Figure 1.

Volume-adjusted proximity probability distributions for a select different combinations of amino acids and nucleotides. Proximity is the closest atom of the nucleotide to the closest atom of the closest of 10 amino acids in the 40 Å periodic box. Proportion of simulation time is adjusted for the volume of the amino acid and nucleotide, so that different systems are comparable. Most interactions demonstrate multiple binding modes, at ~1.9 Å, 2.5 Å, and 4 Å. An additional peak at around 5.5 Å is also visible, which is interpreted as the average distance of the closest amino acid when not bound. The vertical red line indicates the 5 Å threshold for binding. (A) proline; (B) arginine; (C) aspartate; (D) phenylalanine; (E) glycine.