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| Aromatic Stacking Interaction | Hydrophobic Interaction | |
| 1501-MBP | αF54-F91, βF26-F92, βH81-H90 | βN82-V89, βV85-V89 |
| 1501-EBNA-1 | βY78-H407 | βV85-P404 |
| 1601-MBP | αF54-F91, βF26-F92, βR71-F92 | βN82-V89, βV85-V89 |
| 1601-EBNA-1 | Absent | Absent |
The stacking and hydrophobic interaction for the bound and free MHC-peptide are reported below. The interacting pair is given as allele residue - peptide residue.
