Chen Jin, Zhang Linxi, Jing Li, Wang Youxing, Jiang Zhouting, Zhao Delu
Department of Physics, Zhejiang University, Hangzhou 310028, PR China.
Biophys Chem. 2003 Aug 1;105(1):11-21. doi: 10.1016/s0301-4622(03)00033-4.
Short-range and long-range contacts are important in forming protein structure. The proteins can be grouped into four different structural classes according to the content and topology of alpha-helices and beta-strands, and there are all-alpha, all-beta, alpha/beta and alpha+beta proteins. However, there is much difference in statistical property for those classes of proteins. In this paper, we will discuss protein structure in the view of the relative number of long-range (short-range) contacts for each residue. We find the percentage of residues having a large number of long-range contacts in protein is small in all-alpha class of proteins, and large in all-beta class of proteins. However, the percentage of residues is almost the same in alpha/beta and alpha+beta classes of proteins. We calculate the percentage of residues having the number of long-range contacts greater than or equal to (>/=) N(L)=5, and 7 for 428 proteins. The average percentage is 13.3%, 54.8%, 41.4% and 37.0% for all-alpha, all-beta, alpha/beta and alpha+beta classes of proteins with N(L)=5, respectively. With N(L) increasing, the percentage decreases, especially for all-alpha class of proteins. In the meantime, the percentage of residues having the number of short-range contacts greater than or equal to N(S) (>/=N(S)) in protein samples is large for all-alpha class of proteins, and small for all-beta class of proteins, especially for large N(S). We also investigate the ability of amino residues in forming a large number of long-range and short-range contacts. Cys, Val, Ile, Tyr, Trp and Phe can form a large number of long-range contacts easily, and Glu, Lys, Asp, Gln, Arg and Asn can form a large number of long-range contacts, but with difficulty. We also discuss the relative ability in forming short-range contacts for 20 amino residues. Comparison with Fauchere-Pliska hydrophobicity scale and the percentage of residues having large number of long-range contacts is also made. This investigation can provide some insights into the protein structure.
短程和长程接触在蛋白质结构形成中很重要。根据α螺旋和β链的含量及拓扑结构，蛋白质可分为四种不同的结构类别，即全α蛋白、全β蛋白、α/β蛋白和α+β蛋白。然而，这些类别的蛋白质在统计特性上有很大差异。在本文中，我们将从每个残基的长程（短程）接触相对数量的角度来讨论蛋白质结构。我们发现，在全α类蛋白质中，具有大量长程接触的残基百分比很小，而在全β类蛋白质中则很大。然而，在α/β类和α+β类蛋白质中，残基百分比几乎相同。我们计算了428种蛋白质中长程接触数量大于或等于N(L)=5和7的残基百分比。对于N(L)=5的全α、全β、α/β和α+β类蛋白质，平均百分比分别为13.3%、54.8%、41.4%和37.0%。随着N(L)的增加，百分比下降，尤其是全α类蛋白质。同时，在蛋白质样本中，短程接触数量大于或等于N(S)（≥N(S)）的残基百分比在全α类蛋白质中很大，而在全β类蛋白质中很小，尤其是对于较大的N(S)。我们还研究了氨基酸残基形成大量长程和短程接触的能力。半胱氨酸、缬氨酸、异亮氨酸、酪氨酸、色氨酸和苯丙氨酸能够轻松形成大量长程接触，而谷氨酸、赖氨酸、天冬氨酸、谷氨酰胺、精氨酸和天冬酰胺能够形成大量长程接触，但比较困难。我们还讨论了20种氨基酸残基形成短程接触的相对能力。还与福歇尔-普利斯卡疏水性标度以及具有大量长程接触的残基百分比进行了比较。这项研究可以为蛋白质结构提供一些见解。
