Chakrabarti P, Pal D
Department of Biochemistry, Bose Institute, Calcutta, India.
Protein Eng. 1998 Aug;11(8):631-47. doi: 10.1093/protein/11.8.631.
An analysis of the known protein structures has shown that the main-chain torsion angles, phi and psi of a residue can be affected by the side-chain torsion angle, chi1. The (chi1, psi) 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 psi axis by as much as 30 degrees as chi1 is changed from around 180 to -60 to 60 degrees. Because of the lesser steric constraint points are more diffused along the psi axis when chi1 is approximately -60 degrees. Although points are more spread out along the phi axis in the (chi1, phi) plot, the dependence of phi on chi1 shows up in a shortened phi range (by about 30 degrees) when chi1 is around -60 degrees, and a distinct tendency of clustering of points into two regions when chi1 is approximately equal to 60 degrees, 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 Cbeta position (although Thr is atypical), (ii) Leu (branched at the Cgamma 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 chi1 angles have their phi and psi angles in a region that is common to the Ramachandran plots at the two different chi1 angles. The dependence of phi and psi angles on chi1 can be used to understand the helical propensities of some residues. Moreover, the average phi, psi values in the alpha-helices vary with the side-chain conformation.
对已知蛋白质结构的分析表明，一个残基的主链扭转角φ和ψ会受到侧链扭转角χ1的影响。所有残基（除甘氨酸、丙氨酸和脯氨酸外）的（χ1，ψ）图显示出六个不同的点集中区域——尽管在某些特定情况下其中一些区域几乎不存在。当χ1从约180度变化到 -60度再到60度时，这些簇的平均值在ψ轴上可显示出高达30度的偏移。由于空间位阻较小，当χ1约为 -60度时，点在ψ轴上分布更分散。尽管在（χ1，φ）图中，点在φ轴上分布更分散，但当χ1约为 -60度时，φ对χ1的依赖性表现为φ范围缩短（约30度），而当χ1约等于60度时，尤其是对于芳香族残基，点明显倾向于聚集成两个区域。基于主链构象对其侧链的依赖性，17种氨基酸可分为五类：（i）在Cβ位置分支的脂肪族残基（尽管苏氨酸不典型），（ii）亮氨酸（在Cγ位置分支），（iii）芳香族残基（色氨酸可能会有一些偏差），（iv）短极性残基（天冬氨酸和天冬酰胺），以及（v）其余的线性链残基，主要是极性的。丝氨酸和苏氨酸最倾向于以两种不同的侧链取向出现，这可以通过晶体学确定其位置。这种表现出两个χ1角的残基，其φ和ψ角处于两个不同χ1角的拉氏图的共同区域。φ和ψ角对χ1的依赖性可用于理解一些残基的螺旋倾向。此外，α螺旋中的平均φ、ψ值会随侧链构象而变化。
