Calculation of hydrophobicity is important to the identification of various protein features. This can be membrane spanning regions, antigenic sites, exposed loops or buried residues. Usually, these calculations are shown as a plot along the protein sequence, making it easy to identify the location of potential protein features.
Figure 17.9: Plot of hydrophobicity along the amino acid sequence. Hydrophobic regions on the sequence have higher numbers according to the graph below the sequence, furthermore hydrophobic regions are colored on the sequence. Red indicates regions with high hydrophobicity and blue indicates regions with low hydrophobicity.
The hydrophobicity is calculated by sliding a fixed size window (of an odd number) over the protein sequence. At the central position of the window, the average hydrophobicity of the entire window is plotted (see figure 17.9).