Peptide Hydrophobicity Calculator
Enter one or two standard peptide sequences to get the grand average of hydropathy (GRAVY) and a Kyte–Doolittle sliding-window hydropathy plot, with both profiles shown on the same axis for direct comparison.
GRAVY and hydropathy profile
Enter a sequence or select Try comparison to see how residue order changes the plot.
Select a position on the chart, move the slider, or enter a residue number to inspect the window.
Sequence A window
Sequence B window
The chart compares absolute residue positions. Sequence alignment is a separate analysis.
How peptide hydrophobicity is calculated
Assign a score to each residue
Each standard residue receives its published Kyte–Doolittle hydropathy value, ranging from +4.5 for isoleucine to −4.5 for arginine, with leucine at +3.8 and glutamate at −3.5. Scores are dimensionless and describe relative hydropathy on this scale only.
Average the whole sequence
GRAVY is the sum of all residue scores divided by the number of residues. A positive value indicates higher average hydropathy on the Kyte–Doolittle scale, and a negative value indicates lower average hydropathy. As an arithmetic mean, GRAVY is independent of where residues sit in the sequence.
Plot centered windows
For each position with a full window, the calculator averages the central residue and an equal number of neighbors on each side, weighting every residue equally. With a window of 3, the value at position 3 is the mean of residues 2, 3 and 4. Plotting these values along the sequence produces the hydropathy profile.
Same GRAVY, different profiles
The synthetic sequences LLLLEEEE (A) and LELELELE (B) each contain four leucines at +3.8 and four glutamates at −3.5, so both have a GRAVY of +0.150. With a window of 3 centered on position 3, A covers LLL and averages +3.800 while B covers ELE and averages −1.067, revealing a clustered pattern in A and an alternating pattern in B.
| Sequence | GRAVY | Window at position 3 | Peak window |
|---|---|---|---|
LLLLEEEE | +0.150 | LLL · +3.800 | +3.800 |
LELELELE | +0.150 | ELE · −1.067 | +1.367 |
What hydropathy tells you about solubility
GRAVY and the hydropathy plot let you compare sequences on one consistent scale. Solubility is established by measuring your actual sample under your chosen conditions, including pH, peptide concentration and buffer composition, and sample preparation, form and handling can also shape observed behavior. Net charge is another useful property to consider, and you can estimate it at a chosen pH with our Peptide Net Charge Calculator.
Peptide hydrophobicity FAQs
Can I calculate hydrophobicity for a sequence that includes modification tags such as UniMod annotations?
The calculator accepts the 20 standard one-letter residues, which are the residues covered by the Kyte–Doolittle scale, and it rejects inline tags. When you want a score for the parent sequence, you can enter an independently verified parent sequence. That result describes the standard residues only and leaves any effect of the modification outside its scope.
How should I compare hydrophobicity across several candidate sequences?
Use the same scale and the same window settings for every sequence. GRAVY is an arithmetic mean, as described in the ExPASy ProtParam documentation, so sequences with the same composition can share a GRAVY while showing different local profiles. Comparing the plots alongside the averages, as in the LLLLEEEE and LELELELE example above, captures both views.
Why can a peptide with both hydrophobic and hydrophilic residues be hard to dissolve?
Hydropathy is one property of a sequence, and measured behavior depends on the actual sample and the solution conditions, including pH, concentration and buffer composition. A balanced GRAVY can also hide a hydrophobic cluster, which the hydropathy plot can reveal. Whether a given sample dissolves is best determined by measurement.
Can sample handling change how the same sequence dissolves?
The sequence score stays the same regardless of how a sample was made or handled. Published peptide handling recommendations note that preparation, form and handling may affect observed behavior, and these factors sit outside what the calculator assesses.
Can a hydrophobicity score explain how a peptide behaves in RP-HPLC?
Only partly. Kyte–Doolittle hydropathy was developed to describe protein sequences, and chromatographic retention is a separate property. Published research on sequence-specific RP-HPLC retention shows that retention depends on the separation conditions and on sequence features beyond a residue average. Treat GRAVY as a relative sequence property and assess retention separately under your separation conditions.
