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.