Hydropathy plots allow for the visualization of hydrophobicity over the length of a peptide sequence. A hydropathy scale which is based on the hydrophobic and hydrophilic properties of the 20 amino acids is used. A moving “window” determines the summed hydropathy at each point in the sequence (Y coordinate). These sums are then plotted against their respective positions (X coordinate). Such plots are useful in determining the hydrophobic interior portions of globular proteins as well as determining membrane spanning regions of membrane bound proteins.
In this calculation the window size has is variable, allowing the user to change the sensitivity of the calculation. Smaller windows result in “noisier” plots than do larger windows. Window sizes between 7-11 residues were found by Kyte and Doolittle to maximize the information content of the plots. It is advised that the peptide length should be greater than double the window size to get any useful information from the Hydropathy plot.
Reference:Kyte and Doolittle Jol Mol. Bio. (1982) 157 105-132.