SPACE - Tools for protein Structure Prediction and Analysis based on Complemenrtarity and Environment

CMA: Contact Map Analysis

PDB ID: or
Local:
Chain #1: from to
Chain #2: from to
Scale: Threshold, Å2:  
 
 

Description

This program allows to analyse contacts between two chains or within one chain in a given PDB file. The program represents residue-residue contacts in the form of a contact map that, in addition, allows to see a detailed atom-atom contact information for any pair of contacting residues. Refer to LPC/CSU software for more extensive analysis.

Usage

To run the analysis you have to provide the following information:
PDB ID
or
Local
  • Identificator of the protein structure in the Protein Data Bank (4-letter code). Program reports an error if it will find any problem (wrong PDB ID, non-existent PDB ID, etc.)
  • Alternatively, select a local data file.
Chain #1* Identificator of the 1st chain (1-letter code). If chain ID is blank ' ' in the PDB file use '_' character instead.
Chain #2* Identificator of the 2nd chain (1-letter code). If chain ID is blank ' ' in the PDB file use '_' character instead.
from ... to ... Allows to specify a region for analysis in every chain. If any field is left empty (or it contains non-numeric characters) the beginning or the end of the chain is assumed for that field.
Threshold Only residue-residue contacts with contact area above a given threshold (Å2) are displayed. If field is left empty (or it contains non-numeric characters) all contacts are displayed.
Scale This parameters affects the size of the resulting contact map. Make this parameter smaller to get the smaller contact map and vice versa.
*To identify residue-residue contacts within a protein chain provide the same chain ID in both fields "Chain #1" and "Chain #2".

Once you fill the necessary fields and click "Submit" button the program displays a contact map where blue square indicates a contact between pair of residues which are shown at the left and at the top of the contact map. Full lists of atom-atom (see format) and residue-residue contacts are available for download (see links below the contact map).

Program also allows to display a detailed infomartion about all atom-atom contacts between a given pair of contacting residues and to visualize contacting residues using JMol applet (requires installed JAVA plugin for browser).

Comments and suggestions to Vladimir Potapov