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.