Figure 5. The first eigenvector from PCA analysis on trajectory of 10–100 ns of the M170P dilated holo system.

The Cα atoms of HBC residues are shown as spheres. Transitions from white to blue indicated the counterclockwise rotation of TM2 residues associated with the opening of the HBC gate. Thirty frames were generated to describe the collective motion of the eigenvector using the Gromacs inset program g_anaeig and four of them were selected to show for visual clarity.