Kyte-Doolittle Hydropathy Plot Help

An hydropathy plot is a graphical display of the local hydrophobicity of amino acid side chains in a protein. A positive value indicates local hydrophobicity and a negative value suggests a water-exposed region on the face of a protein. Hydropathy plots are generally most useful in predicting transmembrane segments and N-terminal secretion signal sequences.

Hydropathy plots are usually computed for single protein sequences, but Bonsai permits you to compute a hydropathy plot for an alignment. As long as the alignment is correct or nearly correct, this has the advantage that variations in hydrophobicity that occur across individual sequences are muted, permitting easier recognition of hydrophobic stretches characteristic of the family. This may also permit more exact recognition of the beginning and end of transmembrane segments.

The window size on an hydropathy plot is the number of residues across which an average local hydropathy is computed for display. You can change the window size using the numbered buttons. A small window produces "noisier" plots that more accurately reflect highly local hydrophobicity. A window of 9 or 11 is generally optimal for recognizing the long hydrophobic stretches that typify transmembrane stretches.


File Menu

Print: print this hydropathy plot. The printout will reflect what the window is currently showing (below the menu bar line), so change the window to suit before printing. For higher quality print out, save the image as a GIF file and print using another program.

Save as GIF: save this hydropathy plot as a GIF file. As for printing, the GIF image saved will correspond to what the window is currently showing.


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Kyte-Doolittle Help: this help.


James H. Thomas, Department of Genome Sciences, University of Washington
5/18/2002