Variability analysis of HIV-1 gp120 V3 region: IV. Distribution functions for intra- and inter-subtype amino acid hamming distances

Shchelkanov MYu; N S Starikov; I V Yaroslavtsev; P O Tsvetkov; A N Yudin; M V Denisov; A A Slavsky; A A Vedenov; E V Karamov

doi:10.1080/07391102.1998.10508209

Variability analysis of HIV-1 gp120 V3 region: IV. Distribution functions for intra- and inter-subtype amino acid hamming distances

J Biomol Struct Dyn. 1998 Apr;15(5):877-85. doi: 10.1080/07391102.1998.10508209.

Authors

Shchelkanov MYu¹, N S Starikov, I V Yaroslavtsev, P O Tsvetkov, A N Yudin, M V Denisov, A A Slavsky, A A Vedenov, E V Karamov

Affiliation

¹ Moscow Institute of Physics and Technology, Faculty of Physicochemical Biology, Department of Molecular Biophysics, Dolgoprudny, Moscow region, Russia.

PMID: 9619510
DOI: 10.1080/07391102.1998.10508209

Abstract

Distribution functions for intra- and inter- HIV-1 V3-loop subtypes amino acid Hamming distances were calculated (850 V3-loop sequences from the Los Alamos HIV-1 Database (1996) were used). These functions have pronounced bell-like shape. Such shapes of the histograms for HIV-1 V3 intra- and inter-subtype distriutions are discussed to confirm the applicability of different hierarchical cluster procedures for HIV-1 V3 classification. Two-mode distribution for the subtype E could sertificate that this subtype includes two thinner taxons.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Amino Acids
HIV Envelope Protein gp120 / chemistry*
Humans
Mathematical Computing*
Peptide Fragments / chemistry*

Substances

Amino Acids
HIV Envelope Protein gp120
HIV envelope protein gp120 (305-321)
Peptide Fragments