Accessibility and partner number of protein residues, their relationship and a webserver, ContPlot for their display.
BACKGROUND
Depending on chemical features residues have preferred locations -- interior or exterior -- in protein structures, which also determine how many other residues are found around them. The close packing of residues is the hallmark of protein interior and protein-protein interaction sites.


RESULTS
The average values of accessible surface area (ASA) and partner number (PN, the number of other residues within a distance of 4.5 A from any atom of a given residue) of different residues have been determined and a webserver, ContPlot has been designed to display these values (relative to the average values) along the protein sequence. This would be useful to visually identify residues that are densely packed, or those involved in protein-protein interactions. The skewness observed in the distribution of PNs is indicative of the hydrophobic or hydrophilic nature of the residue. The variation of ASA with PN can be analytically expressed in terms of a cubic equation. These equations (one for each residue) can be used to estimate the ASA of a polypeptide chain using the PNs of the individual residues in the structure.


CONCLUSIONS
The atom-based PNs (obtained by counting surrounding atoms) are highly correlated to the residue-based PN, indicating that the latter can adequately capture the atomic details of packing. The average values of ASA and PN associated with each residue should be useful in protein structure prediction or fold-recognition algorithm. ContPlot would provide a handy tool to assess the importance of a residue in the protein structure or interaction site.
Pal
Arumay
A
Department of Biochemistry, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata, India. arumay@boseinst.ernet.in
Bahadur
Ranjit Prasad
RP
Ray
Partha Sarathi
PS
Chakrabarti
Pinak
P
D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D030562:Databases, Protein; D020407:Internet; D008958:Models, Molecular; D011487:Protein Conformation; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry*; D012984:Software
D011506:Proteins