Quantitative peptide binding motifs for 19 human and mouse MHC class I molecules derived using positional scanning combinatorial peptide libraries

Table 4 Comparison of main anchor motifs identified using positional scanning combinatorial libraries with those using other approaches.

		Published motif					Combinatorial library motif
System	Allele	P2	P3	P5	P6	P9	P2	P3	P5	P6	P9
HLA	A*0201	LM [IVATQ]				VL [MIAT]	L [MQ]				VI [LA]
	A*3001	YF				L		RK			KA [LVIY]
	A*3201	[MLITVQS]				[WIFYHT]	TMIQLVS [A]				FIYLW
	A*6802	[LMIVATQS]				[LMIVAT]	VTS [IALMP]				VALI
	B*0702	P				L [FWYIVMA]	P [VA]				LFAVI [M]
	B*0801		RK	RK		LIVM			RHKF	F [RH]	LFMVIA [E]
	B*1501	QL				FY					FY [M]
	B*1503	QK				FY	QMK [LHASE]				F [MY]
	B*2705	R				KRLYANFMIH	R
	B*3501	P				YFMLI [WVA]	PA				FYM [A]
	B*5101	APG				VI [FWYLMA]	PA [GQVS]				I [V]
	B*5301	P				WFL [YIVMA]	PA [IV]				FC [IW]
	B*5401	P				[FWYLIVMA]	A [P]				AV
	B*5801	AST				FW	STA [VG]				WFIY [MC]
	B*5802	ST			R	F					IFL [MW]
H-2	Db			N		LIVM			N [L]		IML [VF]
	Dd	G	P	RK		LFI	G	P			FLI [C]
	Kd	YF				LIVM	Y				ILV [M]
	Kk	E				LIVM	E [D]				IV [FL]

1. Indicates residues preferred in the indicated anchor positions, as reported in the published literature. Motifs are as identified by pool sequencing motifs. Residues in brackets are additional residues identified on the basis of peptide binding studies.
2. Indicates residues preferred in the indicated anchor positions, as identified by the combinatorial library approach. Motifs are as identified using an ARB > 0.2 threshold. Residues in brackets are additional residues identified when the threshold is lowered to 0.1.