Ensembler: Enabling High-Throughput Molecular Simulations at the Superfamily Scale
Fig 9
Src, Abl1, and Flt4 models projected onto the distances between two conserved residue pairs, colored by sequence identity.
Two Src structures (PDB entries 1Y57 [57] and 2SRC [56]) are projected onto the plots for reference, representing active and inactive states respectively. These structures and the residue pairs analyzed here are depicted in Fig 8. Distances are measured between the center of masses of the three terminal sidechain heavy atoms of each residue. The atom names for these atoms, according to the PDB coordinate files for both reference structures, are—Lys: NZ, CD, CE (ethylamine); Glu: OE1, CD, OE2 (carboxylate); Arg: NH1, CZ, NH2 (part of guanidine).