Hydropathy Analysis

Description: You can display one of two types of plots. You can calculate hydropathy with th estandard Kyte-Doolittle values or you can calculate the free energy difference between a lipid and a water environment.

Protein sequences that form transmembrane regions are assumed to have a thermodynamic preference for a hydrophobic environment (inside the membrane lipid bilayer), rather than an aqueous environment in water. The free energy change for each amino acid residue between a lipid and a water environment can be measured experimentally, and the values for peptides can be shown to be additive (White and Wimley 1999). Residues which can be buried inside a lipid bilayer must be in a region of the peptide where most residues show a free energy difference in favour of being in an octanol environment or at least being in the lipid/water interface region. White and Wimley (1999) showed that a sliding window of either free energy difference will indicate the location of probable transmembrane regions, but that the best indicator is the difference between the two values, which is the free energy difference between the interface and octanol environments.

Window: Hydropathy Plot Style:

Please enter the protein sequence with FASTA format you want to analyze:

If you have any questions please e-mail: Can Tran - can@ucsd.edu