Packing of aromatic rings against tryptophan residues in proteins.
The geometry of the interaction of the aromatic side chains of phenylalanine (Phe), tyrosine (Tyr), tryptophan (Trp) and histidine (His) with the indole ring of Trp has been analyzed using the structures in the Protein Data Bank in order to understand the dependence of the packing behaviour on the size and chemical nature of the aromatic rings. The Phe ring prefers to interact either perpendicularly, with its edge pointing towards the Trp face, or in an offset-stacked arrangement. The edge-to-face motif is typical of a Trp-Trp pair. While parallel stacking is the dominant feature of Trp-His interaction, Tyr packs in a more uniform manner around Trp with a higher than expected occurrence at the edge and a few cases of possible OH-pi interaction.
Samanta
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Department of Biochemistry, Bose Institute, P-1/12 CIT Scheme VII-M, Calcutta 700 054, India.
Pal
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Chakrabarti
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D001665:Binding Sites; D018360:Crystallography, X-Ray; D006639:Histidine / Q000737:chemistry; D010649:Phenylalanine / Q000737:chemistry; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D013816:Thermodynamics; D014364:Tryptophan / Q000737:chemistry*; D014443:Tyrosine / Q000737:chemistry
D011506:Proteins; D014443:Tyrosine; D010649:Phenylalanine; D006639:Histidine; D014364:Tryptophan