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.
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.
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 *141) 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.
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.
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.
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 *14Tabulating 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.