Atom density in protein structures

The residue environment in protein structures is studied with respect to th e density of carbon (C), oxygen (O), and nitrogen (N) atoms within a certai n distance (say 5 A) of each residue. Two types of environments are evaluat ed: one based on side-chain atom contacts (abbreviated S-S) and the other b ased on all atom (sidechain + backbone) contacts (abbreviated A-A). Differe nt atom counts are observed about nine-residue structural categories define d by three solvent accessibility levels and three secondary structure state s. Among the structural categories, the S-S atom count ratios generally var y more than the A-A atom count ratios because of the fact that the backbone (O) and (N) atoms contribute equal counts. Secondary structure affects the (C) density for the A-A contacts whereas secondary structure has little in fluence on the (C) density for the S-S contacts. For S-S contacts, a greate r density of (O) over (N) atom neighbors stands out in the environment of m ost amino acid types. By contrast, for A-A contacts, independent of the sol vent accessibility levels, the ratio (O)/(N) is approximate to 1 in helical states, consistent with the geometry of alpha-helical residues whose side- chains tilt oppositely to the amino to carboxy alpha-helical axis. The high est ratio of neighbor (O)/(N) is achieved under solvent exposed conditions. This (O) vs. (N) prevalence is advantageous at the protein surface that ge nerally exhibits an acid excess that helps to enhance protein solubility in the cell and to avoid nonspecific interactions with phosphate groups of DN A, RNA, and other plasma constituents.