Ligand-Protein Contacts & Contacts of Structural Units
Analysis
LPC Analysis of interatomic Contacts in Ligand-Protein complexes
CSU Analysis of interatomic contacts in protein entries
Select one.
Data source
PDB entry ( find it with OCA ) or
Local

Provide either a PDB id or click on 'Browse...' and select a local data file.

Click on 'Run' for analysis.

Note: Your local data file should follow the PDB format:

  1. The first line should a have 4-letter word at columns 63-66 (instead of PDB id).
  2. The lines containing protein atom coordinates must begin with the word ATOM and should have exactly the same format as in PDB.
  3. The lines containing ligand atom coordinates must begin with the word HETATM and should have exactly the same format as in PDB.
  4. In order to have a ligand picture in the Chemscape window, the file should have connectivity information, in lines beginning with the word CONECT and having exactly the same format as in PDB.
  5. The bottom line must contain only the word END in the first three letter positions.
In publications, credits should state:

Ligand-Protein Contacts (LPC) were derived with LPC software (Sobolev V., Sorokine A., Prilusky J., Abola E.E. and Edelman M. (1999) Automated analysis of interatomic contacts in proteins. Bioinformatics, 15, 327-332).

or (and)

Contacts of Structural Units (CSU) were derived with CSU software (Sobolev V., Sorokine A., Prilusky J., Abola E.E. and Edelman M. (1999) Automated analysis of interatomic contacts in proteins. Bioinformatics, 15, 327-332).