Analysis of interactive packing of secondary structural elements in alpha/beta units in proteins

An alpha-helix and a beta-strand are said to be interactively packed if at least one residue in each of the secondary structural elements loses 10% of its solvent accessible contact area on association with the other secondar y structural element. An analysis of all such 5,975 nonidentical alpha/beta units in protein structures, defined at less than or equal to 2.5 Angstrom resolution, shows that the interaxial distance between the alpha-helix and the beta-strand is linearly correlated with the residue-dependent function , log[(V/nda)/n-int], where V is the volume of amino acid residues in the p acking interface, nda is the normalized difference in solvent accessible co ntact area of the residues in packed and unpacked secondary structural elem ents, and n-int is the number of residues in the packing interface. The bet a-sheet unit (beta u), defined as a pair of adjacent parallel or antiparall el hydrogen-bonded beta-strands, packing with an alpha-helix shows a better correlation between the interaxial distance and log(V/nda) for the residue s in the packing interface. This packing relationship is shown to be useful in the prediction of interaxial distances in alpha/beta units using the in teracting residue information of equivalent alpha/beta units of homologous proteins. It is, therefore, of value in comparative modeling of protein str uctures.