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Kyte & Doolittle Plot (hydropathy) with window size of Hopp & Woods Plot (hydrophilic/antigenic) with window size of

How should I interpret the graphs?

Kyte & Doolittle Hydropathy
Hydropathic regions achieve a positive value. Setting window size to 5-7 is suggested to be a good value for finding putative surface-exposed regions, whereas a window size of 19-21 yields a plot in which transmembrane domains stand out sharply, with values of at least 1.6 at their centers.

When the window size is 19, peaks with scores greater than 1.8 indicate possible transmembrane regions.
When the window size is 9, strong negative peaks indicate possible surface regions of globular proteins.

The Window Position values shown on the x-axis of the graph reflect the average hydropathy of the entire window, with the corresponding amino acid as the middle element of that window. For example, if the window size were 19, the score at window position 10 would be the average hydropathy of the 19 amino acids from position 1 to position 19 in the input sequence. Notice that the horizontal axis is scaled to include only those amino acids for which a windowed hydropathy score is computed.

First, each amino acid is given a hydrophobicity score between -4.5 and 4.5. A score of 4.5 is the most hydrophobic and a score of -4.5 is the most hydrophilic. Click here to see each amino acid's score. Then a window size is set. A window size is the number of amino acids whose hydrophobicity scores will be averaged and assigned to the middle amino acid in the window. The default window size is 9 amino acids. The computer program starts with the first window of amino acids and calculates the average of all the hydrophobicity scores in that window. Then the computer program moves down one amino acid and calculates the average of all the hydrophobicity scores in the second window. This pattern continues to the end of the protein, computing the average score for each window and assigning it to the middle amino acid in the window. The averages are then plotted on a graph. The y axis represents the hydrophobicity scores and the x axis represents the position in the protein sequence.

Hopp & Woods Antigenic/Hydrophilic
This scale was developed for predicting potential antigenic sites of globular proteins, which are likely to be rich in charged and polar residues. This scale is essentially a hydrophilic index, with apolar residues assigned negative values. The authors suggest that, using a window size of 6, the region of maximal hydrophilicity is likely to be an antigenic site.

Reference:
Kyte, J. and Doolittle, R. 1982. A simple method for displaying the hydropathic character of a protein. J. Mol. Biol. 157: 105-132.
Hoop TP and Woods KR: Prediction of protein antigenic determinants from amino acid sequences. Proc Natl Acad Sci USA 78:3824, 1981.