Protein Hydrophobicity Calculator

Hydrophobicity measures how strongly a protein or peptide repels water — a key property for predicting membrane interactions, folding behavior, and drug delivery potential. Paste your amino acid sequence in single-letter code into the Protein Hydrophobicity Calculator, then select a hydrophobicity scale (Kyte-Doolittle, Eisenberg, Hopp-Woods, and more), a window size, and any N- or C-terminal modifications. You'll get the average hydrophobicity, plus hydrophobic and hydrophilic residue counts, hydrophobic percentage, and peak min/max hydrophobicity values across the sequence.

Enter protein sequence in single-letter amino acid code format

Choose the hydrophobicity scale for calculations

Size of sliding window for hydrophobicity profile calculation

Results

Average Hydrophobicity

--

Sequence Length

--

Hydrophobic Residues

--

Hydrophilic Residues

--

Maximum Hydrophobicity

--

Minimum Hydrophobicity

--

Hydrophobic Percentage

--

Results Table

More Biology Tools

Frequently Asked Questions

What is protein hydrophobicity and why is it important?

Protein hydrophobicity measures the tendency of amino acid residues to avoid water. It's crucial for understanding protein folding, membrane interactions, and biological activity.

Which hydrophobicity scale should I use for my analysis?

Kyte-Doolittle is the most commonly used scale for general analysis. Eisenberg is good for membrane proteins, while Hopp-Woods is useful for predicting surface accessibility.

What does the window size parameter control?

Window size determines the number of adjacent residues used to calculate the hydrophobicity profile. Larger windows provide smoother profiles, while smaller windows show more detail.

How do N-terminal and C-terminal modifications affect hydrophobicity?

Terminal modifications can significantly alter the overall hydrophobicity of short peptides by adding hydrophobic or hydrophilic groups that change the molecule's properties.

What amino acids are considered hydrophobic vs hydrophilic?

Hydrophobic: F, I, L, M, V, W, Y, A. Hydrophilic: D, E, K, R, H, N, Q, S, T. Some amino acids like G, P, C have intermediate properties depending on the scale used.

Can I analyze both proteins and peptides with this calculator?

Yes, this calculator works for both short peptides and long protein sequences. The analysis methods are the same, though interpretation may differ based on sequence length.

What format should I use for entering the amino acid sequence?

Use standard single-letter amino acid codes (A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, Y). Spaces and line breaks are automatically removed.

How is the hydrophobicity profile calculated?

The profile is calculated using a sliding window approach where the average hydrophobicity of residues within each window is computed and plotted against sequence position.