Figure 2

Cluster analysis of MD simulation trajectories of all HLA-B*57:01 systems. (A,C,E) Residue pairs used for distance measurements. The MHC binding cleft is shown as a cartoon with the α2 helix omitted for clarity and the peptide shown in sticks. The Cα atoms of paired residues in the peptide and β-sheet are shown as spheres, coloured blue for peptide atoms and red for β-sheet atoms. The distance (in Å) is calculated between the atoms in each pair, shown as a yellow dotted line. (B,D,F) Plots of the distance between the Cα of the central peptide residue and the Cα of the underlying β-sheet residue (vertical axis), against the maximum of the distances between the Cα of the N- and C-terminal residues of the peptide and the Cα of the corresponding underlying β-sheet residue (horizontal axis). Each point on the graph corresponds to a single frame from each trajectory, with one frame shown for each nanosecond of simulation time. Each system is displayed in a different colour as per the key displayed with the figure.