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Protein Engineering, Vol. 15, No. 2, 91-100, February 2002
© 2002 Oxford University Press

Aromatic–aromatic interactions in and around {alpha}-helices

Rajasri Bhattacharyya1,2, Uttamkumar Samanta3,2 and Pinak Chakrabarti1,3,4

1 Department of Biochemistry and 3 Bioinformatics Centre, Bose Institute,P-1/12 CIT Scheme VIIM, Calcutta 700 054, India

To understand the role of aromatic–aromatic interactions in imparting specificity to the folding process, the geometries of four aromatic residues with different sequence spacing, located in {alpha}-helices or five residues from helical ends, interacting with each other have been elucidated. The geometry is found to depend on the sequence difference. Specific interactions (C–H···{pi} and N–H···{pi}) which result from this geometry may cause a given pair of residues (such as Phe–His) with a particular sequence difference to occur more than expected. The most conspicuous residue in an aromatic pair in the context of helix stability is His, which is found at the last (C1) position or the two positions (Ncap and Ccap) immediately flanking the helix. An {alpha}-helix and a contiguous 310-helix or two helices separated by a non-helical residue can have interacting aromatic pairs, the geometry of interaction and the relative orientation between the helices being rather fixed. Short helices can also have interacting residues from either side.


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