Spatial assignment of amino acid residues in globular proteins: an approach from information theory.

Abstract

Abstract In the native folded state of globular proteins, amino acid residues place themselves at various positions from the centroid of the molecule. Applying information theory on 19 protein crystals the spatial preferences have been found out from the frequencies of occurrence of residues within various concentric ellipsoidal zones of proteins. The intrinsic spatial preferences of individual residues are related to their physical and chemical properties. The directing power of the individual residues on the chain path and the spatial information contained by doublets of residues have been found out. The derived information is used to predict the spatial/zonal preference of residues in carp myogen using the knowledge of amino acid sequence. The implication of packing densities in different spatial zones are discussed.