- Hydrophilicity plot
A hydrophilicity plot is a
quantitative analysisof the degree of hydrophobicityor hydrophilicityof amino acids of a protein. It is used to characterize or identify possible structure or domains of a protein.
The plot has amino acid sequence of a protein on its
x-axis, and degree of hydrophobicity and hydrophilicity on its y-axis. There are a number of methods to measure the degree of interaction of polar solvents such as water with specific amino acids. For instance, the Kyte-Doolittle scaleindicates hydrophobic amino acids, while the Hopp-Woods scalemeasures hydrophilic residues.
Analyzing the shape of the plot gives information about partial structure of the protein. For instance, if a stretch of about 20 amino acids shows positive for hydrophobicity, then this indicates that these amino acids may be part of
alpha-helixspanning across a lipid bilayer, which is composed of hydrophobic fatty acids. Conversely, amino acids with high hydrophilicity indicate that these residues are in contact with solvent, or water, and that they are therefore likely to reside on the outer surface of the protein.
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