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STATISTICAL PROPERTIES OF LONG-RANGE CONTACTS IN GLOBULAR PROTEINS

Chinese Journal of Polymer Science 2004年第2期22卷 187-194页

作者：王向红 Department of Physics Wenzhou Normal College Wenzhou 325000 China

The analysis of residue-residue contacts in protein structures can shed some light on our understanding of the folding and stability of proteins. In this paper, we study the statistical properties of long-range and short-range residue- residue contacts of 91 globular proteins using CSU software and analyze the importance of long-range contacts in globular protein structure. There are many short-range and long-range contacts in globular proteins, and it is found that the average number of long-range contacts per residue is 5.63 and the percentage of residue-residue contacts which are involved in long- range ones is 59.4%. In more detail, the distribution of long-range contacts in different residue intervals is investigated and it is found that the residues occurring in the interval range of 4-10 residues apart in the sequence contribute more long-range contacts to the stability of globular protein. The number of long-range contacts per residue, which is a measure of ability to form residue-residue contacts, is also calculated for 20 different amino acid residues. It is shown that hydrophobic residues (including Leu, Val, He, Met, Phe, Tyr, Cys and Trp) having a large number of long-range contacts easily form long-range contacts, while the hydrophilic amino acids (including Ala, Gly, Thr, His, Glu, Gln, Asp, Asn, Lys, Ser, Arg, and Pro) form long-range contacts with more difficulty. The relationship between the Fauchere-Pliska hydrophobicity scale (FPH) and the number of short-range and long-range contacts per residue for 20 amino acid residues is also studied. An approximately linear relationship between the Fauchere-Pliska hydrophobicity scale (FPH) and the number of long-range contacts per residue CL, is found and can be expressed as CL = a + b × FPH where a = 5.04 and b = 1.23. These results can help us to understand the role of residue-residue contacts in globular protein structure.

关键词： Long-range and short-range contact structural class Globular protein CSU software

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Study on properties of residue-residue contacts in protein

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Journal of Zhejiang University Science 2004年第8期5卷 941-949页

作者：王向红柯见洪郑亦庄陈爱徐银香 DepartmentofPhysics WenzhouNormalCollegeWenzhou325000China

Residue-residue contacts are very important in forming protein structure. In this work, we calculated the average probability of residue-residue contacts in 470 globular proteins and analyzed the distribution of contacts in the different interval of residues using Contacts of structural Units (CSU) and structural classification (SCOP) software. It was found that the relationship between the average probability PL and the residue distance L for four structural classes of proteins could be expressed as lgPL=a+b×L, where a and b are coefficients. We also discussed the connection between two aspects of proteins which have equal array residue number and found that the distribution probability was stable (or un- stable) if the proteins had the same (or different) compact (for example synthase) in the same structural class.

关键词： Globular protein structural class Residue distance Long- and short-range contact

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