1. What is Peptide Hydrophobicity?

Peptide hydrophobicity is a measure of how water-repellent a peptide sequence is, calculated as the average of individual amino acid hydrophobicity values. It's important for understanding protein folding, membrane interactions, and solubility.

2. How Does the Calculator Work?

The calculator uses the following formula:

Where:

• \( \text{hydrophobicity\_aa} \) — Hydrophobicity value of each amino acid (Kyte-Doolittle scale)
• \( \text{length} \) — Number of amino acids in the peptide

Explanation: The calculator sums the hydrophobicity values of each amino acid in the sequence and divides by the total number of amino acids to get the average hydrophobicity.

3. Importance of Hydrophobicity Calculation

Details: Hydrophobicity is crucial for predicting protein behavior, including membrane insertion, solubility, and aggregation propensity. It's used in drug design and protein engineering.

4. Using the Calculator

Tips: Enter the peptide sequence using standard one-letter amino acid codes (ACDEFGHIKLMNPQRSTVWY). The sequence is case-insensitive.

5. Frequently Asked Questions (FAQ)

Q1: What hydrophobicity scale is used?
A: The calculator uses the Kyte-Doolittle hydrophobicity scale, a widely recognized scale for amino acid hydrophobicity.

Q2: What are typical hydrophobicity values?
A: Values range from about -4.5 (most hydrophilic) to +4.5 (most hydrophobic). Most soluble proteins have slightly negative averages.

Q3: How does hydrophobicity affect protein behavior?
A: More hydrophobic peptides tend to be less soluble in water and more likely to aggregate or insert into membranes.

Q4: Are there other hydrophobicity scales?
A: Yes, other scales like Eisenberg or Hopp-Woods exist, each with slightly different values and applications.

Q5: Can I use modified amino acids?
A: This calculator only handles standard amino acids. Modified residues would require custom hydrophobicity values.