Mechanism of a Herbal Formula Associated with Prognosis and Immune Infiltration in LIHC: Transcriptomics Analysis and Molecular Dynamics Simulations

Figure 13

Nonbonded interactions between the molecules and the residues at the binding site for 1JUN-tanshinone IIA. (a) Timeline representation of the interactions and contacts (H-bonds, Hydrophobic, Ionic, Water bridges). (b) Top panel shows the total number of specific contacts the protein makes with the ligand over the course of the trajectory. The bottom panel shows which residues interact with the ligand in each trajectory frame. Some residues make more than one specific contact with the ligand, which is represented by a darker shade of orange, according to the scale to the right of the plot.

(a)

(b)