Amino acid propensities are position-dependent throughout the length of alpha-helices

J Mol Biol. 2004 Apr 9;337(5):1195-205. doi: 10.1016/j.jmb.2004.02.004.


The 20 commonly occurring amino acids have been shown to have distinct position-dependent, helix-forming propensities near the ends of alpha-helices. Here, we show that the amino acids also have very strong position-dependent propensities throughout the length of a helix. Most helices are amphiphilic, and they have a strong tendency to both begin and end on the solvent-inaccessible face of the helix. These position-specific propensities should provide valuable parameters to guide de novo protein design, and should allow more precise prediction of helical topology in natural proteins.

MeSH terms

  • Amino Acid Sequence
  • Amino Acids / chemistry
  • Databases, Protein
  • Hydrophobic and Hydrophilic Interactions
  • Models, Molecular*
  • Protein Structure, Secondary*
  • Proteins / chemistry*


  • Amino Acids
  • Proteins