Main-chain conformational features at different conformations of the side-chains in proteins

Abstract

An analysis of the known protein structures has shown that the main-chain torsion angles, φ and ψ of a residue can be affected by the side-chain torsion angle, χ₁. The (χ₁, ψ) plot of all residues (except Gly, Ala and Pro) show six distinct regions where points are concentrated-although some of these regions are nearly absent in specific cases. The mean of these clusters can show a shift along the y axis by as much as 30° as χ₁ is changed from around 180 to -60 to 60°. Because of the lesser steric constraint points are more diffused along the ψ axis when χ₁ is approximately -60°. Although points are more spread out along the φ axis in the (χ₁, φ) plot, the dependence of f on χ₁ shows up in a shortened φ range (by about 30°) when χ₁ is around -60°, and a distinct tendency of clustering of points into two regions when χ₁ ≈ 60°, especially for the aromatic residues. Based on the dependence of the backbone conformation on its side-chain the 17 amino acids can be grouped into five classes: (i) aliphatic residues branched at the C_β position (although Thr is atypical), (ii) Leu (branched at the C_γ position), (iii) aromatic residues (Trp can show some deviations), (iv) short polar residues (Asp and Asn), and (v) the remaining linear-chain residues, mainly polar. Ser and Thr have the highest inclination to occur with two different orientations of the side-chain that can be located through crystallography. Such residues exhibiting two χ₁ angles have their φ and ψ angles in a region that is common to the Ramachandran plots at the two different χ₁ angles. The dependence of φ and ψ angles on χ₁ can be used to understand the helical propensities of some residues. Moreover, the average φ, ψ values in the α-helices vary with the side-chain conformation.