Identification of important functional environs in protein tertiary structures from the analysis of residue variation in 3-D: application to cytochromes c and carboxypeptidases A and B

A simple methodology is described to apply to aligned proteinsequence sets for which at least one representative 3-D C structureis known. The evolutionary variation observed at each residueposition in the sequence alignment is qualified by taking intoaccount the residue variation that has occurred at other positionslocated within 7 A (according to the probable chain fold). Thisexpresses the evolutionary behaviour of any residue positionin the more appropriate context of its immediate surroundingsand distinguishes between invariant residues on the basis ofthe variation of their environment. The highest mechanisticsignificance is attached to conserved residues in conservedsurroundings, but the quantitative nature of the analysis meansthat all residue vicinities can be ranked and merged accordingto the degree of conservation that they exhibit and the residuepositions that comprise them. Therefore, with the aid of thechain fold, contour maps can be constructed that show gradedfoci of evolutionary conservation in the underlying superstructureof the protein type, and the irregular shapes and extents oflarge conserved areas. To test the methodology, it was appliedto cytochromes c and the carboxypeptidases A and B.