Function of HIV p6

  • p6 is a structural protein at the C terminus of gag gene [1].

  • p6 can recruit the host machinery to bud the virus outwards from the cell surface [2].

  • Viral protein Vpr and host proteins (e.g. AIP1/ALIX) bind to p6 during viral packaging [1].


  1. Bell NM, Lever AM: HIV Gag polyprotein: processing and early viral particle assembly. Trends Microbiol 2013, 21:136-144.(Download Article)

  2. Morita E, Sundquist WI: Retrovirus budding. Annu Rev Cell Dev Biol 2004, 20:395-425.(Download Article)


(1) Reference sequence for HIV-1 p6

  • Strain: HIV-1 subtype B HXB2 (ID: K03455)

  • Fasta format: Download

  • Reference sequence:

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(2) Reference sequence for HIV-2 and SIV p6

  • Strain: SIV Mac239 (ID: M33262)

  • Fasta format: Download

  • Reference sequence:

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51 60
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(3) Coloring scheme for above amino acids

  1. Amino acids with hydrophobic side chains (normally buried inside the protein core):

    • A - Ala - Alanine

    • I - Ile - Isoleucine

    • L - Leu - Leucine

    • M - Met - Methionine

    • V - Val - Valine

  2. Amino acids with polar uncharged side chains (may participate in hydrogen bonds):

    • N - Asn - Asparagine

    • Q - Gln - Glutamine

    • S - Ser - Serine

    • T - Thr - Threonine

  3. Amino acids with positive charged side chains:

    • H - His - Histidine

    • K - Lys - Lysine

    • R - Arg - Arginine

  4. Amino acids with negative charged side chains:

    • D - Asp - Aspartic acid

    • E - Glu - Glutamic acid

  5. Amino acids with aromatic side chains:

    • F - Phe - Phenylalanine

    • Y - Tyr - Tyrosine

    • W - Trp - Tryptophan

  6. Cysteine: C - Cys - Cysteine

  7. Glycine: G - Gly - Glycine

  8. Proline: P - Pro - Proline

Amino acid variations at HIV-1 p6

Here, we visualize the prevalence of amino acid variations at the HIV-1 p6 from HIV-1 subtype B.

Protocal of our sequence collection

  • For HIV-1 subtype B, one sequence per patient was extracted from HIV Los Alamos database (

  • We removed misclassified sequences or sequences with hypermutations, stop codons, ambiguous nucleotides, which were described in our article [1].

  • We removed sequences conferred partial or full resistance to any of the protease inhibitors, RT inhibitors and integrase inhibitors using HIVdb V6.0 .


Our sequence dataset of HIV-1 subtype B p6 included 4725 sequences. In the following picture, HXB2 indices of individual proteins are shown on top of the colored bars. A consensus amino acid at each position is shown beneath the colored bar. Natural variations are shown below the consensus amino acids; proportions (%) are colored red if they were more than 5%; blue otherwise.

HIV-1 protein interaction patterns.

Please cite our article:

  1. Guangdi Li, Supinya Piampongsant, Nuno Rodrigues Faria, Arnout Voet, Andrea-Clemencia Pineda-Peña, Ricardo Khouri, Philippe Lemey, Anne-Mieke Vandamme, Kristof Theys. An integrated map of HIV genome-wide variation from a population perspective. Retrovirology 12, 18, doi:10.1186/s12977-015-0148-6 (2015). [PDF] [PubMed Link]


(1) Secondary structure of HIV-1 p6

Here, we visualize the secondary structure of HIV-1 p6 using PDBSum (PDB code: 2C55)

(2) Tertiary structure of HIV-1 p6

Here, we provide a structure movie of p6 using PyMOL V1.7 (PDB code: 2C55). Alpha-helix and beta-strand secondary structures are demonstrated by red .


(1) Coding region of p6 at the HIV genome

(2) Localization of p6 during the HIV-1 life cycle

Here, we visualize the localization of p6 during the viral life cycle. Red stars indicate the appearance of HIV-1 p6.

Anti-HIV inhibitor

(1) Drug binding pocket of HIV-1 p6

Here, we visualize the drug binding pocket of HIV-1 p6

(2) List of known inhibitors targeting HIV-1 p6

Here, we summarize the published anti-HIV inhibitors which bind to HIV-1 p6.

Protein-protein interactions