Four Distances between Pairs of Amino Acids Provide a Precise Description of their Interaction
Figure 3
Only cases with correct IUPAC atom name assignment protocol were considered. (A) The CG2–CG1 distance (d21) has a higher occupancy at 4 Å than the CG1–CG1 distance (d11). (B) Val atom notation in the PDB. The CB atom is a prochiral atom, putting the CB hydrogen at the back, and starting at clockwise direction from the CA atom the following atoms are always CG1 then CG2. (B) The V shape objects represent the covalent bond between CG1 CG2 and CB in the Val side chain. The possible Val conformation with CG1–CG1 (d11) and CG2–CG1 (d21) distances of either at 4 Å or at 6 Å (C,D). Two histograms depicting the distance between CG1 (C) and CG2 (D) from the backbone nitrogen and oxygen. (C) CG1 atom is generally closer to the backbone oxygen. (D) CG2 atom is generally closer to backbone nitrogen.