated. You can then compare subset accessibility to the
reference (entire molecule) accessibility. A further advantage is that
if you want to assign special values to atoms or define a subset that
can not be created easily within the program you can edit this
reference file. An example might be that you want to change the Van der
Waals radii of a few individual atoms of a given atom name and residue
type while leaving all the rest at the value assigned in the program.
This would have to be done by editing or creating a file of the "RAD"
format with all the particular values you desire. When this file in
"RAD" FORMAT is read the Van der Waals radius indicated for each atom
is accepted without regard to atom name or residue type. This is
particularly useful when only a few atoms have been assigned default
radii because the radius asignment program wasn't prepared for the
particular residue type or atom name.
3)CREATION OF SUBSETS - There are many different ways for selecting
atoms for input into the accessibility calculation routine. A general
description of the different ways that an atom can be treated by this
routine is described in the FLAG assignment step. The creation of
subsets is done in two basic steps:
1) Defining the flag value to be assigned to the atoms to be
indicated in the second step. To do this you chose among four keywords
1)"OMIT" - assign flag of -1
2)"INCL" - assign flag of 1
3)"CALC" - assign flag of 0
4)"DONE" - no more flag assignments, proceed to next step in program.
If one of the first three options is entered you will be presented
with five different ways to specify what atoms are to be assigned
the particular flag.
1)"FILE" - assign flag if atom came from one of two input files.
This is not available if only one input file was read.
2)"CHAI(N)" - assign flag to an atom if it has the chain number
specified. Many times a molecule will consist of two
separate chains that are identified in the coordinate list.
Two monomers in an asymmetric unit or two subunits in a
dimer are usually identified separately.
3)"ZONE" - assign flag based on a range of the sequence number.
Any atom that has a sequence number greater than or
equal to the starting value entered or less than or equal to
the ending value specified will be assigned the designated
flag. Repeat this operation for as many sequence
pairs as required. Entering the same number twice will
result in the flag assignment to the single residue
specified.
4)"RESI(DUE)" - assign flag to an atom if the residue name is the same
as the one specified. For instance in a protein you may only
be interested in calculating the accessibility of histidine
residues. If you enter the standard three letter notation
"HIS" all histidines will be assigned the flag value
5)"ATOM" - assign flag to an atom if the atom name is the same as the
one specified. This is the same as the "RESI"
option, except that atom types are identified.
6)"SERI(AL) - Assign flag based on a range of serial numbers of atoms
in the coordinate list. An atom of serial number equal to
or greater than the starting value entered or less than or
equal to the ending value entered will be assigned the
designated flag. Repeat through as many serial number pairs
as required. Entering the same number twice will result in
the flag assignment to the single atom specified.
If you have more than one input file you will be asked for the file
number for which flags are to be set.
The ORDER OF OPERATION in setting FLAGS is very important. Any
operation that is performed will overwrite the previouse flag value
assigned to an atom. For example if a zone from 1 to 20 is
assigned a FLAG of -1 by using the "OMIT" flag and the "ZONE"
operation, and then the "CALC" flag is set to a ZONE from 5 to 10.
The end result would be that the ZONE from 1 to 4 is OMITTED, the ZONE
from 5 to 10 is CALCULATED and the ZONE from 11 to 20 is OMITTED.
If CALC was first called for the ZONE from 5 to 10 and the "OMIT" was
called for ZONE 1 to 10 all the atoms associated with residues 1 to
10 would be OMITTED.
===============================================================================
APPENDICES
A) SHORT FORM INTRODUCTION
--------------------------
Summary of Program Startup and Input/Output
1) NAME OF OUTPUT FILE: (X)n.XXX
2) NUMBER OF COORDINATE FILES 1 or 2
3) NAME OF COORDINATE FILE(S) (Y)n.YYY
4) FORMAT OF INPUT FILE: "WAH" Konnert - Hendrickson
"BNL" Brookhaven Data Bank
"RAD" output of this program
5) INPUT FILE FORMAT CHECK: "CHANGE" go to step (2)
"NEXT " continue to next block
"STOP " exit from program
6) PROGRAM READS INPUT FILE(S)
LOADS INTERNAL ARRAYS AND
ASSIGNS VAN DER WAALS RADII
SUMMARY OF OPERATION GIVEN:
"NEXT " continue to next block
"STOP " exit from program
7) PREPARATION OF KEY ARRAY
FLAG ASSIGNMENTS TO ATOMS:
"ALLATM" calculate all atoms
"PRESET" keep existing flags
"SUBSET" define subset of atoms
"OMIT" omit atom
"INCL(UDE)" include atom
"CALC(ULATE" calculate atom
"DONE" enter when done
"FILE"
file #
"CHAIN"
chain #
"ZONE"
begining sequence #
ending sequence #
"RESI(DUE)"
residue name
.
.
enter "END "
"ATOM"
atom name
.
.
enter "END "
"SERI(AL)
begining serial #
ending serial #
8) SUMMARY OF ATOM FLAGS:
"RESET " go back to step (7)
"NEXT " go to next block
9) REDEFINE PARAMETERS: "PROBE " change the probe radius
"ZSTEP " change the step increment
"SKIP "
"NO " do area calculation
"YES" skip area calculation and
make VOLUME output file.
"NEXT " do calculations and create
output files
10) MAKE ANOTHER RUN "YES" go back to step (7)
"NO " stop program and close output
file.
===============================================================================
SAMPLE FORMATS OF INPUT FILE(S) AND OUTPUT FILE(S)
1)KONNERT - HENDRIKSON FORMAT
------------------------------------------------------------------------------
1 ASN N 24CA -32.94390 -9.02940 -2.14060 20.00000 0.00000
1 ASN N 24N -32.80980 -7.59900 -2.82170 30.00000 0.00000
1 ASN N 24C -32.40750 -8.76120 -0.77840 22.00000 0.00000
1 ASN N 24O -31.37940 -7.46490 -0.29190 20.00000 0.00000
1 ASN N 24CB -32.22870 -9.78930 -3.11360 10.00000 0.00000
1 ASN N 24CG -30.53010 -8.94000 -3.21090 6.00000 0.00000
1 ASN N 24OD1 -29.94900 -8.31420 -4.37850 16.00000 0.00000
1 ASN N 24ND2 -29.63610 -8.35890 -2.14060 14.00000 0.00000
1 TYR Y 25CA -32.31810 -10.05750 1.26490 12.00000 0.00000
1 TYR Y 25N -32.85450 -10.01280 -0.09730 16.00000 0.00000
1 TYR Y 25C -30.61950 -9.02940 1.45950 18.00000 0.00000
1 TYR Y 25O -30.08310 -8.04600 2.33520 14.00000 0.00000
1 TYR Y 25CB -32.98860 -11.75610 1.45950 26.00000 0.00000
1 TYR Y 25CG -32.13930 -12.02430 2.52980 22.00000 0.00000
1 TYR Y 25CD1 -32.58630 -11.97960 3.79470 22.00000 0.00000
1 TYR Y 25CD2 -30.97710 -12.29250 2.23790 30.00000 0.00000
1 TYR Y 25CE1 -31.87110 -12.38190 4.86500 30.00000 0.00000
1 TYR Y 25CE2 -29.99370 -12.15840 3.21090 30.00000 0.00000
1 TYR Y 25CZ -30.57480 -12.42660 4.57310 30.00000 0.00000
1 TYR Y 25OH -29.63610 -12.42660 5.64340 30.00000 0.00000
1 CYS C 26CA -28.02690 -8.09070 0.48650 6.00000 0.00000
-------------------------------------------------------------------------------
2) BROOKHAVEN DATA BANK FORMAT
-------------------------------------------------------------------------------
HEADER ELECTRON TRANSPORT (HEME PROTEIN) 01-JUL-80 4CYT 4CYT 3
COMPND CYTOCHROME $C (REDUCED) 4CYT 4
SOURCE ALBACORE TUNA (THUNNUS ALALUNGA) HEART 4CYT 5
AUTHOR T.TAKANO 4CYT 6
JRNL AUTH T.TAKANO,R.E.DICKERSON 4CYT 7
JRNL TITL REDOX CONFORMATION CHANGES IN REFINED TUNA 4CYT 8
JRNL TITL 2 CYTOCHROME $C 4CYT 9
JRNL REF TO BE PUBLISHED 4CYT 10
JRNL REFN 353 4CYT 11
REMARK 1 4CYT 12
REMARK 1 REFERENCE 1 4CYT 13
REMARK 1 AUTH T.TAKANO,R.E.DICKERSON 4CYT 14
REMARK 1 TITL CONFORMATIONAL DIFFERENCES BETWEEN FERRI- AND 4CYT 15
REMARK 1 TITL 2 FERROCYTOCHROME $C 4CYT 16
REMARK 1 REF TO BE PUBLISHED 4CYT 17
.
.
.
REMARK 2 4CYT 57
REMARK 2 RESOLUTION. 1.5 ANGSTROMS. 4CYT 58
REMARK 3 4CYT 59
REMARK 3 REFINEMENT. SIMULTANEOUS MINIMIZATION OF ENERGY AND 4CYT 60
REMARK 3 R-FACTOR (SEE A.JACK,M.LEVITT, ACTA CRYST., V. A34, 4CYT 61
REMARK 3 P. 931, 1978). 4CYT 62
REMARK 4 4CYT 63
REMARK 4 STANDARD PROTEIN DATA BANK PROCEDURE IS TO USE A NULL 4CYT 64
REMARK 4 (BLANK) CHARACTER FOR THE CHAIN INDICATOR IN STRUCTURES 4CYT 65
REMARK 4 COMPRISING ONLY ONE CHAIN. IN THIS CASE THE CHARACTER R 4CYT 66
REMARK 4 (FOR REDUCED) WAS USED TO CONFORM TO THE DEPOSITOR*S 4CYT 67
REMARK 4 PUBLICATIONS AND TO EMPHASIZE THE RELATIONSHIP BETWEEN THIS 4CYT 68
REMARK 4 STRUCTURE AND THE OXIDIZED FORM WHICH IS AVAILABLE FROM THE 4CYT 69
REMARK 4 PROTEIN DATA BANK AS ENTRY 3CYT. 4CYT 70
REMARK 5 4CYT 71
REMARK 5 STRUCTURE FACTOR DATA FROM THIS ANALYSIS ARE AVAILABLE FROM 4CYT 72
REMARK 5 THE PROTEIN DATA BANK AS A SEPARATE ENTRY (R4CYTSF). 4CYT 73
REMARK 6 4CYT 74
REMARK 6 THE TRANSFORMATION WHICH WILL PLACE THE COORDINATES OF 4CYT 75
REMARK 6 THIS (REDUCED) MOLECULE INTO BEST ALIGNMENT WITH THOSE OF 4CYT 76
REMARK 6 THE OXIDIZED INNER MOLECULE IN THE SPACE OF THE LATTER IS 4CYT 77
REMARK 6 GIVEN BELOW 4CYT 78
REMARK 6 .2868 .8127 -.5072 47.2662 4CYT 79
REMARK 6 .5553 -.5724 -.6033 17.5577 4CYT 80
REMARK 6 -.7806 -.1086 -.6155 16.3160 4CYT 81
REMARK 7 4CYTA 12
REMARK 7 CORRECTION. INSERT NEW PUBLICATION AS REFERENCE 3 AND 4CYTA 13
REMARK 7 RENUMBER SUCCESSIVE REFERENCES. 04-DEC-80. 4CYTA 14
SEQRES 1 R 104 ACE GLY ASP VAL ALA LYS GLY LYS LYS THR PHE VAL GLN 4CYT 82
SEQRES 2 R 104 LYS CYS ALA GLN CYS HIS THR VAL GLU ASN GLY GLY LYS 4CYT 83
SEQRES 3 R 104 HIS LYS VAL GLY PRO ASN LEU TRP GLY LEU PHE GLY ARG 4CYT 84
SEQRES 4 R 104 LYS THR GLY GLN ALA GLU GLY TYR SER TYR THR ASP ALA 4CYT 85
SEQRES 5 R 104 ASN LYS SER LYS GLY ILE VAL TRP ASN ASN ASP THR LEU 4CYT 86
SEQRES 6 R 104 MET GLU TYR LEU GLU ASN PRO LYS LYS TYR ILE PRO GLY 4CYT 87
SEQRES 7 R 104 THR LYS MET ILE PHE ALA GLY ILE LYS LYS LYS GLY GLU 4CYT 88
SEQRES 8 R 104 ARG GLN ASP LEU VAL ALA TYR LEU LYS SER ALA THR SER 4CYT 89
HET HEM R 1 43 PROTOPORPHYRIN IX CONTAINS FE(II) 4CYT 90
FORMUL 2 HEM C34 H34 N4 O4 FE1 ++ 4CYT 91
FORMUL 3 HOH *54(H2 O1) 4CYT 92
HELIX 1 NR ASP R 2 CYS R 14 1 4CYT 93
HELIX 2 50R THR R 49 LYS R 55 1 4CYT 94
HELIX 3 60R ASN R 60 GLU R 69 1 4CYT 95
HELIX 4 70R GLU R 69 ILE R 75 1 INCOMPLETE DUE TO PRO 76 4CYT 96
HELIX 5 CR LYS R 87 THR R 102 1 4CYT 97
TURN 1 T1R GLU R 21 GLY R 24 TYPE II 3(10) 4CYT 98
TURN 2 T2R LEU R 32 LEU R 35 TYPE II 3(10) 4CYT 99
TURN 3 T3R LEU R 35 ARG R 38 TYPE II 3(10) 4CYT 100
TURN 4 T4R ALA R 43 TYR R 46 TYPE II 3(10) 4CYT 101
TURN 5 T5R ILE R 75 THR R 78 TYPE II 3(10) 4CYT 102
CRYST1 37.330 87.100 34.440 90.00 90.00 90.00 P 21 21 2 4 4CYT 103
ORIGX1 1.000000 0.000000 0.000000 0.00000 4CYT 104
ORIGX2 0.000000 1.000000 0.000000 0.00000 4CYT 105
ORIGX3 0.000000 0.000000 1.000000 0.00000 4CYT 106
SCALE1 .026788 0.000000 0.000000 0.00000 4CYT 107
SCALE2 0.000000 .011481 0.000000 0.00000 4CYT 108
SCALE3 0.000000 0.000000 .029036 0.00000 4CYT 109
ATOM 1 C ACE R 0 -4.908 -1.959 10.948 1.00 26.26 4CYT 110
ATOM 2 O ACE R 0 -5.892 -2.598 10.550 1.00 23.47 4CYT 111
ATOM 3 CH3 ACE R 0 -4.713 -.521 10.460 1.00 18.24 4CYT 112
.
.
.
ATOM 800 O SER R 103 1.518 -5.558 28.026 1.00 29.45 4CYT 909
ATOM 801 CB SER R 103 4.397 -3.919 27.306 1.00 32.25 4CYT 910
ATOM 802 OG SER R 103 3.511 -3.293 26.400 1.00 24.64 4CYT 911
ATOM 803 OXT SER R 103 2.573 -4.368 29.502 1.00 40.45 4CYT 912
TER 804 SER R 103 4CYT 913
HETATM 805 FE HEM R 1 10.847 -15.938 15.534 1.00 7.22 4CYT 914
HETATM 806 CHA HEM R 1 13.726 -14.615 16.758 1.00 11.33 4CYT 915
HETATM 807 CHB HEM R 1 9.227 -12.941 15.857 1.00 15.40 4CYT 916
.
.
.
CONECT 624 623 625 805 4CYT1014
CONECT 805 137 624 810 821 4CYT1015
.
.
.
CONECT 846 845 4CYT1057
CONECT 847 845 4CYT1058
MASTER 79 0 1 5 0 5 0 6 900 1 48 8 4CYTA 15
END 4CYT1060
-------------------------------------------------------------------------------
3) "RAD" FORMAT INPUT FILE (EQUIVALENT TO FORMAT OF OUPUT FILE)
-------------------------------------------------------------------------------
ACCESSIBILITY PROGRAM BY MARK HANDSCHUMACHER AND F.M. RICHARDS - 5/4/83
OUTPUT FILE NAME: SAMPLE.ACC
INPUT FILE NUMBER: 1 FILE NAME: SAMPLE.WH
ATMTYP = NAME ASSOCIATED WITH PARTICULAR ATOM TYPE
RCOV = COVALENT RADIUS OF ATOM TYPE
RVDW = VAN DER WAALS RADIUS OF ATOM TYPE
ATMTYP DESCRIPTION RCOV RVDW
------ ---------------------- ------ ------
C4 C - TETRAHEDRAL - 0 H 0.77 0.00
C4H C - TETRAHEDRAL - 1 H 0.77 2.00
C4HH C - TETRAHEDRAL - 2 H 0.77 2.00
C4HHH C - TETRAHEDRAL - 3 H 0.77 2.00
C3 C - TRIGONAL - 0 H 0.77 1.70
C3H C - TRIGONAL - 1 H 0.77 1.85
C3HH C - TRIGONAL - 2 H 0.77 1.85
O1 O - CARBONYL - 0 H 0.66 1.40
O2H O - HYDROXYL - 1 H 0.66 1.60
O1O2H O - CARBOXYL -1/2 H 0.66 1.50
N4 N - TETRAHEDRAL - 0 H 0.70 0.00
N4H N - TETRAHEDRAL - 1 H 0.70 2.00
N4HH N - TETRAHEDRAL - 2 H 0.70 2.00
N4HHH N - TETRAHEDRAL - 3 H 0.70 2.00
N3 N - TRIGONAL - 0 H 0.70 1.50
N3H N - TRIGONAL - 1 H 0.70 1.70
N3HH N - TRIGONAL - 2 H 0.70 1.80
S2 S - DIVALENT - 0 H 1.04 1.85
S2H S - SULFHYDRYL - 1 H 1.04 2.00
P4 P - PENTAVALENT - 0 H 1.10 0.00
O1N3HH A - (O OR N) - 0.68 1.60
Z2ION ZN- PLUS 2 ION - 0.74 0.74
FE FE- HEME IRON - 0.70 1.70
------ ---------------------- ------ ------
NUMBER OF ATOMS READ FROM INPUT FILE(S) = 21
NUMBER OF ATOMS ASSIGNED DEFAULT RADII = 0
SETTYP ALLATM
X MIN = -32.989 X MAX = -28.027 DELTA X = 4.962
Y MIN = -12.427 Y MAX = -7.465 DELTA Y = 4.962
Z MIN = -4.378 Z MAX = 5.643 DELTA Z = 10.022
NUMBER OF ATOMS CALCULATED = 21
NUMBER OF ATOMS INCLUDED = 0
NUMBER OF ATOMS OMMITED = 0
MINIMUM EFFECTIVE RADIUS = 2.80
MAXIMUM EFFECTIVE RADIUS = 3.40
PROBE RADIUS = 1.400
STEP INTERVAL = 0.250
KEY = PROGRAM FLAG: "OMIT", "INCLUDE", "CALCULATE"
INDEX = SERIAL NUMBER OF ATOM
IC = CHAIN NUMBER
IF = FILE NUMBER
ATM = ATOM TYPE
RES = RESIDUE TYPE
NUM = SEQUENCE NUMBER
X,Y,Z = ATOM COORDINATES
VDW = VAN WAALS RADIUS OF ATOM
COV = COVALENT RADIUS OF ATOM
AAREA = SURFACE AREA OF CONTACT IN SQUARE ANGSTROMS
OF THE PROBE WITH THE EFFECTIVE SURFACE
CAREA = SURFACE AREA OF CONTACT IN SQUARE ANGSTROMS
OF THE PROBE WITH THE VAN DER WAALS SURFACE
FRCT = FRACTIONAL ACCESSIBILITY (NOT IN USE)
KEY INDEX IC IF ATM RES NUM X Y Z VDW COV AAREA CAREA FRCT
-- ----- -- -- -------- --- ------- ------- ------- ---- ---- ----- ----- ----
BEGIN
0 1 1 1 CA ASN 24 -32.944 -9.029 -2.141 2.00 0.77 18.7 6.5 0.00
0 2 1 1 N ASN 24 -32.810 -7.599 -2.822 1.70 0.70 38.2 11.5 0.00
0 3 1 1 C ASN 24 -32.408 -8.761 -0.778 1.70 0.77 3.4 1.0 0.00
0 4 1 1 O ASN 24 -31.379 -7.465 -0.292 1.40 0.66 15.5 3.9 0.00
0 5 1 1 CB ASN 24 -32.229 -9.789 -3.114 2.00 0.77 45.5 15.7 0.00
0 6 1 1 CG ASN 24 -30.530 -8.940 -3.211 1.70 0.77 5.6 1.7 0.00
0 7 1 1 OD1 ASN 24 -29.949 -8.314 -4.378 1.40 0.66 38.3 9.6 0.00
0 8 1 1 ND2 ASN 24 -29.636 -8.359 -2.141 1.80 0.70 22.0 7.0 0.00
0 9 1 1 CA TYR 25 -32.318 -10.057 1.265 2.00 0.77 13.7 4.8 0.00
0 10 1 1 N TYR 25 -32.854 -10.013 -0.097 1.70 0.70 5.0 1.5 0.00
0 11 1 1 C TYR 25 -30.619 -9.029 1.459 1.70 0.77 0.1 0.0 0.00
0 12 1 1 O TYR 25 -30.083 -8.046 2.335 1.40 0.66 26.7 6.7 0.00
0 13 1 1 CB TYR 25 -32.989 -11.756 1.459 2.00 0.77 39.4 13.6 0.00
0 14 1 1 CG TYR 25 -32.139 -12.024 2.530 1.70 0.77 0.2 0.1 0.00
0 15 1 1 CD1 TYR 25 -32.586 -11.980 3.795 1.85 0.77 24.3 7.9 0.00
0 16 1 1 CD2 TYR 25 -30.977 -12.292 2.238 1.85 0.77 21.4 6.9 0.00
0 17 1 1 CE1 TYR 25 -31.871 -12.382 4.865 1.85 0.77 38.0 12.3 0.00
0 18 1 1 CE2 TYR 25 -29.994 -12.158 3.211 1.85 0.77 24.9 8.1 0.00
0 19 1 1 CZ TYR 25 -30.575 -12.427 4.573 1.70 0.77 3.6 1.1 0.00
0 20 1 1 OH TYR 25 -29.636 -12.427 5.643 1.60 0.66 53.5 15.2 0.00
0 21 1 1 CA CYS 26 -28.027 -8.091 0.486 2.00 0.77 71.9 24.9 0.00
-------------------------------------------------------------------------------
TYPICAL OUTPUT OF AN AREA FILE FROM ACCESS (above) PRODUCED
BY THE PROGRAM ACCFMT
(This has not been modified for UNIX yet).
-------------------------------------------------------------------------------
**************************************************
RUN : 15-JUN-88 14:55:17
**************************************************
PROGRAM ACCFMT
FORMATTED OUTPUT BY RESIDUE TYPE
OF AREA FILE FROM PROGRAM ACCESS
**************************************************
INPUT FILE NAME = 1PCY.DAT
OUTPUT FILE NAME = 1PCY.ARE
**************************************************
ATOM SEARCH STOPPED AT THE FOLLOWING ENTRY
U CU 1
NO MATCH FOR RESIDUE TYPE
**************************************************
GLY N CA C O MAIN SIDE TOTAL
6 0.0 0.0 0.0 0.0 0.0 0.0 0.0
10 1.5 20.1 1.9 13.5 37.0 0.0 37.0
24 0.0 22.7 0.0 15.6 38.3 0.0 38.3
34 0.0 16.9 0.0 0.0 16.9 0.0 16.9
49 1.6 41.2 2.1 27.9 72.8 0.0 72.8
67 0.0 17.8 2.5 15.0 35.3 0.0 35.3
78 0.0 23.2 0.0 0.0 23.2 0.0 23.2
89 4.4 40.6 2.5 25.5 73.0 0.0 73.0
91 0.0 22.8 0.0 8.1 30.9 0.0 30.9
94 0.0 5.0 0.9 0.9 6.8 0.0 6.8
AVE 0.8 21.0 1.0 10.6 33.4 0.0 33.4
ALA N CA C O CB MAIN SIDE TOTAL
7 0.0 0.0 0.0 0.0 15.4 0.0 15.4 15.4
13 0.0 0.0 0.0 0.0 16.7 0.0 16.7 16.7
33 0.0 0.4 0.0 0.0 12.6 0.4 12.6 13.0
52 0.0 0.0 0.0 0.0 6.2 0.0 6.2 6.2
65 0.0 0.0 0.0 0.0 41.0 0.0 41.0 41.0
73 3.0 0.0 0.0 11.7 24.7 14.7 24.7 39.4
90 0.6 6.1 0.6 3.1 14.2 10.4 14.2 24.6
AVE 0.5 0.9 0.1 2.1 18.7 3.6 18.7 22.3
--------------
PRO N CA C O CB CG CD MAIN SIDE TOTAL
16 0.0 4.4 0.0 0.0 26.8 5.9 3.5 4.4 36.2 40.6
23 0.0 0.0 0.4 1.6 14.3 3.2 0.1 2.0 17.6 19.6
36 0.0 0.0 0.0 0.5 0.6 16.9 36.8 0.5 54.3 54.8
47 0.0 3.9 0.0 0.0 5.8 0.4 0.0 3.9 6.2 10.1
86 0.0 14.6 0.5 16.9 32.8 1.0 0.9 32.0 34.7 66.7
AVE 0.0 4.6 0.2 3.8 16.1 5.5 8.3 8.6 29.8 38.4
---------------
THR N CA C O CB OG1 CG2 MAIN SIDE TOTAL
69 2.5 0.0 0.0 16.0 0.4 21.9 20.0 18.5 42.3 60.8
97 0.0 0.0 0.0 0.0 1.1 5.3 16.1 0.0 22.5 22.5
AVE 1.3 0.0 0.0 8.0 0.8 13.6 18.1 9.3 32.4 41.7
---------------
ASP N CA C O CB CG OD1 OD2 MAIN SIDE TOTAL
2 0.0 0.0 0.0 0.0 4.7 0.5 29.0 16.6 0.0 50.8 50.8
8 1.2 3.1 0.4 27.9 28.2 3.7 5.9 22.7 32.6 60.5 93.1
9 0.8 11.4 2.5 25.7 39.7 2.5 0.0 37.9 40.4 80.1 120.5
42 0.0 2.5 0.0 0.0 0.0 2.1 4.6 28.7 2.5 35.4 37.9
44 0.0 5.0 0.0 17.5 14.0 3.8 38.3 33.9 22.5 90.0 112.5
51 1.8 4.0 0.0 0.0 18.5 3.4 25.6 9.2 5.8 56.7 62.5
61 0.0 7.1 0.0 0.0 10.0 3.0 28.3 14.8 7.1 56.1 63.2
AVE 0.5 4.7 0.4 10.2 16.4 2.7 18.8 23.4 15.8 61.4 77.2
----------------
**************************************************
GRAND TOTALS: MAIN CHAIN = 881.9
SIDE CHAIN = 3084.0
ALL = 3965.9
**************************************************