Selection of class I MHC-restricted peptides with the strip-of-helix hydrophobicity algorithm

Victor E. Reyes, L. Thomas Chin, Robert E. Humphreys

Research output: Contribution to journalArticlepeer-review

17 Scopus citations


A strip-of-helix hydrophobicity algorithm to predict class II MHC-restricted peptides, on the basis of their structural similarity to an amphipathic, α -helix in Ii, also predicted peptides which were presented to cytotoxic T-cells by class I MHC molecules. This algorithm ranked peptides according to mean Kyte-Doolittle hydrophobicity values of amino acids at positions n, n + 4, n + 7, n + 11, n + 14 and n + 18 in a sequence which when coiled as a putative α-helix, had the indicated residues in an axial strip along one side of the helix. Sequences selected for highly scoring, hydrophobic strips were required to have at least 1 of the 4 adjacent strips scoring more negatively than -1 in the strip-of-helix hydrophobicity index and the entire sequence could contain no prolines. This algorithm predicted the class I MHC-restricted, T-cell-presented peptides in sequences of 4 proteins from which some class I MHC-restricted, T-cell-presented sequences had been experimentally determined. Since both class I and class II MHC-restricted peptides could be identified with this algorithm, one can propose that: (I) foreign peptide-binding sites (desetopes) of the class I and class II MHC molecules are structurally similar; and (2) any one T-cell-presented peptide can be presented by some specific allele of both a class I and a class II MHC antigen.

Original languageEnglish (US)
Pages (from-to)867-871
Number of pages5
JournalMolecular Immunology
Issue number9
StatePublished - Sep 1988
Externally publishedYes

ASJC Scopus subject areas

  • Immunology
  • Molecular Biology


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