Representation of noncovalent interactions in protein structures.

The energetics of solvent-atom and atom-atom nonbonded interactions can be described, for protein structures, in terms of the accessible and the contact atomic surface areas, respectively. This type of description emphasizes the importance of the local environment around groups in the three-dimensional structure of protein molecules. The graphical representation of nonbonded interactions according to this description allows one to visualize the spatial extent and distribution of these interactions and the relative stability of atoms or atomic groups in known or modified protein conformations. Applications of this short range description and of its graphical representation will be discussed.