Can three-dimensional contacts in protein structures be predicted by analysis of correlated mutations?
A method has been developed to detect pairs of positions with correlated mutations in protein multiple sequence alignments. The method is based on reconstruction of the phylogenetic tree for a set of sequences and statistical analysis of the distribution of mutations in the branches of the tree. The database of homology-derived protein structures (HSSP) is used as the source of multiple sequence alignments for proteins of known three-dimensional structure. We analyse pairs of positions with correlated mutations in 67 protein families and show quantitatively that the presence of such positions is a typical feature of protein families. A significant but weak tendency is observed for correlated residue pairs to be close in the three-dimensional structure. With further improvements, methods of this type may be useful for the prediction of residue-residue contacts and subsequent prediction of protein structure using distance geometry algorithms. In conclusion, we suggest a new experimental
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