Table 5.
B pocket structures of reference panel alleles.
| Residues1 | Key residues | Reference panel allele(s) | Associated supertype(s) | Specificity |
| YDSVENIFNY | DENIFNY | B*0801-2 | B08 | Undefined |
| YFAVMEKVHC | FMEKVHC | A*0207 | A02 | Small and aliphatic |
| YFAVMEKVHF | FMEKVHF | A*0217 | A02 | Small and aliphatic |
| YFAVMEKVHY | FMEKVHY | A*0201-4 | A02 | Small and aliphatic |
| YFAVMENMHY | FMENMHY | A*0101 | A01 | Small and aliphatic |
| YFAVMENVHY | FMENVHY | A*3201, A*7401 | A01 A03 | Small and aliphatic |
| YFAVMENVQY | FMENVQY | A*0301 | A03 | Small and aliphatic |
| YHSVTEISNS | HTEISNS | B*3701 | B44 | Acidic |
| YHSVTNISNY | HTNISNY | B*1801 | B44 | Acidic |
| YHTVEEICKY | HEEICKY | B*2702-7, B*2709 | B27 | Basic |
| YHTVENICKY | HENICKY | B*7301 | B27 | Basic |
| YHTVKEISNY | HKEISNY | B*4001-2, B*4006, B*4501 | B44 | Acidic |
| YSAVMEKVHF | SMEKVHF | A*2301, A*2402 | A24 | Aromatic and aliphatic |
| YSAVMENVHY | SMENVHY | A*3002-4 | A01 | Small and aliphatic |
| YSAVMENVQY | SMENVQY | A*3001 | A01 A03 | Small and aliphatic |
| YTAVMENVHY | TMENVHY | A*3101 | A03 | Small and aliphatic |
| YTAVMNNVHY | TMNNVHY | A*3301, A*3303 | A03 | Small and aliphatic |
| YTAVMQNVQY | TMQNVQY | A*2902 | A01 A24 | Small, aliphatic and aromatic |
| YYAVENIYQY | YENIYQY | B*5501-2, B*5601 | B07 | Proline |
| YYAVGNIYQY | YGNIYQY | B*5401 | B07 | Proline |
| YYAVMEISNY | YMEISNY | B*1501, B*1512 | B62 | Aliphatic |
| YYAVMEKVHY | YMEKVHY | A*0205, A*0206, A*0214 | A02 | Small and aliphatic |
| YYAVMEKYQY | YMEKYQY | B*4601 | B62 | Aliphatic |
| YYAVMENMSY | YMENMSY | B*1516-17, B*5701-2 | B58 | Small |
| YYAVMENVQY | YMENVQY | A*1101 | A03 | Small and aliphatic |
| YYAVMNIFNY | YMNIFNY | B*1508 | B07 | Proline |
| YYAVMNISNY | YMNISNY | B*1502, B*1513 | B62 | Aliphatic |
| YYAVMNNVHY | YMNNVHY | A*2601-3 | A01 | Small and aliphatic |
| YYAVMNNVQY | YMNNVQY | A*6601, A*6801-2, A*6901 | A02 A03 | Small and aliphatic |
| YYAVTEISNY | YTEISNY | B*5201 | B62 | Aliphatic |
| YYAVTENMSY | YTENMSY | B*5801-2 | B58 | Small |
| YYAVTNIFNY | YTNIFNY | B*3501, B*3503, B*5101-3, B*5301, B*7801 | B07 | Proline |
| YYSVEEISNY | YEEISNY | B*1503, B*3902, B*4801 | B27 | Basic |
| YYSVENICNS | YENICNS | B*3909 | B27 | Basic |
| YYSVENICNY | YENICNY | B*1402, B*1509-10, B*1518, B*3801, B*3901 | B27 | Basic |
| YYSVENIYNY | YENIYNY | B*0703 | B07 | Proline |
| YYSVENIYQY | YENIYQY | B*0702, B*0705, B*4201, B*6701 | B07 | Proline |
| YYTVKEISNY | YKEISNY | B*4402-3 | B44 | Acidic |
1. Based on data presented in Saper et al, and Madden (see Methods), the MHC residues utilized as constituting the B pocket are: 7, 9, 24, 34, 45, 63, 66, 67, 70, and 99. Key residues are those in positions 9, 45, 63, 66, 67, 70, and 99.