Ramakrishnan C, Soman K V
Int J Pept Protein Res. 1982 Sep;20(3):218-37. doi: 10.1111/j.1399-3011.1982.tb03052.x.
A new algorithm has been developed for identifying helices, extended structures, and bends from the positions of the alpha-carbon atoms using the virtual bond approach. The parameters used are two virtual bond angles (delta 1 and delta 2), the virtual dihedral angle (theta), and the distance (D) between the terminal alpha-carbon atoms of the tripeptide. The criteria for classification have been worked out by model building as well as from proteins whose complete secondary structures are known. These criteria are as follows: (i) magnitude of theta less than or equal to 60 degrees and (delta 1 + delta 2) less than or equal to 230 degrees for a bend, (ii) for a helix, successive thetas should not differ by more than 30 degrees, and (iii) for an extended structure, the cumulative deviation of the above parameters should not vary by more than 20% from the ideal extended chain. The method developed has been applied successfully to three proteins wherein the coordinates of alpha-carbon atoms alone are known and a complete mapping of the secondary structures has now been obtained. One interesting observation is that the percentage of residues not taking part in helices, extended structures, and bends is very small--of the order of 4%.
已经开发出一种新算法，用于使用虚拟键方法从α-碳原子的位置识别螺旋、伸展结构和转角。所使用的参数是两个虚拟键角（δ1和δ2）、虚拟二面角（θ）以及三肽末端α-碳原子之间的距离（D）。分类标准是通过模型构建以及从已知完整二级结构的蛋白质中得出的。这些标准如下：（i）对于转角，θ的大小小于或等于60度且（δ1 + δ2）小于或等于230度；（ii）对于螺旋，连续的θ相差不应超过30度；（iii）对于伸展结构，上述参数的累积偏差与理想伸展链的偏差不应超过20%。所开发的方法已成功应用于三种仅知道α-碳原子坐标的蛋白质，现在已经获得了二级结构的完整图谱。一个有趣的发现是，不参与螺旋、伸展结构和转角的残基百分比非常小——约为4%。
