Table 2.

HIV-1C V3 sequence characteristics.

ID	Pheno- type	# of clones	V3 loopa	V3 length	Net charge	N- glyco	11/25 Prediction	C-PSSM prediction	Change in GPGQb
DM8		MRCA	CTRPGNNTGRSVRIGPRKAFYTTRKIIGDIRAAHC
	R5	10	------R-----GQ---GE--------	35	4	1	R5	X4	0
	R5	1	------R-----GQ---GE---V----	35	4	1	R5	X4	0
	X4	1	-------------LRT--~--------	34	7	1	X4	X4	1
DM146		MRCA	CTRPDNNTRRSVRMGIGPGQVFYTNDIIGDIRQAHC
	Dual	8	--------R-------T-------R---	36	5	1	X4	X4	0
	R5	5	-----------~~----------R---	34	4	1	R5	X4	0
	R5	2	-----------~~--------------	34	3	1	R5	X4	0
	R5	1	-----------~~-----------Y--	34	2	1	R5	X4	0
	R5	1	-----------~~--A-----------	34	3	1	R5	X4	0
	R5	1	-I-------I---~~----A-----E-S-	34	1	1	R5	X4	0
DM159		MRCA	CTRPNNNTRKSVRIGPGQTFYATGEIIGDIRRAHC
	R5	2	-I------R-M----ALFT---N-Q---	35	5	1	R5	X4	0
	R5	2	-I------R-M----AYFT---N-Q---	35	5	1	R5	X4	0
	R5	1	--------------------------	35	5	1	R5	R5	0
	Dual	1	---I-RERK----RA-FR-QMT---Q-S-	35	6	0	R5	X4	1
	Dual	1	---I-RERK----RA-FR-QMT---Q-S-	35	5	0	R5	X4	1
	X4	1	---I-RERK----RA-FR-QMT---Q-S-	35	5	0	X4	X4	1
	X4	1	---I-RERK----RA-FR-QMT---Q-S-	35	6	0	X4	X4	1
	X4	1	---I-NVRN----RALFK-KMT---Q-S-	35	6	0	X4	X4	1
DM173		MRCA	CVRPNNNTRKSVRIGIGRGQTFYANRIIGDIRQAHC
	Dual	6	---------------------------	36	7	1	R5	X4	6
	X4	3	---------------------------	36	7	1	R5	X4	3
DM172		MRCA	CIRPGNNTRRRVRMGIGPGQTFYATGNIIGDIRQAHC
	Dual	6	-M-------------------------	37	6	1	X4	X4	0
	Dual	1	---------------------------	37	6	1	X4	X4	0
	X4	1	---------------------------	37	6	1	X4	X4	0
	X4	1	-M-------------------------	37	6	1	X4	X4	0
DM192		MRCA	CTRPNNNTSQSIRIGPGQTFYAMGRIIGDIRQAHC
	R5	5	--------------------------	35	4	2	X4	X4	0
	R5	1	--------------Y-----------	35	4	2	X4	X4	0
	R5	1	------RE-------Y--D--------	35	2	1	R5	R5	0
	R5	1	------RE-------Y--D--------	35	2	1	R5	R5	0
	Dual	1	-----RRK---------I-GV-----Y-	35	5	0	R5	X4	0
DM202		MRCA	CTRPGNNTSRSIRIGPGQTFYATGRITGNIRQAHC
	R5	1	-I-----------------V-D--L--	35	5	2	X4	X4	0
	R5	3	--------------------D-----	35	5	2	X4	X4	0
	R5	1	-I-----------------V-D-----	35	6	2	X4	X4	0
	Dual	2	-I-----------------V-D-----	35	5	2	X4	X4	0
	Dual	1	-M----K------R-----V-D--K--	35	8	1	X4	X4	1
	Dual	1	-M----R------R-----V-D--K--	35	8	1	X4	X4	1
	Dual	1	-M----K------R-----V-D-----	35	7	1	X4	X4	1
DM263		MRCA	CIRPGNNTRKSMRIGPGQTFYATGDIIGDIRKAHC
	R5	3	--------------------------	37	5	1	R5	R5	0
	R5	3	------------------E--------	37	5	1	R5	R5	0
	R5	1	-T-------------------N-Q---	37	5	1	R5	R5	0
	Dual	1	------------------E--------	37	5	1	R5	R5	0
	Dual	1	----K------I-H-----K--------	37	9	1	X4	X4	1
	Dual	1	----K------I-H-----K--------	37	9	1	X4	X4	1
	Dual	1	----K------I-H-----K--------	37	9	1	X4	X4	1
DM268		MRCA	CTRPSNNTRRRVRIGIGPGQAFDATGEIIGDIRQAHC
	X4	11	------------R------Q-------	37	6	1	X4	X4	11
	R5	5	--------S-~~---YT----------	35	4	1	R5	R5	0
	R5	2	--------S-~~---YT----------	35	4	1	R5	R5	0
DM269		MRCA	CIRPGNNTSRSIRIGPGQAFYATGRIVGDIRQAHC
	R5	10	-------------T------------	35	5	2	X4	X4	0
	R5	1	--------------------------	35	5	2	X4	X4	0
	Dual	6	-M----K------RT---K----K---	35	8	1	X4	X4	6

^aV3 crow n motif in bold.

^bNumber of clones with substitution in GPGQ crow n.