Contact analysis (ANACON)

Introduction.

Using WHAT IF atomic contact analysis can be done in many different ways. Throughout the WHAT IF menus you will find contact analysis related options. The HBONDS menu deals with the special class of contacts called hydrogen bonds. This menu, activated with the ANACON command, holds a set of options to analyze contacts within one molecule or between molecules that are present in the soup. See the SYMTRY menu if you want to include symmetry contacts.

There are two ways to visualize contacts. The first one simply lists, and indicates with dashed lines at the screen, all atomic contacts. The second way of looking at contacts is more complicated, and utilizes a 2D-plot. The main principle is that you create a two dimensional contact plot, and that you can than analyze the local structures by picking the square in the contact map that belongs with the contact you are interested in.

You will often be prompted for a "Maximal allowed Van der Waals radius limit" or something related. This is the distance between the Van der Waals radii that is maximally allowed between two atoms in order to be called in contact. If you, for example, put this distance at 0.5 Angstrom, two carbons (Carbon has a default Van der Waals radius of 1.8 Angstrom) are still called in contact if they are 2*1.8+0.5=4.1 Angstrom away from each other.

Graphical contact analysis

Evaluating the hand of structures (CONHAN)

The command CONHAN does roughly the same as the command CONRES. It draws squares for contacting residues. The difference is that CONHAN gives the whole square one color. This color is a function of the local chiralities of the two contacting residues. Red means negative hand; Green positive; and Blue means no noticeable hand. You will be prompted for the contact distance and for the chirality cutoff. With this parameter you will have to experiment a little. The suggested cutoff is 10.0.

As usual you will be prompted for the mol-object number and the mol-item name. After typing go this plot is just as pickable as all other contact plots.

Analyzing residue contacts (CONRES)

The command CONRES will make WHAT IF loop over both ranges. It will then search for all inter range residue pairs that have at least one atom pair within contact distance (you will be prompted for that distance). For every pair it will draw a square. The dimensions of the square are either proportional with the number of atoms in the residues, or homogeneous, depending on the program parameters. The left and upper line of the square get the color of the alpha carbon of the residue in the second (vertical) range. The right and bottom line get the color of the alpha carbon of the residue in the first (horizontal) range.

Analyzing atomic contacts (CONATM)

The command CONATM does the same as the command CONRES (see above). However, on top of that, it will fill the squares with little squares that are indicative of the individual atomic contacts. For all pairs of inter range atoms that are within contact distance a little square will be put in the residue square. The same coloring rules as for the residue square are used for the atomic squares.

Analyzing residue contacts (RSCACA)

The CONRES command depends a bit on the side chain conformations. If the sidechain gets another rotamer, different contacts will be found. Sometimes this is not desirable. For such cases the options RSCACA and RSCBCB exist. The command RSCACA will make WHAT IF loop over two ranges you are prompted for. It will then search for all inter C-alpha - C-alpha distances that are shorter than a cutoff you will be prompted for. Each such pair will be represented by a square. The dimensions of the square are either proportional with the number of atoms in the residues, or homogeneous, depending on the program parameters. The left and upper line of the square get the color of the alpha carbon of the residue in the second (vertical) range. The right and bottom line get the color of the alpha carbon of the residue in the first (horizontal) range.

Analyzing residue contacts (RSCBCB)

The command RSCBCB functions virtually identical as the RSCACA command. The only difference is that C-beta - C-beta distances will be used instead of C-alpha - C-alpha distances.

Counting contacts

Counting residue contacts (CNTRES)

The command CNTRES will list all residues from the first range, and give for all of them the number of residues in the second range that have at least one atom within the given distance cutoff.

Counting atomic contacts (CNTATM)

The command CNTATM will list all residues from the first range, and give for each of them the number of atoms in the second range that are within the given distance cutoff of at least one atom in the residue in the first range.

Other contact related options

All options that list contacts in the text window use roughly the same output format. Typically such output looks like (some blank columns are remove here, to make the output fit on the page...):
1   59 ASP  (  59 ) E  OD1 <>  57 ASP  (  57 ) E    OD2  D= 2.603  H-ene=   --   (S-S)
2   59 ASP  (  59 ) E  OD1 <>  59 ASP  (  59 ) E    N    D= 2.718  H-ene=  0.31  (S-B) 
3   59 ASP  (  59 ) E  OD1 <>  59 ASP  (  59 ) E    CA   D= 2.771  H-ene=   --   (S-B)
4   59 ASP  (  59 ) E  OD1 <>  59 ASP  (  59 ) E    C    D= 3.001  H-ene=   --   (S-B)
5   59 ASP  (  59 ) E  OD1 <>  61 GLN  (  61 ) E    N    D= 3.219  H-ene=  0.55  (S-B) 
6   59 ASP  (  59 ) E  OD1 <> 322  CA  ( 319 )     CA    D= 2.296  H-ene=   --   (S-B)
7   59 ASP  (  59 ) E  OD1 <> 327 HOH  (HOH  )      482  D= 2.979  H-ene=  0.60  (S-W)
*1  *2  *3     *4  *5   *6     *7  *8     *9  *10  *11      *12        *13        *14
1) Contact counter

2) Residue number of first contact partner.

3) Residue type of first contact partner.

4) PDB number of first contact partner.

5) Chain identifier of the first contact partner.

6) First of the two atoms making the contact. In case of water, the number of the water in its group is listed rather than the redundant atom type oxygen.

7) Residue number of second contact partner.

8) Residue type of second contact partner.

9) PDB number of second contact partner.

10) Chain identifier of the second contact partner.

11) Second of the two atoms making the contact. In case of water, the number of the water in its group is listed rather than the redundant atom type oxygen.

12) Distance between the two contacting atoms.

13) In case of hydrogen bonds, the quality of this hydrogen bond. 0.0 or -- means that there is no hydrogen bond. 1.0 is a perfevt hydrogen bond.

14) What kind of atoms make the contact: (B-B) both partners sit in backbone; (B-S) first partner sit in backbone, second in side chain, etc.

In case you use symmetry related molecules, the number of the symmetry matrix that had to be used to find the contact is listed between 13 and 14.

Listing contact analysis (CONTAC)

The command CONTAC allows you to list all contacts between the two ranges set. A contact is defined as two atoms who's Van der Waals surfaces come within X Angstrom. You will be prompted for X. If the appropriate parameter has been set (see chapter on parameters) then dotted lines will be drawn in the graphics window between all contacting atoms. Every contact will only be listed once. You are asked (if it is possible) if you want symmetry to be used for the second range. If you say yes, the second range will be replaced by all symmetry related residues of the residues that you gave as second range.

Listing contact analysis (CONDBL)

The command CONDBL allows you to list all contacts between the two ranges set. A contact is defined as two atoms who's Van der Waals surfaces come within X Angstrom. You will be prompted for X. If the appropriate parameter has been set (see chapter on parameters) then dotted lines will be drawn in the graphics window between all contacting atoms. All contacts will be listed in both directions. So, for any residue all contacts will be listed. This means that all contacts will normally be printed twice.

Listing contacts (CONTYP)

The command CONTYP allows you to list all contacts between the two ranges set. Rather then the CONTAC option, you will not get ALL contacts, but only those between the residues and atoms you asked for. You will be prompted first for the residues in the first range to be used, and then for the atoms in those residues. If you only gave one residue type, you can specify individual atoms. If you gave more residues, you can only answer `main chain` or `side chain`, or take all atoms by just hitting return. Thereafter you will be prompted the same way for the residues and atoms in the second range. Then the contacts will be listed, and drawn at the screen.

A contact is defined as two atoms who's Van der Waals surfaces come within X Angstrom. You will be prompted for X. If the graphics screen is present, dotted lines will be drawn between all contacting atoms.

Listing contacts (CONTPS)

The command CONTPS allows you to list all contacts between the two ranges set. Rather then the CONTAC option, you will not get ALL contacts, but only those between the residues you asked for. You will be prompted first for the residues in the first range to be used, thereafter you will be prompted the same way for the residues in the second range. Then the contacts will be listed, and drawn at the screen.

A contact is defined as two atoms who's Van der Waals surfaces come within X Angstrom. You will be prompted for X. If the graphics screen is present, dotted lines will be drawn between all contacting atoms.

Bump analysis (BUMPS)

The command BUMPS allows you to list all bumps between the two ranges set. A bump is defined as two atoms who's Van der Waals surfaces overlap more than X Angstrom. You will be prompted for X. The default value for X is 0.25 A. Several cases are treated special, for example, bumps within one residue are not listed, and bumps of a cysteine with the sidechain of its partner in a cys-cys bridge is are based on statistically derived distances rather than on the sum of the Van der Waals radii. If a graphics screen is present, then dotted lines will be drawn between all bumping atoms. I

Listing all contacts of one atom (LSTATC)

This option will prompt you first for one atom in one residue and second for residue ranges. All contacts between the one selected atom and all atoms in the given ranges will be listed. The output typically looks like:
1   59 ASP  (  59 ) E  OD1 <>  57 ASP  (  57 ) E    OD2  D= 2.603  H-ene=   --   (S-S)
2   59 ASP  (  59 ) E  OD1 <>  59 ASP  (  59 ) E    N    D= 2.718  H-ene=  0.31  (S-B) 
3   59 ASP  (  59 ) E  OD1 <>  59 ASP  (  59 ) E    CA   D= 2.771  H-ene=   --   (S-B)
4   59 ASP  (  59 ) E  OD1 <>  59 ASP  (  59 ) E    C    D= 3.001  H-ene=   --   (S-B)
5   59 ASP  (  59 ) E  OD1 <>  61 GLN  (  61 ) E    N    D= 3.219  H-ene=  0.55  (S-B) 
6   59 ASP  (  59 ) E  OD1 <> 322  CA  ( 319 )     CA    D= 2.296  H-ene=   --   (S-B)
7   59 ASP  (  59 ) E  OD1 <> 327 HOH  (HOH  )      482  D= 2.979  H-ene=  0.60  (S-W)
*1  *2  *3     *4  *5   *6     *7  *8     *9  *10  *11      *12        *13        *14

Tabulating bumps (BMPTAB)

The command BMPTAB will cause WHAT IF to prompt you for a range of residues, a table number and a table name. Thereafter you are asked for a second range. The total 'bump' value for the residues in the first range will be stored in the table. WHAT IF will ask you if you want to use symmetry. If you do want to use symmetry (see USESYM in the chapter on symmetry) symmetry related copies of the second range will be used in addition to the normal range. (This in contrast to the CONTAC and BUMPS option where you can use either the normal second range, or its symmetry partners, but not both at the same time.

Showing salt bridges (SHOSBR)

The command SHOSBR will cause WHAT IF to search for salt-bridges. A salt-bridge is defined as a basic nitrogen and an acidic oxygen being 'near' each other. 'Near' has a default of 4.5 A Angstrom between their atom centers, but can be changed because WHAT IF prompts you for it. You will also be prompted for a decision on histidines. They can either be considered as basic, or being left out of the determination.

Parameter options

Changing parameters (PARAMS)

The command PARAMS brings you in the menu from which you can change the parameters relevant for the ANACON option.

There are ten parameters that can be changed to influence what the pictures at the screen will look like. The user changes these parameters by name. They are called:

BOXTYP = Type of contact boxes used
FRMCOL = Colour of frame around plot
SEQCOL = Colour of sequence characters in frame
NEICOL = Colour of neighboring residues after picking
LABCOL = Colour of labels after picking
CACFLG = Flag for making Ca-crosses or not
1O3FLG = Flag for one or three letter code residues
HOFFLG = Flag to skip lower triangle
CACCOL = Colour of Ca-crosses in squares
CONLIN = Display lines in CONTAC, BUMPS, etc., or not

(BOXTYP)

The contact boxes can be perfect aquares (BOXTYP=1) or have the lengths of their axes as function of the number of atoms in the residues that make the contact they represent (BOXTYP=0). In case BOXTYP=0, the residues can no longer be shown on the diagonal.

(FRMCOL)

This is the color of the frame around the plot. (As usual blue=0, red=120, green=240, and 360 is blue again).

(SEQCOL)

This is the color with which the sequence will be drawn in the frame around the plot. (As usual blue=0, red=120, green=240, and 360 is blue again).

(NEICOL)

After picking NEIM at the screen menu, you will see the two contacting residues colored by atom type. The residues around this pair can get one fixed color, determined by this parameter, or can be colored by atom type too. To color by atom type this parameter should be set to -1. Otherwise to 0-360.

(CACFLG)

The squares used to indicate the contacts are scaled by the number of atoms in the residues. Especially if you use the CONATM option it might be nice to know what are backbone and what are side chain atoms. The CACFLG parameter can be used to draw lines between the main chain and side chain atoms in the two residues. This then results of course in crosses being drawn in the squares.

(1O3FLG)

This flag allows you to choose whether the sequence in the frame is written in one- or in three- letter code.

(HOFFLG)

If this parameter is set to one, the CONRES results will only use the upper half of the triangle, and the CONATM results the lower one.

(CACCOL)

This is the color of the crosses drawn if the CACFLG parameter is activated.

(CONLIN)

The command CONLIN determines whethet the contact calculation related options like CONTAC, BUMPS, etc. will only list the contacts, or will also display them at the screen.

Showing parameters (SHOPAR)

The command SHOPAR will show the present value for all parameters relevant for the ANACON option.