The packing density in proteins: Standard radii and volumes

The sizes of atomic groups are a fundamental aspect of protein structure. T hey are usually expressed in terms of standard sets of radii for atomic gro ups and of volumes for both these groups and whole residues. Atomic groups, which subsume a heavy-atom and its covalently attached hydrogen atoms into one moiety, are used because the positions of hydrogen atoms in protein st ructures are generally not known. We have calculated new values for the rad ii of atomic groups and for the volumes of atomic groups. These values shou ld prove useful in the analysis of protein packing, protein recognition and ligand design. Our radii for atomic groups were derived from intermolecula r distance calculations on a large number (similar to 30,000) of crystal st ructures of small organic compounds that contain the same atomic groups to those found in proteins. Our radii show significant differences to previous ly reported values. We also use this new radii set to determine the packing efficiency in different regions of the protein interior. This analysis sho ws that, if the surface water molecules are included in the calculations, t he overall packing efficiency throughout the protein interior is high and f airly uniform. However, if the water structure is removed, the packing effi ciency in peripheral regions of the protein interior is underestimated, by similar to 3.5%. (C) 1994 Academic Press.