Download

Please click following links to download whole protein-protein interaction data in PiSITE. User can also download the data for each protein chain from interaction viewer.

March 2024

• All files (367,855 chains, 1,612.0MB)
• Non redundant files (28,947 chains, 28.0MB)

Previous versions

January 2019

• All files (263,002 chains, 918.0MB)
• Non redundant files (22,654 chains, 22.0MB)

[Legacy version] August 2008

• All files (110,325 chains, 146.0MB)
• Non redundant files (7,739 chains, 6.0MB)

Data format

PiSITE flat-file format

PiSITE prepared protein-protein interaction data for all protein chains. Each file contains the interaction data for a protein chain. PiSITE flat-file formatted file is a ASCII text file and easy to handle. The data line of a PiSITE flat-file format is a simple space-separated list, and a line with first letter "#" are comment line. PiSITE flat-file formatted file consists three parts, "header", "Binding states" and "Interaction of each residue".

Header

First four lines are header information and contain PDB ID and chain name. The first letter of these lines are always "#".

example
#PiSITE data for 1byuB generated at 2019-03
#PDBID: 1BYU
#CHAIN: B
#----

Binding states

Second part includes information about binding states and partners of a protein chain. Each line shows information about binding states and partners of a protein chain similar to target protein chain. The first column is a pdbcode (PDB ID and chain ID delimited by colon) of a similar protein chain. The second column is a cluster number of a similar protein chain. The third column is a sequence identity between target protein chain and a similar protein (in percentage). The fourth column is a sequence coverage of a similar protein chain for target protein chain (in percentage). The fifth or later column shows the pdbcode of binding partners with their model number and partner cluster number (partner_cluster_no:pdb_id:chain_id:model_no).

example
1wa5:A 17 99.43 81.48 11:1wa5:C:1 12:1wa5:B:1

Interaction of each residue

Third part includes information of interactions for each residue. Each line corresponds to a residue. The first column is a residue number. The second column is an insertion code. The third column is an amino acid type of a residue. The fourth column means the number of the clusters of binding partners that interact the residue. The fifth or later column shows the binding partners that interact the residue. In these column, first digit is a cluster number of a binding partner, and second four letter code is a PDB ID, next letter is a chain ID and last letter is model number of a binding partner.

example
35 . F 4 1|3ea5:B:1 1|2bku:B:1 3|5ysu:B:1 12|1wa5:C:1 7|3ch5:A:2