1. What is Peptide Hydrophobicity?

Hydrophobicity is a measure of how water-repellent a peptide is, based on the sum of hydrophobicity values of its constituent amino acids divided by the peptide length. It influences protein folding, membrane interactions, and solubility.

2. How Does the Calculator Work?

The calculator uses the hydrophobicity equation:

Where:

• \( hydrophobicity_{aa} \) — Kyte-Doolittle hydrophobicity value for each amino acid (dimensionless)
• \( length \) — Number of amino acids in the peptide

Explanation: The equation calculates the average hydrophobicity per residue using standard Kyte-Doolittle hydrophobicity values for each amino acid.

3. Importance of Hydrophobicity Calculation

Details: Hydrophobicity is crucial for predicting peptide behavior in solution, membrane interactions, and protein-protein interactions. It helps in drug design and understanding protein folding.

4. Using the Calculator

Tips: Enter the peptide sequence using standard one-letter amino acid codes (ACDEFGHIKLMNPQRSTVWY). The sequence should contain only valid amino acid characters.

5. Frequently Asked Questions (FAQ)

Q1: What hydrophobicity scale is used?
A: This calculator uses the Kyte-Doolittle hydrophobicity scale, which is one of the most widely used scales.

Q2: What do positive and negative values mean?
A: Positive values indicate hydrophobic residues/peptides, while negative values indicate hydrophilic ones.

Q3: How does length affect hydrophobicity?
A: The calculator normalizes by length, giving average hydrophobicity per residue, making values comparable across different length peptides.

Q4: Are modifications supported?
A: This calculator only handles standard amino acids. Modified residues would need special consideration.

Q5: What's a typical hydrophobicity range?
A: Most natural peptides fall between -2.0 (very hydrophilic) to +4.5 (very hydrophobic) on the Kyte-Doolittle scale.