Local interactions as a structure determinant for protein molecules: II.

Van der Waals interactions between sidechains are indicated to be important in determining the native state of the proteins of known structure by the following observations: 1. the average radial distribution of polarity increases continuously from the center of the molecule to its periphery. 2. nonpolar sidechains tend to occur in clusters. 3. the frequencies of long-range nearest-neighbor pairs are markedly non-random; each type of sidechain seeks nearest-neighbors of similar polarity. To investigate how these interactions affect the overall structure of the protein molecule, three simplified models are treated: a sheath-core model composed of independent residues, a modification accounting approximately for the connected nature of the chain, and a model consisting of three concentric spherical phases.