Hydropathicity Plots

Protein Hydropathicity Plots Tutorial

Cell Membrane: Lipid Bilayer

To explain protein hydropathicity plots, you must understand the cell membrane structure. It is made up of two layers of lipids that surround the cell and proteins that provide protection and signaling for the cell. The membrane is selectively permeable, meaning certain substances are allowed to come inside the cell and certain substances are banned from coming inside the cell. Transmembrane proteins can be channels or pores that allow materials to cross the membrane when they are needed inside the cell. Peripheral proteins are used in communication between cells or for identification for the immune system. Using protein hydropathicity plots, we can identify which kind of protein is being analyzed by examining the hydrophobic and hydrophilic regions of that protein.

What is a protein hydropathicity plot?

  • It is a method to display the hydrophobic and hydrophilic regions of a protein sequence and predict the structure based on these regions.
    • Hydrophobic- “water fearing”
      • Nonpolar regions and unable to interact with water
      • Located on the inside of the membrane
      • Usually membrane-spanning proteins: channels or pores
      • Must have a stretch of 18-20 amino acids to cross the membrane
    • Hydrophilic- “water loving”
      • Polar regions and able to interact with water
      • Located on the outside of the membrane
      • Usually peripheral proteins: antigens or receptors
  • It gives you information about the structure of the protein based on its hydrophobicity and hydrophilicity.

How it works…

To make a hydropathicity plot, a protein sequence and window size are chosen. A protein sequence can be obtained from a database. A window size refers to the number of amino acids scored at once. If three are examined at once, the first number plotted will be an average of those three. The window moves down one amino acid each time, and each set receives a score that is plotted. After the whole sequence has been plotted, you can determine the hydrophobic or hydrophilic regions by examining the plot. For example, if you are using the Kyte-Doolittle method that shows hydrophobicity, the peaks of the plot are hydrophobic regions.

  • A protein sequence is scanned with a moving window of some size.
    • Window Size
      • Number of amino acids examined at one time
      • Range from 5 to 25
      • Depends on expected structure
  • At each position, the average hydrophobic or hydrophilic (depending on method used) index of the amino acids within the window is calculated.
    • Each amino acid has a score depending on the method you are using.
    • Each amino acid has an R group that determines whether the protein is hydrophobic or hydrophilic.
    • These scales for the amino acids have been developed experimentally.
    • Link to amino acid Kyte-Doolittle Hydrophobicity scores: http://gcat.davidson.edu/rakarnik/aminoacidscores.htm
  • This value is plotted on a graph.
    • X-axis is the window size.
    • Y-axis is the hydrophobicity or hydrophilicity.
  • Methods:
    • Kyte-Doolittle
      • Hydrophobicity plot
      • Window size= 19-21
      • >0 means hydrophobic region
    • Hopp-Woods
      • Hydrophilicity plot
      • Window size= 5-7
      • >0 means hydrophilic region
  • The structure of proteins define their function. Using hydropathicity plots, we can make predictions about the structure, which will enable us to make predictions about functions of proteins.

Try it out!


  • Enter a protein sequence with single letter codes only into the text box.
  • Choose the type of plot you want to use and the appropriate window size.
  • Click on the plot button.
  • Helpful Hints:
    • If you change parameters, you must click plot again to see the new results.
    • To test the program without entering a sequence, click demo protein.
    • By clicking on the graph, it will tell you at what amino acid position you are.

Hydrophobicity Plot: Cystic Fibrosis Transmembrane Conductance Regulator (AAA35680)

Hydrophilicity Plot: Beta-Globin (AAA88054)



27 Feb 2002. Amino Acid Hydropathy Scores. http://gcat.davidson.edu/rakarnik/aminoacidscores.html. 2011 Mar 6.

20 Jun 1998. Background on Hydrophobicity Plots. http://www.vivo.colostate.edu/molkit/hydropathy/scales.html. 2011 Mar 6.

Hoop TP and Woods KR: Prediction of protein antigenic determinants from amino acid sequences. Proc Natl Acad Sci USA 78:3824, 1981. 2011 Mar 6.

27 Feb 2002. Kyte-Doolittle Hydropathy Plots. http://gcat.davidson.edu/rakarnik/kyte-doolittle-background.htm#protein. 2011 Mar 6.

Kyte J and Doolittle RF: A simple method for displaying the hydropathic character of a protien. J Mol Biol 157:105, 1982. 2011 Mar 6.

Wikipedia. 17 Mar 2011. Lipid Bilayer. http://en.wikipedia.org/wiki/Lipid_bilayer.2011 Mar 6.



http://www.cartoonstock.com/directory/h/hydrophobic.asp. 2011 Mar 9.

http://www.northallegheny.org. 2011 Mar 9.

March 11, 2011

Brooke Bailey: ebailey@samford.edu

Biology 306: Bioinformatics

Samford University



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