Propensities of polar and aromatic amino acids in noncanonical interactions: nonbonded contacts analysis of protein-ligand complexes in crystal structures

J Med Chem. 2007 Mar 22;50(6):1189-96. doi: 10.1021/jm061038a. Epub 2007 Feb 22.


The nonbonded contacts analysis of 14 polar and aromatic amino acid side chains was carried out for protein-ligand complexes derived from the crystal structures in the Protein Data Bank. Through the exhaustive analysis, several unusual contacts were observed as well as the well-known interactions. CH-S interactions were frequently found in Met-related contacts, which have not yet been the subject of systematic investigations. We have also described the propensity of each amino acid for nonbonded interactions. All amino acids studied in this work showed high frequencies for the canonical hydrogen-bonding NH-O, OH-N, and OH-O interactions, while the preferences in noncanonical interactions such as CH- pi interactions were not always consistent among the side chains with similar characteristics. Understanding such amino acid side chain propensities is important for improving the accuracy of structure-based drug design, and this study will open new possibilities for developing unique compounds with high binding affinity.

MeSH terms

  • Amino Acids / chemistry*
  • Crystallography, X-Ray
  • Databases, Protein
  • Hydrogen Bonding
  • Ligands*
  • Models, Molecular
  • Molecular Structure
  • Proteins / chemistry*


  • Amino Acids
  • Ligands
  • Proteins