The Journal of Biological Physics and Chemistry

2007

Volume 7, Number 1, p.p. 7-14


Amino acid similarities based on side chain terminal group contacts

G. Managadze,+ B. Vishnepolsky,+ M. Grigolava and M. Pirtskhalava*

Institute of Molecular Biology and Biological Physics, 12 Gotua St, 0160 Tbilisi, Georgia

Sequence alignment is a standard method to infer evolutionary, structural and functional relationships among sequences of amino acids. The quality of alignments depends on the similarity matrix used. Contact-based matrices are applicable for the comparison of distantly related sequences. Differences between amino acid sequences are revealed mainly at the level of side chain terminal groups (SCTG). Distances between the heavy atoms in the SCTG are fixed. Contact between amino acids was estimated on the basis of evaluation of the distance between SCTGs. Here, collection and analysis of terminal group contact data is reported. On the basis of the results, a new amino acid similarity matrix (TGC) was constructed, and a comparison made between the TGC, evolutionary change-based matrices and other contact-based matrices. Essential differences between TGC and the contact-based matrices reveal the origin of the interactions that are the basis of SCTG close contact-based similarity. Hence, the information reflected in TGC can be used in addition to other structural information that is frequently used in fold recognition.

Keywords: fold recognition, side chain terminal group contact, substitution matrix


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