Figure 5.

(A) Snapshot of tweezer/K214 complex extracted from the MD trajectory of the centroid conformation of the maximum cluster of the last 200 ns. (B) Zoom-in view representation. (C) 2-D Protein-ligand interaction depictions of K214/tweezer complex by the end of MD simulation (300 ns). Green circles represent hydrophobic residues, purple circles represent polar residues, red ring represent acidic residues, and blue interior rings represent basic residues. Hydrogen bonding interactions are drawn with an arrowhead, sidechain in green and backbone in blue. Green benzol rings with a “+” describe an arene–cation binding; two benzol rings, an arene–arene binding. The solvent accessible surface area is plotted onto the atoms in blue smudge for ligand and over the constituent atoms as turquoise halo for receptor residues, respectively. (For detailed interpretation of the color definitions, the reader is referred to the web version of this article (Clark and Labute, 2007).