As of December 25, 2012 there are 87,090 structure entries in PDB. The number of PDB entries that contain at least one protein interaction (either protein-protein or protein-peptide interaction) determined using our method is 66,838.
Statistics for different interaction types is obtained based on the annotation of protein subunits using either SCOP domain family annotation extracted from SCOP database (version 1.75) or predicted domain using an HMM-based approach. The six subunit types, domain, C-terminal, Linker, N-terminal, Peptide and Undefined Chain, are abbreviated as D, C, L, N, P and U, correspondingly.
The statistics below is calculated for the inter-chain interactions and intra-chain interactions. In addition, there are 12 interactions of the mixed type (when a SCOP domain spans more than one chain). The above two numbers are calculated for the whole set of interactions as well as individually for (i) the interactions with both subunits being SCOP- annotated or (ii) interactions with at least one subunit annotated using the SCOP annotation prediction method.
Figure below represents statistics for extracted protein subunits of a given subunit type. Similarly to the previous plot, the numbers are calculated using either SCOP database-annotated subunits or subunits annotated using the SCOP annotation prediction method.
The following is the statistics for inter organism and intra organism interactions. Here, we only consider the interactions that have corresponding organism information in PDB files.
