Statistical analysis of predicted transmembrane α-helices

Isaiah T. Arkin*, Axel T. Brunger

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

166 Scopus citations


Statistical analyses were undertaken for putative transmembrane α-helices obtained from a database representing the subset of membrane proteins available in Swiss-Prot. The average length of a transmembrane α-helix was found to be 22-21 amino acids with a large variation around the mean. The transfer free energy from water to oil of a transmembrane α-helix in bitopic proteins, -48 kcal/mol, is higher than that in polytopic proteins, -39 kcal/mol, and is nearly identical to that obtained by assuming a random distribution of solely hydrophobic amino acids in the α-helix. The amino acid composition of hydrophobic residues is similar in bitopic and polytopic proteins. In contrast, the more polar the amino acids are, the less likely they are to be found in bitopic proteins compared to polytopic ones. This most likely reflects the ability of α-helical bundles to shield the polarity of residues from the hydrophobic bilayer. One half of all amino acids were distributed non-randomly in both bitopic and polytopic proteins. A preference was found for tyrosine and tryptophan residues to be at the ends of transmembrane α-helices. Correlated distribution analysis of amino acid pairs indicated that most amino acids are independently distributed in each helix. Exceptions are cysteine, tyrosine, and tryptophan which appear to cluster closely to one another and glycines which are preferentially found on the same side of α-helices. Copyright (C) 1998 Elsevier Science B.V.

Original languageAmerican English
Pages (from-to)113-128
Number of pages16
JournalBiochimica et Biophysica Acta - Protein Structure and Molecular Enzymology
Issue number1
StatePublished - 8 Dec 1998
Externally publishedYes

Bibliographical note

Funding Information:
The authors wish to thank Drs. D.M. Engelman, K.R. MacKenzie and P.D. Adams for helpful discussions and W.P. Russ for help in manuscript preparation. This work was funded in part by a grant from NIH (GM-54160-01) to A.T.B.


  • Lipid bilayer
  • Membrane protein
  • Protein database
  • α-Helix


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