Looking for the contacts

Slide 1. To illustrate ligand-protein interactions we have studied formation of hydrogen bonds (hbonds) between [MPG]616 ligand and it's surrounding. At first, we have selected all amino acid residues disposed in less then 4.0Å from ligand. Then atoms that may hypothetically form hbonds, were carefully weeded, using principle, that average length of hbond is 3.5A. Hypothetical bonds were compared with bonds presented in PDB database^[0]. The length of observed hydrogen bonds corresponds to theoretical data^[2].

Slide 2. Obvious interactions were detected using "calculate hbonds" command. Then we selected contacts, that were not taking part in supporting any kind of secondary structures (alpha-helixes or beta-strands).

Slide 3. To detect salt bridges oppositely charged amino acids were selected.

Slide 4. Firstly we selected every cystein. Then we manually filtered out cysteins that are not connected.

Slide 5. "Cationic sidechain nitrogens (lysine or arginine) within 6.0 Å of the face of an aromatic ring (phenylalanine, tyrosine, or tryptophan) may engage in polar interactions called "cation pi interactions" (Gallivan & Dougherty, 1999)

To detect cation-pi interactions firstglance software was used.