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Open Access Highly Accessed Research article

Accessibility and partner number of protein residues, their relationship and a webserver, ContPlot for their display

Arumay Pal1, Ranjit Prasad Bahadur1, Partha Sarathi Ray2 and Pinak Chakrabarti12*

Author Affiliations

1 Department of Biochemistry, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata 700 054, India

2 Bioinformatics Centre, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata 700 054, India

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BMC Bioinformatics 2009, 10:103  doi:10.1186/1471-2105-10-103

Published: 8 April 2009

Abstract

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 Å 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.

Conclusion

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.