Fig. 6: Interactions stabilizing the retinal conformation of K.

a The NCI plot for the EC side of the SB linkage. Hydrogen atoms are added according to the optimization with the QM/MM calculation. The reduced density gradient isosurface at s(ρ) = 0.5 is added as colored surfaces. The nature of the interaction can be visualized by the color according to the value of sign(λ₂)ρ in an atomic unit (e a₀⁻³), where λ₂ and sign(λ₂) are the second eigenvalue of the Hesse matrix of ρ and its sign, respectively. The color scale are given at the right bottom of the panel. Blue, green and red correspond to attraction, weak attraction and repulsion, respectively. The blue arrows indicate the interaction between H atoms of Cε in Lys216 and Thr89. The green arrow indicates the interaction between H of Cε in Lys216 and Asp85. The orange arrow indicates the interaction between H of Nς in Lys216 and W402. The purple arrow indicates the interaction between H of Nς in Lys216 and Asp212. b Interactions with surrounding residues (Asp85, Thr89 and Asp212) and Water402 prevent torsional rotation at Nς–Cε and Cε–Cδ bonds in Lys216. c The torsional potential energy curve for the Nς–Cε bond. The torsion angles in K/bR and L are ~+240° and +120°, respectively. d The torsional potential energy curve for the Cε–Cδ bond. The torsion angles in K/bR and L are approximately +60° and −60°, respectively.