3. Results
The dataset used for the analysis consists of 895 cases, corresponding to a set of proteins that includes 285 enzymes, few transport protein complexes, and other structural oligomers. Proteins from diverse organisms including eukaryotes, plants and various animals are also present in this working dataset. 366 cases in the dataset are human proteins of which 96 are known to have enzymatic activity. In each case, the protein chain from the bound complex is compared against its corresponding chain in the unbound form. The structures are aligned to identify topologically equivalent residues, modelled as nodes in the PSN construct. Those residues that are in contact between the binding partners are considered as interfacial sites and those in contact with the interface are primary contacts.
A threshold of a minimum of 50 residues is used so that globular domains are considered and not peptides. The smallest case with least number of nodes is the ovalbumin enzyme inhibitor bound to different binding partners (PDB ID 1HJA). Here, turkey ovalbumin protein of 51 residues is complexed with the trimeric alpha-chymotrypsin to inhibit its function (with 16 interfacial sites and 21 are primary contact sites). The largest case, from PDB ID 2J8S, is the Acriflavine resistance protein B trimer of 1032 residues in each chain bound to two molecules of designed inhibitor (DARPin). One of the chains from the trimer is unbound and the other two have differential contact. While one chain has 20 interfacial sites with 31 primary contacts, the other has only 7 interfacial sites with 20 primary contacts.