Table 2.

Conserved fragments in ectodomain of HIV-1 gp41

N	Start	End	Sequence
1	1	7	S T M G A A S
2	9	25	T L T V Q A R Q L L S G I V Q Q Q
3	27	55	N L L R A I E A Q Q H L L Q L T V W G I K Q L Q A R V L A
4	62	67	D Q Q L L G
5	69	74	W G C S G K
6	87	92	S W S N K S
7	153	158	W L W Y I K

Fragments were selected to have six or more consecutive residues with H ≤ 1, and were obtained from an MSA of the HIV-1 gp41 ectodomain (residues 528–674 in gp160 from HIV-1 strain H2XB2). The MSA includes 359 representative sequences of HIV-1 clades A (73), B (85), C (85), D (51) and 01_AE (65) that were aligned using MUSCLE (29). The MSA is available at http://imed.med.ucm.es/PVS/supplemental/gp41_ecto_aln.html