Abstract
Protein-Protein Interaction Sitesbase (PPInS), a high-performance database of protein-protein interacting interfaces, is presented. The atomic level information of the molecular interaction happening amongst various protein chains in protein-protein complexes (as reported in the Protein Data Bank [PDB]) together with their evolutionary information in Structural Classification of Proteins (SCOPe release 2.06), is made available in PPInS. Total 32468 PDB files representing X-ray crystallized multimeric protein-protein complexes with structural resolution better than 2.5 Å had been shortlisted to demarcate the protein-protein interaction interfaces (PPIIs). A total of 111857 PPIIs with ~32.24 million atomic contact pairs (ACPs) were generated and made available on a web server for on-site analysis and downloading purpose. All these PPIIs and protein-protein interacting patches (PPIPs) involved in them, were also analyzed in terms of a number of residues contributing in patch formation, their hydrophobic nature, amount of surface area they contributed in binding, and their homo and heterodimeric nature, to describe the diversity of information covered in PPInS. It was observed that 42.37% of total PPIPs were made up of 6–20 interacting residues, 53.08% PPIPs had interface area ≤1000 Å2 in PPII formation, 82.64% PPIPs were reported with hydrophobicity score of ≤10, and 73.26% PPIPs were homologous to each other with the sequence similarity score ranging from 75–100%. A subset “Non-Redundant Database (NRDB)” of the PPInS containing 2265 PPIIs, with over 1.8 million ACPs corresponding to the 1931 protein-protein complexes (PDBs), was also designed by removing structural redundancies at the level of SCOP superfamily (SCOP release 1.75). The web interface of the PPInS (http://www.cup.edu.in:99/ppins/home.php) offers an easy-to-navigate, intuitive and user-friendly environment, and can be accessed by providing PDB ID, SCOP superfamily ID, and protein sequence.
Highlights
Protein-Protein Interaction Sitesbase (PPInS), a high-performance database of protein-protein interacting interfaces, is presented
It covers a vast diversity of protein-protein interaction patches (PPIPs) in terms of a number of residues involved in protein-protein interacting patches (PPIPs) formation, their hydrophobicity level, homo and heterodimeric nature of interacting PPIPs, and the amount of surface of the PPIPs devoted to protein-protein interaction interfaces (PPIIs) formation
A PPIP with the less hydrophobic score on this scale implies its high hydrophobicity. Observations made from this analysis underlined the hydrophobic nature of protein-protein interactions (PPIs) sites as it was observed that 82.64% PPIPs were reported with hydrophobicity score of less than 10 and 14.2% PPIPs were reported with hydrophobicity score in the range of 11–20 (Fig. 7)
Summary
Web server for PPInS (http://www.cup.edu.in:99/ppins/home.php) was designed using php scripts and Apache web server. On inputting SCOP superfamily “63707” to the PPInS, a list of 10 PPIIs will be displayed with an option to download them Each of these 10 PPIIs has at least one interacting protein chain which belongs to SCOP superfamily “63707”. Homo and heterodimeric nature of PPIPs in PPIIs. The sequence similarity between the interacting PPIPs of PPInS had revealed that 73.26% of total PPIPs were homologous to each other with the sequence similarity score ranging from 75% to the absolute similarity. The sequence similarity between the interacting PPIPs of PPInS had revealed that 73.26% of total PPIPs were homologous to each other with the sequence similarity score ranging from 75% to the absolute similarity This is in line with the earlier reports in the literature which state that homodimers are more prevalent in nature. On the other hand, when the sequence similarity further reduces (say around 75%) the heterodimeric complex formation is favoured
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Free) 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
