Abstract 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.
Received: 17 February 2006
Revised: 13 October 2006
Accepted manuscript online:
Fund: Project supported by the National Natural Science
Foundation of China (Grant Nos10204013, 90103031, 10074030,
10474041, 90403120 and 10021001), and the Nonlinear Project (973)
of the National Science Ministry, China.
Cite this article:
Chen Ying(陈颖), Wang Jun(王骏), and Wang Wei(王炜) The preferences of orientations between the pairs of amino acids 2007 Chinese Physics 16 868
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