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HMOMENT application details page
Hydrophobic moment calculation
hmoment plots or writes out the hydrophobic moment. Hydrophicmoment is the hydrophobicity of a peptide measured for a specified angleof rotation per residue. Periodicities in the polar/apolar character of the amino acid sequenceof a protein can be examined by assigning to each residue a numericalhydrophobicity and searching for periodicity in the resultingone-dimensional function. The strength of each periodic component isthe quantity that has been termed the hydrophobic moment. When proteins of known three-dimensional structure are examined, it isfound that sequences that form alpha helices tend to have, on average, astrong periodicity in the hydrophobicity of af 3.6 residues, the periodof the alpha helix. The angle of rotation per residue in alpha helices is 100 degrees.Similarly, many sequences that form strands of beta sheets tend to havea periodicity in their hydrophobicity of about 2.3 residues, the periodtypical of beta structure. The angle of rotation per residue in betasheets is 160 degrees. This means that many protein sequences tend to form the periodicstructure that maximizes their amphiphilicity. The hydrophobic moment is measured within a moving window using the methodof Eisenberg et al. The default angle of 100 degrees is used for thealpha-helix results and the default of 160 degrees is used for thebeta-sheet results. These angles can be changed if required using theappropriate options. hmoment can plot two graphs when the option '-double' is given,one for the alpha helix moment and one for the beta sheet moment. Otherwise it just plots the alpha helix moment.
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