MMTSB
Tool Set Documentation

contact.pl

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Usage

usage:   contact.pl [options] [refPDB] cmpPDB
options: [-l min:max[...]]
         [-read file]
         [-list]
         [-mindist value]
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Description

This script calculates residue contact maps and compares them between different structures. Residues are considered in contact when the minimum inter-residue distance of all pairs of heavy atoms is less than 4.2 Å.

In the default mode with two structures as arguments the fraction of contacts present in the second structure with respect to the first is determined. Also calculated is the continuous quantity rho that uses a sigmoidal function for the minimum inter-residue distance around 4.2 A to effectively include residue pairs that are slightly further apart with a reduced weight. An extended output is available with -list to get a list of all residue contacts in the reference structure with the minimum distances in the reference as well as the test structures.

If only one structure is given as an argument no comparison is done. A residue contact list is printed out instead. This list can be used in later comparisons with -read to save time if multiple structures are compared to the same reference. The more costly calculation of the reference residue map then has to be done only once.

The option -l is available to limit the residue map to contacts with a subset of residues as might be useful for loop modeling.

Options

-help 
usage information
-l min:max[...] 
restrict contact map calculation to given residue range
-read file 
read reference contact list from file
-list 
write out contact list

Examples

contact.pl 1vii.exp.pdb 1vii.exp.min.pdb
compares the residue contact map between two structures and reports the number of contacts present in the second structure with respect to the first. Also reported is the continuous quantity rho that takes near-contacts into consideration.

23 contacts ( fraction: 0.958333 ), rho: 0.999182


contact.pl 1vii.exp.pdb
writes the contact list for the given structure to standard output

2 7 3.525115
2 10 3.383307
2 11 3.541492
2 15 2.839893
2 34 2.930046
2 36 3.797043
7 12 3.996071
7 13 2.808753
7 14 2.851043
7 15 2.858498

...


contact.pl -read 1vii.exp.contacts 1vii.exp.min.pdb
compares the residue contact map of the given structure with the contact list read from a file and reports the number of contacts present with respect to the reference. Also reported is the continuous quantity rho that takes near-contacts into consideration.

23 contacts ( fraction: 0.958333 ), rho: 0.999182


contact.pl -l 10:21 -list 1vii.exp.pdb 1vii.exp.min.pdb
compares the residue contact map involving only contacts with residues 10 through 21 between two structures. In addition to the fraction of contacts present in the second structure a detailed list is printed out for all contacts with the minimum distances in the reference and test structures.

19 contacts ( fraction: 0.950000 ), rho: 0.999018
   LEU:2     - VAL:10      3.383307 4.250682
 * LEU:2     - PHE:11      3.541492 3.911385
 * LEU:2     - ARG:15      2.839893 2.706345
 * PHE:7     - GLY:12      3.996071 2.764539
 * PHE:7     - MET:13      2.808753 3.330530
 * PHE:7     - THR:14      2.851043 3.908893
 * PHE:7     - ARG:15      2.858498 3.255971
 * PHE:7     - PHE:18      3.632217 3.699490
 * VAL:10    - LYS:33      3.377613 2.759139

...