Table 2.

Comparison of the position the bound peptide in the original crystal structure and after docking back into the MHC groove

Class	Allele	PDB	Res (Å)	Length	RMSD (Å)	Sequence
I	HLA-A*0201	1DUZ	1.80	9	0.33	LLFGYPVYV
I	HLA-A*0201	1HHG	2.60	9	0.46	TLTSCNTSV
I	HLA-A*0201	1HHJ	2.50	9	0.87	ILKEPVHGV
I	HLA-A*0201	1HHH	3.00	10	1.10	FLPSDFFPSV
I	HLA-A*0201	1I1Y	2.20	9	0.70	YLKEPVHGV
I	HLA-A*0201	1I4F	1.40	10	0.49	GVYDGREHTV
I	HLA-A*0201	1I7R	2.20	9	0.59	FAPGFFPYL
I	HLA-A*0201	1I7U	1.80	9	0.32	ALWGFVPVL
I	HLA-A*0201	1JF1	1.85	10	1.53	ELAGIGILTV
I	HLA-A*0201	1JHT	2.15	9	0.54	ALGIGILTV
I	HLA-A*0201	1OGA	1.40	9	0.32	GILGFVFTL
I	HLA-A*0201	1QRN	2.80	9	0.46	LLFGYAVYV
I	HLA-A*0201	1QSE	2.80	9	0.26	LLFGYPRYV
I	HLA-A*0201	1QSF	2.80	9	0.54	LLFGYPVAV
I	HLA-A*6801	1TMC	2.30	10	0.52	EVAPPEYHRK
I	HLA-B*0801	1AGD	2.05	8	0.28	GGKKKYKL
I	HLA-B*0801	1AGF	2.20	8	0.66	GGKKRYKL
I	HLA-B*3501	1A1N	2.00	8	0.10	VPLRPMTY
I	HLA-B*3501	1A9E	2.50	9	1.09	LPPLDITPY
I	HLA-B*5101	1E27	2.20	9	1.27	LPPVVAKEI
I	HLA-B*5301	1A1M	2.30	9	0.59	TPYDINQML
I	HLA-B*5301	1A1O	2.30	9	0.78	KPIVQYDNF
I	H2-Db	1JPF	2.18	11	1.14	SGVENPGGYCL
I	H2-Db	1JPG	2.20	9	0.33	FQPQNGQFI
I	H2-Dd	1BII	2.40	10	1.49	RGPGRAFVTI
I	H2-Kb	1FZM	1.80	8	0.32	RGYVYQGL
I	H2-Kb	1FZO	1.80	9	0.40	FAPGNYPAL
I	H2-Kb	1G7P	1.50	9	0.97	SRDHSRTPM
I	H2-Kb	1G7Q	1.60	8	0.09	SAPDTRPA
II	HLA-DR1	1AQD	2.45	10	0.63	DWRFLRGYHQ
II	HLA-DR1	1AQD	2.45	10	1.08	DWRFLRGYHQ
II	HLA-DR2	1BX2	2.60	10	0.60	VVHFFKNIVT
II	HLA-DR2	1BX2	2.60	10	0.81	VVHFFKNIVT
II	HLA-DR2	1FV1	1.90	10	0.47	HFFKNIVTPR
II	HLA-DR2	1FV1	1.90	10	0.58	HFFKNIVTPR
II	HLA-DR3	1A6A	2.75	10	0.38	KMRMATPLLM
II	HLA-DR4	1J8H	2.40	10	0.59	KYVKQNTLKL
II	HLA-DR4	2SEB	2.50	10	0.43	YMRADAAAGG
II	HLA I-Ak	1IAK	1.90	10	0.42	TDYGILQINS
II	HLA-DQ8	1JK8	2.40	10	0.21	VEALYLVCGE

RMSD values are calculated for the ligand interface Cα atoms of the lowest energy solution, superimposed onto the experimental structure.