Pfam assignments have been used previously to catalogue the physical interaction of different domain families within the PDB. With a larger and more accurate set of assignments, we have investigated the number of such interactions that are now present in the biological assemblies of the PDB. An interaction is defined if there are at least 5 pairs of residues with any atomic distance < 5Å, or at least 10 pairs of residues with C-beta/C-alpha distance < 12Å and at least one atomic distance < 5Å.

The interactions in biological assemblies provide more accurate estimates of our structural knowledge of how proteins interact with each other, and how this information might be used to investigate protein-protein interaction networks. In the following Table, we show the Pfams that interact with 30 or more other Pfams within the PDB. Several of these are domains which typically bind short peptides from other proteins, including MHC_I, Pkinase, WD40, and efhand domains. Many are also repeat modules that serve as protein-protein interaction scaffolds.