Abstract
The relations of the binding free energies in a dataset of 69 protein complexes with the numbers of interfacial atom pairs, as well as with the atomic distances of the pairs, are analyzed. It is found that the interfacial main-chain atom pairs contribute more to the correlation than the interfacial side chain atom pairs do, and the polar atom pairs contribute more than the non-polar atom pairs do. Interfacial atom pairs with atomic distance in the range of 6–12 Å are the most important to explain the differences in binding free energies in the datasets.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
References
Zhou, H., and Zhou, Y. Q. (2002) Protein Sci., 11, 2714–2726.
Liu, S., Zhang, C., Zhou, H. Y., and Zhou, Y. Q. (2004) Proteins: Structure, Function, and Bioinformatics, 56, 93–101.
Jiang, L., Gao, Y., Mao, F., Liu, Z., and Lai, L. (2002) Proteins, 46, 190–196.
Sippl, M. J. (1990) J. Mol. Biol., 213, 859–883.
Marsden, P. M., Puvanendrampillai, D., Mitchell, J. B. O., and Glen, R. C. (2004) Org. Biomol. Chem., 22, 3267–3273.
Mitchell, J. B. O., Roman, A. L., Alexander, A., and Janet, M. T. (1999) J. Comput. Chem., 20, 1165–1176.
Mitchell, J. B. O., Roman, A. L., Alexander, A., Mark, J. F., and Janet, M. T. (1999) J. Comput. Chem., 20, 1177–1185.
Sippl, M. J. (1995) Curr. Opin. Struct. Biol., 5, 229–235.
Moont, G., Gabb, H. A., and Sternberg, M. J. E. (1999) Proteins: Structure, Function, and Genetics, 35, 364–373.
Robert, C. H., and Janin, J. (1998) J. Mol. Biol., 283, 1037–1047.
Thomas, P. D., and Dill, K. A. (1996) J. Mol. Biol., 257, 457–469.
Samudrala, R., and Moult, J. (1998) J. Mol. Biol., 275, 895–916.
Lee, C. H., Saksela, K., Mirza, U. A., Chait, B. T., and Kuriyan, J. (1996) Cell, 85, 931–942.
Chothia, C., and Janin, J. (1975) Nature, 256, 705–708.
Xu, D., Lin, S. L., and Nussinov, R. (1997) J. Mol. Biol., 265, 68–84.
Ma, X. H., Wang, C. X., Li, C. H., and Chen, W. Z. (2002) Protein Eng., 15, 677–681.
Matthew, J. B. (1985) Annu. Rev. Biophys. Biophys. Chem., 14, 387–417.
Vajda, S., Weng, Z. P., Rosenfld, R., and DelLisi, C. (1994) Biochemistry, 33, 13977–13988.
Zhang, C., Vasmatzis, G., Cornette, J. L., and DeLisi, C. (1997) J. Mol. Biol., 267, 707–726.
Author information
Authors and Affiliations
Corresponding author
Additional information
Published in Russian in Biokhimiya, 2008, Vol. 73, No. 2, pp. 283–286.
Rights and permissions
About this article
Cite this article
Li, YC., Zeng, ZH. Interfacial atom pair analysis. Biochemistry Moscow 73, 231–233 (2008). https://doi.org/10.1134/S0006297908020156
Received:
Revised:
Published:
Issue Date:
DOI: https://doi.org/10.1134/S0006297908020156