Skip to main content
. 2021 Nov 18;6(47):32043–32071. doi: 10.1021/acsomega.1c04817

Table 5. Binding Affinities and Interaction between Selected CTL Epitopes and HLA Alleles.

alleles epitopes grid box size (Å) docking score (kcal mol–1) hydrogen bond interactions hydrophobic bond interactions attractive charges unfavorable bumps
HLA-B*35:01 RTTAPAAAF 62.33 × 45.41 × 70.54 –10.0 Tyr84, Arg97, Trp147 Tyr74 (pi-sigma), Lys146(pi-alkyl), Tyr159 (pi-sigma), Leu163 (pi-alkyl), Trp167 (pi–pi stacked)   Arg97, Ser116, Lys146, Trp147
  WTIGNRAPY   –9.4 Tyr9, Arg62, Ser77, Thr143, Trp147 Ile95 (pi-alkyl), Trp147 (pi–pi T shaped), Tyr159 (pi-sigma), Trp167 (pi–pi stacked) Lys146 Arg62
  NPHAQGIAL   –8.8 Arg97, Tyr99, Trp147, Trp167 Tyr7 (pi-alkyl), Ile66 (pi-alkyl), Phe67 (pi-alkyl), Tyr74 (pi-alkyl), Ile95 (pi-alkyl), Trp147 (pi-alkyl)   Ser77
  control   –9.3 Asn70, Asn80, Tyr84, Thr143, Lys146, Trp147, Tyr171 Tyr59 (pi-alkyl), Asn63 (carbon–hydrogen), Ile95 (pi-alkyl), Trp147 (pi–pi stacked), Tyr159 (pi-alkyl), Trp167 (pi-alkyl) Tyr7  
HLA-A*01:01 ISPNLLGIY 60.64 × 73.76 × 45.49 –7.8 Tyr84, Asp116, Trp147, Arg156 Leu81 (pi-alkyl), Lys146 (pi-alkyl), Trp147 (pi-sigma), Val158 (alkyl), Arg163 (pi-alkyl) Lys146, Tyr159 Arg163
  FTYNLTNLV   –7.8 Asn66, Thr73, Asn77, Tyr84, Lys146, Trp147, Arg156 Leu81 (pi-alkyl), Ile95 (pi-alkyl), Lys146 (pi-alkyl), Val150 (pi-alkyl), Tyr159 (pi-sigma) Arg156 Trp147
  GSNDTELNY   –7.7 Ala76, Thr80, Arg82, Tyr84, His93, Asp116, Tyr118, Lys146, Trp147 Gly79 (carbon–hydrogen), Leu81 (pi-alkyl), Gly83 (carbon–hydrogen), Glu89 (carbon–hydrogen), Thr143 (carbon–hydrogen) Arg75, Arg82, Lys146  
  Control   –8.0 Glu63, Asn66, Ala69, Thr73, Asn77, Arg114, Asp116, Lys146, Trp147, Gln155, Arg156 Ala69 (pi-alkyl), His70 (pi-alkyl), Thr73 (pi-sigma), Ala76 (pi-alkyl), Leu81 (pi-alkyl), Thr143 (carbon–hydrogen), Tyr159 (pi-sigma)   Arg156
HLA-B*14:02 FDERRHVAM 61.25 × 48.69 × 72.95 –8.6 Tyr7, Asn63, Asn70, Asp74, Ser77, Trp147 Ile66 (carbon–hydrogen), Leu81 (pi-alkyl), Leu95 (pi-alkyl), Trp97 (pi-alkyl), Tyr99 (pi-sigma), Phe116 (pi–pi T shaped), Tyr159 (pi-sigma) Asp74, Glu152, Trp167 Glu76, Asn80, Tyr159
  RPMNRPTAL   –7.8 Asn70, Thr73, Ser77, Lys146, Trp147, Glu152 Ser77 (carbon–hydrogen), Trp97 (pi-sigma), Trp147 (pi-sigma) Glu152 Asp74, Ser77
  control   –10.0 Glu55, Arg62, Asn63, Asn70 Leu81 (pi-alkyl), Leu95 (pi-alkyl), Phe116 (pi–pi T shaped), Tyr123 (pi–pi stacked), Trp133 (alkyl),Trp147 (pi-sigma), Leu156 (alkyl), Trp167 (pi-sigma) Trp167 Tyr7, Gly56, Asn63
HLA-A*03:01 SLTCAGIRK 73.20 × 52.65 × 53.24 –6.5 Glu63, Asn66, Glu152, Gln155 Glu63 (carbon–hydrogen), Tyr99 (pi-sigma), Tyr159 (pi-sigma) Tyr7, Glu63, Trp167 Tyr99
  control   –7.1 Tyr7, Asn66, Thr73, Tyr99, Trp147, Glu152, Gln155, Tyr159 Tyr7 (pi-sigma), Ala69 (pi-alkyl), Tyr99 (carbon–hydrogen), Tyr159 (pi-sigma), Trp167 (pi-sigma) Glu63, Glu152, Trp167 Arg114