Table 3.

Dynamic protein/protein side chain contacts appearing in MD simulations. For improved sampling, three independent MD simulations were carried out with each ligand in each protein model. Contact types: H-bond: hydrogen bonding; vdW: van der Waals-contact. Colour coding: white: <30% contact occurrence during simulation; blue: contact present 30% to 60% of simulated time; yellow: contact present in 60% to 90% of simulated time; red: contact present in >90% of simulated time. Van der Waals contacts were counted as present if the distance between any atom of ligand and protein were within a distance that was equal or smaller than the sum of their van der Waals radii. Hydrogen bonds were counted as present if the distance between hydrogen bond donor and acceptor was 2.5–3.5 Å, and if the off-axis angle between O/N–H–O/N was smaller than 30°. Like in the case of protein/ligand contacts, contacts were judged to be significant if they existed in at least two simulation runs with >60% of simulated time.