Abstract
BackgroundDepending 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.ResultsThe 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.ConclusionThe 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.
Highlights
Depending on chemical features residues have preferred locations – interior or exterior – in protein structures, which determine how many other residues are found around them
As the earlier work [7] defined the partner number (PN) in terms of atoms, the present study examines it in terms of residues and finds the relationship with the solvent accessible surface area (ASA)
The hydrophilic residues have lesser partner number compared to the hydrophobic residues of similar volume, for example, Lys vis-à-vis Met
Summary
Depending on chemical features residues have preferred locations – interior or exterior – in protein structures, which determine how many other residues are found around them. It has been shown that when the contact is defined in terms of the number of atoms (i.e., partner number) surrounding a given residue the above two parameters are related [7] Parameters such as these obtained from a database of known protein structures constitute the knowledge base for deriving scoring functions or statistical potentials used in protein fold recognition, usually by threading, concerned with proteinstructure prediction for cases in which a target sequence does not have unambiguous sequence homology to any known structure [8,9,10,11,12]. A webserver is described that scans a protein sequence in a structure to indicate the residues for which the two parameters deviated significantly from the corresponding average value for the same residue
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