A Web Server for Interactive Analysis of Protein Interatomic Contacts

COCαDA-web is a user-friendly Web Server for interatomic contact calculation in proteins, as well as a database comprising precomputed contacts from the PDB. COCαDA-web uses the COCαDA algorithm, which improves search space pruning using alpha-carbon (Cα) distance matrices.

Run Examples

746,598,264

CONTACTS

690,741,959

INTRA-CHAIN CONTACTS

55,856,305

INTER-CHAIN CONTACTS

243,382

3D STRUCTURES

*Last updated on: Mar 26, 2026

How to cite:

Lemos RP, Mariano D, Silveira SDA and de Melo-Minardi RC (2025) COCαDA - a fast and scalable algorithm for interatomic contact detection in proteins using Cα distance matrices. Front. Bioinform. 5:1630078. doi: 10.3389/fbinf.2025.1630078

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: 10.5753/bsb.2024.245545

Run COCαDA-web

Calculate interatomic contacts for a protein file using the COCαDA-web interface

There are three ways to run COCαDA-web: (i) Upload a file in PDB or CIF format (below - left); (ii) enter the PDB/UniProt code to query data from PDB/AlphaFoldDB API (below - right); (iii) use the search bar (Examples section - right) to access COCαDA-db pre-calculated contacts from the PDB. COCαDA-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 or consider using the COCαDA command-line version.

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

Or access an entry by typing the 4-characters PDB code :

PDB search bar