TABLE 2.
Peptide-MHC contact table
SB, salt bridge; BSA, buried surface area between the peptide and MHC; r.m.s. deviation, root mean square deviation calculated by aligning each pMHC complex (α-chain, peptide, and β2m) in PyMOL. A 3.4 Å cut-off was used for HBs and salt bridges, and a 4 Å cut-off was used for vdWs.
| Peptide | H-2Kd·G9G |
H-2Kd·G9V |
||
|---|---|---|---|---|
| vdW | HB/SB | vdW | HB/SB | |
| Leu-1 | 27 | 2 | 28 | 3 |
| Tyr-2 | 21 | 3 | 24 | 5 |
| Leu-3 | 18 | 2 | 19 | 2 |
| Val-4 | 13 | 1 | 12 | 1 |
| Cys-5 | 25 | 1 | 19 | 1 |
| Gly-6 | 6 | 2 | 6 | 2 |
| Glu-7 | 12 | 3 | 14 | 3 |
| Arg-8 | 19 | 1 | 18 | 1 |
| Gly/Val-9 | 17 | 4 | 21 | 4 |
| Total | 158 | 19 | 161 | 22 |
| BSA (Å2) | 1,909.4 | 1,983.4 | ||
| r.m.s. deviation | G9G/G9V | 0.355 | G9V/G9GF | 0.647 |
| G9G/G9GF | 0.491 | |||