A representation of the hydrophobic character of a protein sequence which may be useful in predicting membrane-spanning domains, potential antigenic sites, and regions that are likely to be exposed on the surface. Various algorithms are used, based on a moving average spanning a ‘window’ of 2n + 1 amino acids: Kyte–Doolittle is a widely applied scale in which the window is 7; a much larger window of 19–25 is generally thought appropriate for detecting transmembrane helices. The Hopp–Woods scale was designed for predicting potentially antigenic regions of polypeptides. Various websites enable an enquirer to input sequence and obtain a graphical plot. More sophisticated approaches involve estimating the proportion of the surface of a globular protein that will be occupied by a particular residue or the orientation of the residues in the protein to calculate a hydrophobic moment analysis.
http://www.vivo.colostate.edu/molkit/hydropathy/ Useful lead into web resources for hydropathy plots.
Subjects: Medicine and Health — Chemistry.