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: 2608–2615.

 

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: 4758–4770.

 

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