Verification of Protein Structures: Side-Chain Planarity

Nine of the 20 natural amino acids contain a planar group in their side chains. For these groups, normal deviations from planarity were derived by the study of similar fragments in accurately determined small molecule structures. Comparison of these deviations with values found from a representative set of high-quality protein structures revealed that the planarity of the aromatic residues and arginine in protein structures is comparable to similar fragments in small molecules. For Asn, Gin, Asp and Glu, however, the deviations are up to twice as large as in comparable small-molecule structures, suggesting that adding an extra planarity restraint for these residue types could improve refinement procedures.