Hydrogen bond network protein

There seems to be two major reasons for this improvement in calculated geometries improved hydrogen-bond networks and a better description of metal coordination. Apart from these two effects, we did not find any major changes in active-site geometry that could be attributed to the surrounding protein. 

Hydrocarbons (both aromatic and aliphatic) do not have many (or any) groups that can participate in the hydrogen-bonding network of water. They re greasy and prefer to be on the interior of proteins (away from water). Note that a couple of the aromatics, Tyr and Trp, have O and N, and Met has an S, but these amino acids are still pretty hydrophobic. The hydrophobic nature usually dominates however, the O, N, and S atoms often participate in hydrogen bonds in the interior of the protein. 

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