Table I. Peptide contacts in the HLA-B*18:01–SELEIKRY and HLA-B*44:03–EECDSELEIKRY binary structures
Peptide ResidueInteraction TypeContact a,bPeptide ResidueInteraction TypeContact
Ser1VDWY7, Y59, N63, Y159, W167Glu1VDWM5, Y7, Y59, R62, E63, Y159, L163, S167, R170, Y171
Ser1°HBY159Glu1N, OHBY7, Y159, S167, Y171
Ser1NWmY7, Y59, H171Nε2
Ser1OγHBN63Nδ2Glu1Oε1, Oε2HB, SBR62Nε, Nη2, R170Nη1, Nη2
Glu1Oε1, Oε2WmR62, E63Oε2, R170Nη1
Glu2VDWY7, H9, S24, N63, I66, S67, Y99, Y159Glu2VDWY7, Y9, T24, K45, E63, I66, S67, N70, Y99, Y159, L163
Glu2Oε1, Oε2HB, SBH9Nε2, S24, Y99Glu2Oε1, Oε2HB, SBY9, K45, Y99
Glu2Oε1, Oε2WmH9Nε2, T45Oγ1, S67, N70Nδ2Glu2Oε1, Oε2WmY9, T24Oγ1, S67, N70Nδ2
Cys3VDWI66, Y99, Y159
Cys3°WmY9, N70Nδ2
Leu3VDWI66, N70, Y99, Q155, L156, Y159
Leu3N, OHBN70Nδ2, Y99
Glu4VDWI66, T69, N70Glu8VDWT73, R11
Glu4°HBQ155Nε2Glu8°R11N, Nε
Glu4Oε1, Oε1WmT69Oγ1, Q155Nε2, K6Glu8Oε1HBT73Oγ1
Ile5VDWN70, T73, Y74, R97Ile9VDWW147, V152, Q155, S5
Ile5NWmN70Oδ1, T73Oγ1
Lys6VDWT73, R97, W147, V152, Q155Lys10VDWT73, Y74, N77, R97, D114, D116, W147
Lys10°HBN77Oδ1 Nδ2
Lys6N, OWmR97Nη2
Lys10NζHB, SBD114Oδ1 Oδ2, D116Oδ2
Lys10NζWmD114°, D116Oδ2
Arg7VDWT73, E76, S77, N80, W147Arg11VDWT73, E76, N77, W147, E8
Arg7°HBW147Nε1Arg11N, OHBW147Nε1, E8°
Arg7Nε, Nη2HB, SBE76Oε1, Oε2Arg11NεHBE8°
Tyr8VDWY74, S77, N80, L81, Y84, L95, R97, S116, Y123, T143, K146, W147Tyr12VDWY74, N77, T80, Y84, I95, D116, Y123, T143, K146, W147
Tyr8N, O, OXTHB, SBS77, N80Nδ2, Y84, T143Oγ1, K146Tyr12N, O, OXTHBN77Oδ1, Y84, T143Oγ1, K146
Tyr12N, OXTWmE76Oε2, T80Oγ1
Tyr8OηHBR97Nε, Nη2, S116Tyr12OηHBD116Oδ1
  • HB, hydrogen bond interactions, defined as contact distances of ≤ 3.5 Å between suitable atoms at appropriate angles, as determined in COOT; SB, ionic interactions, defined as contact distances of ≤ 4.0 Å between suitable residue atoms; Wm, hydrogen bond mediated by one water molecule (see HB); VDW, Van der Waals interactions, defined as non–hydrogen bond contact distances of ≤ 4.0 Å.

  • a Atomic contacts determined using the CCP4i implementation of CONTACT and a cutoff of 4.0 Å.

  • b Selected contacts between peptide residues are set in italics.