Motivation: An amphiphilicity index of amino acid residues was developed for improving the method of transmembrane helix prediction. Results: The transfer energy of a hydrocarbon stem group beyond the gamma-carbon was calculated from the accessible surface area, and used to index the amphiphilicity of the residue, Non-zero amphiphilicity index values were obtained for lysine, arginine, histidine, glutamic acid, glutamine, tyrosine and tryptophan. Those residues were found to be abundant in the end regions of transmembrane helices, indicating their preference for the membrane-water interface. The moving average of the amphiphilicity index actually showed significant peaks in the end regions of most transmembrane helices. A dispersion diagram of average amphiphilicity index versus average hydrophobicity index was devised to facilitate discrimination of transmembrane helices. Availability: The amphiphilicity index has been incorporated into a system, SOSUI, for the discrimination of membrane proteins and the prdiction of tranmembrane helical regions (http://sosui.proteome.bio.tuat.ac.jp/sosuiframe0.html). Contact: mitaku@cc.tuat.ac.jp.
