How to Interpret a Protein Hydropathy Plot
Read the axes and compare two sliding windows on the same sequence to see what a Kyte–Doolittle hydropathy plot can tell you.
Read the axes and the zero line
The horizontal axis shows the center of each window, measured from the first residue of the sequence at position 1. An odd window is centered on a residue. An even window is centered between two residues, so its position ends in .5. The calculator plots only complete windows, which leaves gaps at the ends when the window spans several residues.
The vertical axis shows the unitless mean Kyte–Doolittle score of the residues in each window. Positive values indicate more hydrophobic windows on this scale, and negative values indicate more hydrophilic windows. A value near the dashed zero line can come from positive and negative residue scores averaging out.
Compare two windows on the same sequence
Load the calculator example VVVLLLDDDKKK, choose Calculate hydropathy, and compare the default window of 9 with a window of 3. To apply the smaller window, enter 3 and choose Update window. Both plots below use the same axes.
With a window of 3, the first three valines give (4.2 + 4.2 + 4.2) / 3 = 4.2000 at position 2. The three aspartates at positions 7–9 give −3.5000 at position 8. The shorter window shows the shift from the hydrophobic start to the hydrophilic end in more detail.
With a window of 9, the first window includes three valines, three leucines, and three aspartates. Its mean is (12.6 + 11.4 − 10.5) / 9 = 1.5000 at position 5. The larger window averages across more residues, smoothing the transition and leaving only four points. The whole-sequence average (GRAVY) is 0.1500 for either window.
| Window size | Residues | Center | Mean score |
|---|---|---|---|
| 3 | 1–3 | 2 | 4.2000 |
| 3 | 2–4 | 3 | 4.0667 |
| 3 | 3–5 | 4 | 3.9333 |
| 3 | 4–6 | 5 | 3.8000 |
| 3 | 5–7 | 6 | 1.3667 |
| 3 | 6–8 | 7 | -1.0667 |
| 3 | 7–9 | 8 | -3.5000 |
| 3 | 8–10 | 9 | -3.6333 |
| 3 | 9–11 | 10 | -3.7667 |
| 3 | 10–12 | 11 | -3.9000 |
| 9 | 1–9 | 5 | 1.5000 |
| 9 | 2–10 | 6 | 0.6000 |
| 9 | 3–11 | 7 | -0.3000 |
| 9 | 4–12 | 8 | -1.2000 |
What the curve can tell you
Use the curve to locate relatively hydrophobic and hydrophilic stretches and see whether they persist across window sizes. In a longer protein, a broad hydrophobic stretch can flag a candidate membrane-spanning segment for further analysis.
The curve summarizes sequence composition. Confirming membrane location, topology, or three-dimensional structure requires other evidence. A single positive peak, such as the one in this short example, is only a local score on the chosen scale.