Strain in protein structures as viewed through nonrotameric side chains: I. their position and interaction

We studied the relative spatial positioning of nonrotameric side chains with atypical and strained dihedral angles in well-refined protein tertiary structures. The analysis was confined to buried protein cores, which are less error prone to side-chain positioning. More than half of the proteins with two or more nonrotameric residues displayed clusters of two or more (and up to five) nonrotameric residues. The clusters exhibited lower average crystallographic temperature factors compared with isolated nonrotameric residues. Nonrotameric clusters showed significantly tighter packing than corresponding rotameric clusters and had distinct residue compositions that did not correlate with amino acid characteristics such as size, hydrophobicity, turn preference, and the like. Such nonrotameric residue biases would suggest that spatially concentrated strain in protein folds would be minimized by lowered vibrational energy. Furthermore, nonrotameric residues avoided helices and strands and mostly preferred coil regions. If they were in the helical conformation, then they preferred to be within N-terminal segments. Proteins 1999;37:30-43.