You can paste plain sequence or FASTA format. Header lines beginning with > are ignored.
What this peptide hydrophobicity calculator does
This tool estimates how hydrophobic (water-avoiding) or hydrophilic (water-friendly) a peptide sequence is. Hydrophobicity is one of the most important sequence-level properties in peptide science because it strongly affects solubility, membrane interaction, aggregation risk, purification behavior, and biological activity.
The calculator reports both a global score and local information. Global scores summarize the entire sequence, while the sliding window score helps identify short hydrophobic segments that may behave like membrane-active or aggregation-prone motifs.
How the score is calculated
Each amino acid has a numeric hydrophobicity value in a selected scale. The sequence score is calculated by summing those values and then dividing by peptide length:
Average hydrophobicity (GRAVY-like) = (sum of residue hydrophobicity values) / (number of residues)
Positive averages usually indicate a more hydrophobic peptide, while negative averages indicate greater hydrophilicity. Exact interpretation depends on the scale you choose.
Supported scales
- Kyte-Doolittle: commonly used for proteins and transmembrane region screening.
- Eisenberg: a balanced consensus scale useful for comparing peptide designs.
How to use this calculator
- Paste your peptide sequence (or FASTA content) in the input box.
- Select a hydrophobicity scale.
- Choose a sliding window size (typical values: 5 to 11 for short peptides).
- Click Calculate Hydrophobicity.
The output includes sequence length, total score, average score, percent hydrophobic residues, the most hydrophobic/hydrophilic positions, and the highest-scoring local region.
Interpreting your results
Global average hydrophobicity
- Higher positive value: more hydrophobic; often lower aqueous solubility.
- Near zero: mixed behavior; context and sequence pattern matter.
- More negative value: more hydrophilic; often better water solubility.
Local hydrophobic windows
A sequence can have a modest global average but still contain a short strongly hydrophobic patch. These local peaks may drive membrane insertion, self-association, or nonspecific binding. That is why window-based analysis is included.
Design tips for peptide engineering
- Increase Lys/Arg/Asp/Glu content if your peptide is too hydrophobic and insoluble.
- Replace one or two highly hydrophobic residues (I, L, F, W, V) to tune aggregation behavior.
- Monitor local peaks, not just the global average, during optimization cycles.
- Combine hydrophobicity with charge, helicity, and amphipathicity for best predictions.
Important limitations
Hydrophobicity scores are useful heuristics, but they are not full biophysical simulations. Real peptide behavior also depends on pH, ionic strength, structure, post-translational modifications, concentration, temperature, and experimental assay conditions.
For critical decisions, treat this tool as a fast screening method and confirm experimentally.
Frequently asked questions
Can I paste FASTA files?
Yes. Header lines beginning with > are ignored automatically.
What sequence characters are accepted?
Standard amino acids: A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, Y. Non-standard letters such as B, J, O, U, X, and Z are rejected.
Is this the same as predicting membrane proteins?
Not exactly. It is a useful first pass, especially with sliding windows, but membrane prediction requires broader context and often additional structural modeling.