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Kyte-Doolittle Hydropathy Plot

A Secondary Structure Prediction Tool for Proteins

Hydropathy Plot Input

Type or Paste an Amino Acid Sequence Here:

Window Size (odd integer):     

The plot will appear in a separate window.

Plot Interpretation

The plot produced by this program represents the average hydropathy along the amino acid sequence.  The plot may help predict whether or not the protein segment has enough hydrophobicity to either interact with or reside in a membrane.  Regions of the graph that show hydrophobic nature are more likely to be found in a nonaqueous environment (such as the interior of a plasma membrane), while those showing  hydrophilic nature are more likely to be found in an aqueous environment (such as the cytosol or nucleus).  

Background Information

Algorithm

  • The algorithm used by this program calculates an average hydropathy value for each position in the given sequence.  For each position, the algorithm considers the hydropathy index of the surrounding amino acids (within the given window size, centered around that position), and then calculates their average.  This average value is the one plotted on the graph for that position.  Because it considers some number of surrounding amino acids on each side (one less than 1/2 the window size), the average values cannot be calculated for that number of amino acids at the beginning and end of the sequence.  So the algorithm skips these positions, and no value is plotted on the graph.

Hydropathy

  • Molecules can be hydrophobic (water-fearing) or hydrophilic (water-loving).  The hydropathy of a molecule is one factor in determining its structure.  In the case of proteins, structure has been correlated to function.
  • The hydropathy plot displays the hydrophobic and hydrophilic tendencies of an amino acid sequence. A hydropathy scale is used, which has assigned a hydropathy index to each amino acid, based on its relative hydrophobicity (positive value) or hydrophilicity (negative value). 
  • The graph plots the average hydropathy of a moving segment of a fixed window size (which the user enters), moving along the entire sequence. On the plot, a positive peak indicates a probability that the corresponding polypeptide fragment is hydrophobic (a negative peak indicating a probable hydrophilic segment).
Bioinformatics
  • Bioinformatics is the use of computer programming to sort and analyze biological data.

Perl

  • Perl is the programming language that was used to create the tool provided at this site.

Structure

  • The primary structure of the protein is the amino acid sequence.

  • The secondary structure is the two dimensional folding - alpha helixes, beta pleated sheets, and random coil.

  • The tertiary structure is the three dimensional folding - globular, transmembrane or integral membrane, etc.

  • The quaternary structure is the interaction of multiple proteins of the same or different amino acid sequence.

Kyte-Doolittle

  • Kyte and Doolittle were the authors of the paper entitled "A Simple Method for Displaying the Hydropathic Character of a Protein" which was published in the Journal of Molecular Biology, 1982.

About this Project

This page was created by Frank Chemotti, Cecilia Mendiondo, and La Powell for Dr. Laurie Heyer's Computational Biology course at Davidson College. Please, feel free to email us with questions, comments, suggestions, and general concerns.

References

Kyte, Jack, and Russel F. Doolittle.  "A Simple Method for Displaying the Hydropathic Character of a Protein."  Journal of Molecular Biology 1982; (157) 105-132.

Kyte-Doolittle Hydropathy Plots. Pearson, William R. 1998. U of Virginia. 28 Feb 2002 <http://fasta.bioch.virginia.edu/fasta/grease.htm>.

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