fig6

Figure 6. Contact analysis of the ARN12502-USP14 complex from molecular dynamics (MD) simulations. (A) Bar plots showing interactions of ARN12502 with USP14, averaged over three replicates; error bars represent standard error. The left panel shows the persistence of contacts (% simulation time) between the ligand and the top 20 residues. The middle and right panels report the percentage of trajectory frames in which each interaction type was present, globally and by residue (top five mostly contacted), respectively; (B) 3D illustration of the most representative structure obtained by RMSD clustering, with ARN12502 in cyan and surrounding USP14 residues in grey, showing the coordination of the ligand inside the binding pocket; hydrogen atoms are omitted for clarity; (C) Schematic 2D representation corresponding to panel B, showing specific contacts; only interacting hydrogens of ARN12502 are displayed. Interaction types and residue classes are indicated in the legend. For clarity, representation is split into two panels. USP14: Ubiquitin-specific protease 14; 3D: three-dimensional; 2D: two-dimensional.