Biology Reference
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Once the Hydropathy Index for the amino acids is established, the next step is to plot
the Index value for each amino acid in the protein's sequence from N-terminal to
C-terminal. Also a mid-point line that is the Hydropathy Index average of all the amino
acids is drawn. Unfortunately the first pass through the amino acid sequence assigning
the actual Hydropathy Index value for each amino acid in sequence is extremely 'noisy'
and cannot be interpreted. Therefore a second and even a third pass are required where
the Hydropathy Index of a window of amino acids surrounding a central amino acid is
averaged and this value is assigned to the central amino acid in the window. This is
referred to as a 'rolling average'. For example using a window of 7 amino acids, amino
acid 15 would be assigned the average Hydropathy Index of amino acids 12 through
18. The window would then be shifted to amino acid 16 and the average Hydropathy
Index for amino acids 13 through 19 assigned to this central amino acid (amino acid
16). This continues down the entire amino acid chain. A third smoothing pass ('rolling
average') may be required to further diminish noise. Readily available computer
programs allow the user to easily change the window size from 5 to 25 amino acids
and does all of the calculations automatically. Kyte and Doolittle applied this method-
ology to several proteins whose structure had been determined by crystallography.
They found for water-soluble globular proteins a 'remarkable correspondence between
the interior positions of their sequence and the regions on the hydrophobic side of the
midpoint line, as well as the exterior portions and the regions on the hydrophilic side.'
With membrane proteins whose crystallography structures are far less available, possible
trans-membrane amino acid stretches can be readily determined. For example, a stretch of
21 hydrophobic amino acids (~33 ˚ ) is enough to cross the lipid bilayer. According to the
Kyte Doolittle Index, the hydrophobic stretch of amino acids that may cross the
membrane must have averaged Index values of
1.25. Figure 6.3 is a Kyte Doolittle
Hydropathy Index plot of the single membrane span protein glycophorin [5] . This plot
was made from a single pass with a window set at 7 amino acids. The membrane span-
ning a -helix can be readily picked out between amino acids 75 to 94.
>
FIGURE 6.3 Hydropathy plot for
the single membrane span protein gly-
cophorin. The membrane spanning
a -helix can be found between amino
acids 75 to 94 [5] .
GLYC 7
40
20
0
-20
-40
0
20
40
60
80
100
120
140
Sequence number
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