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Protein Engineering, Vol. 12, No. 7, 523-526, July 1999
© 1999 Oxford University Press

Short Communication

Graphical representation of the salient conformational features of protein residues

Debnath Pal and Pinak Chakrabarti1

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

A composite plot for depicting in two dimensions the conformation and the secondary structural features of protein residues has been developed. Instead of presenting the exact values of the main- and side-chain torsion angles ({phi}, {psi} and {chi}1), it indicates the region in the three-dimensional conformational space to which a residue belongs. Other structural aspects, like the presence of a cis peptide bond and disulfide linkages, are also displayed. The plot may be used to recognize patterns in the backbone and side-chain conformation along a polypeptide chain and to compare protein structures derived from X-ray crystallography, NMR spectroscopy or molecular modelling studies and also to highlight the effect of mutation on structure.

Keywords: conformation/protein engineering/protein structural comparison/secondary structure/structural plot

1 To whom correspondence should be addressed


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