Alignments of sequences coding for HIV1 gp120 and its predicted 3D epitopes

Alignments have been performed by MEGA 4 program, they can be downloaded in form of *.mas files from the table below.

Standard PAM matrix included in MEGA4 has been used for the alignment.

This page is an on-line resource for the publication: Khrustalev V.V. (2010) Levels of HIV1 gp120 3D B-cell epitopes mutability and variability: searching for possible vaccine epitopes. Immunological Investigations 39(6): 551-569.

 

Patient's code Complete sequences

coding for gp120

Epitope#1 Epitope#2 Epitope#3 Epitope#4 Epitope#5
H1 H1 gp120 Epitope#1 H1 Epitope#2 H1 Epitope#3 H1 Epitope#4 H1 Epitope#5 H1
H2 H2 gp120 Epitope#1 H2 Epitope#2 H2 Epitope#3 H2 Epitope#4 H2 Epitope#5 H2
H3 H3 gp120 Epitope#1 H3 Epitope#2 H3 Epitope#3 H3 Epitope#4 H3 Epitope#5 H3
H4 H4 gp120 Epitope#1 H4 Epitope#2 H4 Epitope#3 H4 Epitope#4 H4 Epitope#5 H4
H5 H5 gp120 Epitope#1 H5 Epitope#2 H5 Epitope#3 H5 Epitope#4 H5 Epitope#5 H5
S33 S33 gp120 Epitope#1 S33 Epitope#2 S33 Epitope#3 S33 Epitope#4 S33 Epitope#5 S33
S35 S35 gp120 Epitope#1 S35 Epitope#2 S35 Epitope#3 S35 Epitope#4 S35 Epitope#5 S35
ES4 ES4 gp120 Epitope#1 ES4 Epitope#2 ES4 Epitope#3 ES4 Epitope#4 ES4 Epitope#5 ES4
ES8 ES8 gp120 Epitope#1 ES8 Epitope#2 ES8 Epitope#3 ES8 Epitope#4 ES8 Epitope#5 ES8
ES9 ES9 gp120 Epitope#1 ES9 Epitope#2 ES9 Epitope#3 ES9 Epitope#4 ES9 Epitope#5 ES9

 

H1 - H5 sequences (EU743973 EU744175) are from the work of

Bunnik, E.M., Pisas, L. van Nuenen, A.C. and Schuitemaker, H. Autologous neutralizing humoral immunity and evolution of the viral envelope in the course of subtype B human immunodeficiency virus type 1 infection. J Virol. 82: 7932-7941.

 

S33 and S35 sequences (EU604549 EU604642) are from the work of

Fransen, S., Bridger, G., Whitcomb, J.M., Toma, J., Stawiski, E., Parkin, N., Petropoulos, C.J. and Huang, W. Suppression of dualtropic human immunodeficiency virus type 1 by the CXCR4 antagonist AMD3100 is associated with efficiency of CXCR4 use and baseline virus composition. Antimicrob Agents Chemother 52: 26082615.

 

ES4 (DQ410069 DQ410086), ES8 (DQ410131 DQ410178) and ES9 (DQ410188 DQ410214) sequences are from the work of

Bailey, J.R., Lassen, K.G., Yang, H.C. Neutralizing antibodies do not mediate suppression of human immunodeficiency virus type 1 in elite suppressors or selection of plasma virus variants in patients on highly active antiretroviral therapy. J Virol. 80: 47584770.

 

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