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A hydrophilicity plot is a quantitative analysis of the degree of 
The data in the above table was generated using a computer program that evaluates the average hydrophobicity of segments within a protein and uses data collected from literature.
ExPASy ProtScaleProtein Hydrophobicity Plots from Colorado StateHydropathicity Plots from The World of Bioinformatics
Plots (graphics) Protein structure
hydrophobicity
In chemistry, hydrophobicity is the physical property of a molecule that is seemingly repelled from a mass of water (known as a hydrophobe). In contrast, hydrophiles are attracted to water.
Hydrophobic molecules tend to be nonpolar and, th ...
or hydrophilicity
A hydrophile is a molecule or other molecular entity that is attracted to water molecules and tends to be dissolved by water.Liddell, H.G. & Scott, R. (1940). ''A Greek-English Lexicon'' Oxford: Clarendon Press.
In contrast, hydrophobes are no ...
of amino acid
Amino acids are organic compounds that contain both amino and carboxylic acid functional groups. Although hundreds of amino acids exist in nature, by far the most important are the alpha-amino acids, which comprise proteins. Only 22 alpha am ...
s of a protein
Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, respo ...
. 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
A Cartesian coordinate system (, ) in a plane is a coordinate system that specifies each point uniquely by a pair of numerical coordinates, which are the signed distances to the point from two fixed perpendicular oriented lines, measured in t ...
, and degree of hydrophobicity and hydrophilicity on its y-axis
A Cartesian coordinate system (, ) in a plane is a coordinate system that specifies each point uniquely by a pair of numerical coordinates, which are the signed distances to the point from two fixed perpendicular oriented lines, measured i ...
. There are a number of methods to measure the degree of interaction of polar solvent
A solvent (s) (from the Latin '' solvÅ'', "loosen, untie, solve") is a substance that dissolves a solute, resulting in a solution. A solvent is usually a liquid but can also be a solid, a gas, or a supercritical fluid. Water is a solvent for p ...
s such as water with specific amino acids. For instance, the Kyte-Doolittle scale Hydrophobicity scales are values that define the relative hydrophobicity or hydrophilicity of amino acid residues. The more positive the value, the more hydrophobic are the amino acids located in that region of the protein. These scales are commonly ...
indicates hydrophobic amino acids, whereas the Hopp-Woods scale measures 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, these amino acids may be part of alpha-helix spanning across a lipid bilayer
The lipid bilayer (or phospholipid bilayer) is a thin polar membrane made of two layers of lipid molecules. These membranes are flat sheets that form a continuous barrier around all cells. The cell membranes of almost all organisms and many vir ...
, which is composed of hydrophobic fatty acids. On the converse, 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.
The data in the above table was generated using a computer program that evaluates the average hydrophobicity of segments within a protein and uses data collected from literature.
References
{{ReflistExternal links
ExPASy ProtScale
Plots (graphics) Protein structure