Characterization of the backbone geometry of protein native state structures

We present a simple method for analyzing the geometry of noncovalent residue–residue interactions stabilizing the protein structure, which takes into account the constraints on the local backbone geometry. We find that the principal geometrical constraints are amino acid aspecific and are associated with hydrogen bond formation in helices and sheets. In contrast, amino acid residues in nonhelical and nonextended conformations, which make noncovalent interactions stabilizing the protein tertiary structure, display greater flexibility. We apply the method to an analysis of the packing of helices in helical bundle proteins requiring an efficient packing of amino acid side‐chains of the interacting helices. Proteins 2006. © 2006 Wiley‐Liss, Inc.