A CONTACT SCORING MATRIX FOR QUALITATIVE PREDICTION OF CHANGE IN FOLDING OF ALPHA-HELICES IN GLOBULAR-PROTEINS CAUSED BY A MUTATION

The atomic pairs in contact for atoms from pairs of amino-acid residue s on pairs of helices in a protein database consisting of 48 proteins of known tertiary structure from the Brookhaven Protein Data Bank are searched and counted to construct a primary scoring system. Each score in the primary scoring system is weighted further with the possibilit y of occurrence of each residue pair in the protein database to give a final scoring matrix. Scores for predicting change in folding of alph a-helices in a mutant protein are calculated by assuming that every pa ir of helices in the protein can closely interact with each other. It is shown that the change in folding of alpha-helices in several mutant proteins are reflected in both the change of the contact scores and t he helix geometry calculated.