The Interatomic Contact Database & Tool

COCaDA-web is a tool and a database that presents contacts in all structures available in the PDB database. COCaDA calculates seven types of contacts: hydrogen bonds, hydrophobic, aromatic, attractive, repulsive, salt bridges and disulfide bridges.

Run Examples

700,960,631

CONTACTS

649,736,592

INTRA-CHAIN CONTACTS

51,224,039

INTER-CHAIN CONTACTS

233,346

3D STRUCTURES

*Last updated on: ago 17, 2025

How to cite:

LEMOS, Rafael P.; MARIANO, Diego; SILVEIRA, Sabrina A.; MELO-MINARDI, Raquel C. de. COCαDA - Large-Scale Protein Interatomic Contact Cutoff Optimization by Cα Distance Matrices. In: Proceedings of the XVII Brazilian Symposium on Bioinformatics (BSB), 17, p. 59-70, 2024. DOI: https://doi.org/10.5753/bsb.2024.245545

Run COCαDA-web

There are two ways to run COCaDA-web: (1) Upload a file in PDB or CIF format; or (2) enter the 4-digit corresponding PDB code to access COCaDA-db pre-calculated structure contacts. COCaDA-db only supports PDB structures with up to 10,000 amino acid residues. To access structures with more than 10,000 residues, please upload your file.

Cutoffs

Change contact cutoff values (check default values here):

Hydrogen bonds
Min Max
Disulfide Bond
Min Max
Hydrophobic
Min Max
Repulsive
Min Max
Attractive
Min Max
Salt Bridge
Min Max
Aromatic Stacking
Min Max

Filter chains

Select the chains you want to calculate contacts for.

All
Only interchain contacts
Only contacts in the chains:

pH

Change the pH value (default is 7.4):

7.4

Use the pH value defined in the CIF/PDB file

Examples

Click on one of the following PDB-IDs to explore the corresponding entry:

1K0P 1TPM 2LZM 4MDP
1SHR
1A1M
3L1P
4PMI