COCADA - Contacts detected for Protein Data Bank (PDB) entries

COCaDA-web is the database of intramolecular and intermolecular contacts. COCaDA command line interface calculates seven types of contacts: hydrogen bonds, hydrophobic, attractive, repulsive, salt bridges, aromatic, and disulfide bridges.

This dataset contains all contacts calculated for all PDB files available until January 21, 2025. Data extracted from Protein Data Bank (https://www.rcsb.org/). Contacts were calculated using COCaDA v1.0.

For each PDB entry, consisting of a set of four digits, there is a subdirectory with two files in CSV format:

0ABC_contacts.csv: contains the list of contacts of the PDB entry in question. Each line is composed of the following entries: Chain1 (chain of residue 1), Res1 (code of residue 1), ResName1 (name of residue 1), Atom1 (atom of residue 1), Chain2 (chain of residue 2), Res2 (code of residue 2), ResName2 (name of residue 2), Atom2 (atom of residue 2), Distance (distance between atoms - in angstroms), Type (type of contact)

0ABC_info.csv: contains information about the entry.

COCaDA-web is available at http://bioinfo.dcc.ufmg.br/cocada-webCOCaDA command line (source code) is available at https://github.com/LBS-UFMG/cocada