Email updates

Keep up to date with the latest news and content from BMC Structural Biology and BioMed Central.

Open Access Highly Accessed Research article

An automatic method for assessing structural importance of amino acid positions

Michael I Sadowski2 and David T Jones1*

Author Affiliations

1 Computer Science Department, University College London, Gower St, London, WC1E 6BT, UK

2 Division of Mathematical Biology, National Institute for Medical Research, The Ridgeway, Mill Hill, London, NW7 1AA, UK

For all author emails, please log on.

BMC Structural Biology 2009, 9:10  doi:10.1186/1472-6807-9-10

Published: 4 March 2009

Abstract

Background

A great deal is known about the qualitative aspects of the sequence-structure relationship, for example that buried residues are usually more conserved between structurally similar homologues, but no attempts have been made to quantitate the relationship between evolutionary conservation at a sequence position and change to global tertiary structure. In this paper we demonstrate that the Spearman correlation between sequence and structural change is suitable for this purpose.

Results

Buried residues, bends, cysteines, prolines and leucines were significantly more likely to occupy positions highly correlated with structural change than expected by chance. Some buried residues were found to be less informative than expected, particularly residues involved in active sites and the binding of small molecules.

Conclusion

The correlation-based method generates predictions of structural importance for superfamily positions which agree well with previous results of manual analyses, and may be of use in automated residue annotation piplines. A PERL script which implements the method is provided.