Binding affinities and interaction between selected epitopes and HLA alleles.

Protein	Allele	Epitope	Docking score (kcal mol−1)	Hydrogen bond interaction	Hydrophobic bond interaction	Unfavorable bumps	Attractive charges
E	HLA-B*15:01	LVKPSFYVY	−8.4	Arg62, Asn80, Arg97, Gln155	Tyr7 (pi–alkyl), Asn70 (carbon–hydrogen bond), Leu95 (pi–sigma), Trp147 (pi–pi T-shaped), Tyr159 (carbon–hydrogen bond)	—	Lys146
		VSLVKPSFY	−7.5	Arg62, Asn70, Tyr74, Asn80, Tyr84, Lys146, Ala150, Glu152, Gln155	Ile66 (pi–alkyl), Ser77 (carbon–hydrogen bond), Tyr99 (pi–pi stacked), Tyr159 (pi–pi stacked)	Trp147	—
		Control	−8.8	Glu63, Arg97, Trp147, Glu152, Gln155	Tyr7 (pi–sigma), Met45 (pi–alkyl), Ile66 (pi–alkyl), Lys146 (pi–alkyl), Trp147 (pi–alkyl), Trp167 (pi–sigma)	Arg62, Tyr99, Tyr159	Glu63
M	HLA-B*35:01	AGDSGFAAY	−7.7	Tyr7	Tyr99 (pi–pi stacked), Val152 (pi–alkyl), Leu156 (pi–alkyl), Trp167 (pi–sigma)	—	Arg62, Arg97
		LVGLMWLSY	−8.5	Tyr7, Asn70, Trp147, Gln155, Trp167	Tyr7 (pi–pi stacked), Ile66 (pi–alkyl), Tyr99 (pi–pi stacked), Lys146 (pi–alkyl)	Lys146, Trp147	Trp167
		Control	−9.3	Asn70, Asn80, Tyr84, Thr143, Lys146, Trp147, Tyr171	Tyr59 (pi–alkyl), Asn63 (carbon–hydrogen bond), Ile95 (pi–alkyl), Trp147 (pi–pi T-shaped), Tyr159 (pi–alkyl), Trp167 (pi–alkyl)	—	Tyr7