A survey of atom packing in globular proteins.
This survey of the atom packing in the high resolution X-ray crystal structures of 21 proteins indicates that the atom density around a given central atom is determined primarily by its covalently bonded neighbors and proximity to the surface of the protein. Long-range hydrophobic, hydrogen bonding, and electrostatic interactions are strictly of secondary importance. Both radial and angular atom densities were calculated about various central atoms of several residue types, averaged over all occurrences of the chosen residue type in all 21 proteins. Polar interactions, such as hydrogen bonding, involve on the average shorter distances than hydrophobic interactions do, and are more directional. Spatial segregation of polar and non-polar atoms is never complete in long-range interactions since the types of atoms are linked together covalently.
D055598:Chemical Phenomena; D002627:Chemistry, Physical; D003461:Crystallography; D008961:Models, Structural; D011487:Protein Conformation