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\(\bar P_L \) and the residue distanceL for four structural classes of proteins could be expressed as lgP L =a+b×L, wherea andb 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 unstable) if the proteins had the same (or different) compact (for example synthase) in the same structural class.
This is a preview of subscription content, log in to check access.
Buy single article
Instant access to the full article PDF.
Price includes VAT for USA
Bahar, I., Kaplan, M., Jernigan, R.L., 1997. Short-range conformational energies, secondary structure propensities, and recognition of correct sequence-structure matches.Proteins,29:292–308.
Berman, H.M., Westbrook, J., Feng, Z., 2000. The protein data bank.Nucleic Acids Res.,28:235–242.
Bernstein, F.C., Koetzle, T.F., Williams, G.J.B., Meyer, E.F., Brice, M.D., Rodgers, J.R., Kennard, Q., Shimanouchi, T., Tasumi, M., 1977. The protein data bank: a computer-based archival file for molecular structures.J. Mol. Biol.,112:535–542.
Chan, H.S., Dill, K.A., 1998. Compact polymers.Macro-molecules,22:4559–4573.
Fiser, A., Dosztanyi, Z., Simon, I., 1997. The role of long-range interactions in defining the secondary structure of proteins is overestimated.Computer Applications in the Biosciences,13:297–301.
Gromiha, M.M., Selvaraj, S., 1997. Influence of medium and long-range interactions in different structural classes of globular proteins.J. Biol. Phys.,23:151–162.
Gromiha, M.M., Selvaraj, S., 1998. Protein secondary structure prediction in different structural classes.Prot. Eng.,11:249–251.
Gromiha, M.M., Selvaraj, S., 1999. Important of long-range interactions in protein folding.Biophysical Chemistry,77:49–68.
Gromiha, M.M., 2001. Important inter-residue contacts for enhancing the thermal stability of thermophilic proteins.Biophysical Chemistry,91:71–77.
Hubbard, T.J.P., Ailey, B., Brenner, S.E., Murzin, A.G., Chothia, C., 1999. SCOP: A structural classification of proteins database.Nucleic Acids Res.,27:535–542.
McDonald, K., Thornton, J.M., 1994. Satisfying hydrogen bonding potential in proteins.J. Mol Biol.,238:777–793.
Miyazawa, S., Jernigan, R.L., 1985. Estimation of effective inter-residue contact energies from protein crystal structures: quasi-chemical approximation.Macromolecules,18:543–552.
Miyazawa, S., Jernigan, R.L., 1993. A new subatitution matrix for protein sequence searches basedn contact frequencies in protein structures.Protein Eng.,6:267–278.
Miyazawa, S., Jernigan, R.L., 1996. Residue-residue potentials with a favorable contact pair term and an unfavorable high packing density term, for simulation and threading.J. Mol. Biol.,256:623–644.
Russell, R.B., Barton, G.J., 1994. Structural features can be umconservated in proteins with similar folds.J Mol Biol.,244:332–350.
Selbig, J., Argos, P., 1998. Relationships between protein sequence and structure patterns based on residue contacts.Proteins,31:172–185.
Sobolev, V., Sorokine, A., Prilusky, J., 1999. Automated analysis of interatomic contacts in proteins.Bioinformatics,15:327–332.
Wang, X.H., Ke, J.H., Hu, M.X., 2004. Statistical properties of long-range contacts in globular proteins.Chinese of Journal of Polymer Science,22(4):187–194 (in Chinese).
Zhang, C., Kim, S.H., 2000. Environment-dependent residue contacts energies for proteins.Proc. Natl. Acda. Sci.,97(6):2550–2555.
Project supported by the National Natural Science Foundation of China (Nos. 29874012, 20174036, 20274040), and the Natural Science Foundation of Zhejiang Province (No. 10102), and the Science Technology Development Plan of Wenzhou City (No. S2002A014), China
About this article
Cite this article
Xiang-hong, W., Jian-hong, K., Yi-zhuang, Z. et al. Study on properties of residue-residue contacts in protein. J. Zheijang Univ.-Sci. 5, 941–949 (2004). https://doi.org/10.1007/BF02947603
- Globular protein
- Structural class
- Residue distance
- Long-and short-range contact