The preferences of orientations between the pairs of amino acids  

作　　者：陈颖 王骏 王炜 

机构地区：[1]National Laboratory of Solid State Microstructure, Department of Physics, and Institute of Biophysics, Nanjing University, Nanjing 210093, China

出　　处：《Chinese Physics B》2007年第3期868-875,共8页中国物理B（英文版）

基　　金：Project supported by the National Natural Science Foundation of China （Grant Nos 10204013, 90103031, 10074030, 10474041, 90403120 and 10021001）, and the Nonlinear Project （973） of the National Science Ministry, China.

摘　　要：In this work, we make an investigation on the preferences of orientations between amino acids using the orientation defined based on the local geometry of the amino acids concerned. It is found that there are common preferences of orientations （70°, 30°, 140°） and （110°, 340°, 100°） for various pairs of amino acids. Different side chains may strengthen or weaken the common preferences, which is related to the effect of packing. Some amino acids having specific local flexibility may possess some preferences of orientations besides the common ones, such as （10°, 280°, 210°）. Another analysis on the pairs of the amino acids with different secondary-structure preferences shows that the directional interaction may affect the distribution of orientation more effectively than the packing or local flexibility. All these results provide us some insight of the organization of amino acids in protein, and their relation with some related interactions.In this work, we make an investigation on the preferences of orientations between amino acids using the orientation defined based on the local geometry of the amino acids concerned. It is found that there are common preferences of orientations （70°, 30°, 140°） and （110°, 340°, 100°） for various pairs of amino acids. Different side chains may strengthen or weaken the common preferences, which is related to the effect of packing. Some amino acids having specific local flexibility may possess some preferences of orientations besides the common ones, such as （10°, 280°, 210°）. Another analysis on the pairs of the amino acids with different secondary-structure preferences shows that the directional interaction may affect the distribution of orientation more effectively than the packing or local flexibility. All these results provide us some insight of the organization of amino acids in protein, and their relation with some related interactions.

关 键 词：native structure of protein preferences of orientation preferences of secondary structures 

分 类 号：Q517[生物学—生物化学] Q518.1