Aromatic side‐chain interactions in proteins. II. Near‐ and far‐sequence Phe‐X pairs

We have collected all aromatic pairs (3152) involving an N ‐phenyl partner in a dataset of 593 proteins of the PDB: 728 of these pairs involve a partner residue less than 6 apart in the sequence. These near‐sequence Phe‐X pairs correspond to specific conformations that stabilize secondary structures, mainly α‐helices when the residues are 1, 3, and 4 apart, and β‐strands when they are 2 apart in the sequence. These conformations are not spatially random and have been examined in detail. The remaining phenylalanine pairs (2424) are between partners more than 5 apart in the sequence. Of these far‐sequence pairs, 34% of occurrences are in sheets. Next in frequencies are pairs that bridge a β‐strand to a helix (24%), followed by pairs that bridge a β‐strand to a random coiled structure (15%). Helix to helix pairs only constitute 12% of these far‐sequence pairs. Analysis of the pairing frequency supports the hypothesis that aromatic interactions are late events of protein folding. Proteins 2002;48:635–644. © 2002 Wiley‐Liss, Inc.