Calculator Input
Example Data Table
Use these examples to understand common input settings and expected interpretation.
| Example Sequence | Suggested Scale | Window | Use Case | Expected Review |
|---|---|---|---|---|
MKWVTFISLLFLFSSAYS |
Kyte-Doolittle | 9 | Signal peptide screening | Look for a strong positive local region. |
ACDEFGHIKLMNPQRSTVWY |
Eisenberg Consensus | 7 | Mixed residue comparison | Compare hydrophobic and charged residue balance. |
KKLLKLLKKLLKLLKK |
Eisenberg Consensus | 5 | Amphipathic peptide review | Check hydrophobic moment and charge together. |
VVVVVVVVVVVVVVVVVVVV |
Kyte-Doolittle | 11 | Hydrophobic segment test | Expect a high continuous window score. |
Formula Used
Havg = Σhi / N
Here, hi is the residue score from the selected scale.
Wj = Σhi / m
The score is averaged across residues inside the selected window.
GRAVY = Σ Kyte-Doolittle residue values / N
Positive values suggest stronger hydrophobic tendency.
MW = Σ residue masses + 18.01528
Water is added for the peptide termini.
μH = √[(Σhicosθi)² + (Σhisinθi)²] / N
This estimates amphipathic pattern strength.
Positive groups use 1 / (1 + 10pH-pKa). Negative groups use -1 / (1 + 10pKa-pH).
How to Use This Calculator
- Paste a protein or peptide sequence in one-letter amino acid format.
- Select the hydrophobicity scale that matches your review goal.
- Choose a sliding window size. Use larger values for membrane region screening.
- Set a hydrophobicity threshold to mark strong local segments.
- Adjust pH when you need an estimated charge value.
- Press the calculate button and review the result above the form.
- Use the chart to inspect local peaks and valleys.
- Download CSV for residue data or PDF for a quick report.
Understanding Amino Acid Hydrophobicity
Amino acid hydrophobicity explains how strongly a residue prefers water or a nonpolar environment. This property guides protein folding, membrane insertion, ligand binding, and surface exposure. A single sequence can show many local patterns. Average scores help describe the complete chain. Sliding windows reveal short stretches that may form transmembrane helices, buried cores, or exposed loops.
Why Hydrophobicity Matters
Hydrophobic residues often cluster inside soluble proteins. They avoid water and stabilize the folded core. In membrane proteins, long positive windows often mark lipid facing helices. Polar and charged residues often appear on exposed surfaces. They also help active sites, salt bridges, and recognition regions. A hydrophobicity calculator makes these patterns visible before deeper modeling begins.
Using Several Scales
Different hydrophobicity scales were built from different experiments. Kyte Doolittle is widely used for GRAVY and membrane profile work. Eisenberg values support amphipathic helix review. Hopp Woods highlights hydrophilic regions, so high positive values suggest likely surface exposure. Comparing scales prevents overconfidence from one method. The best interpretation uses sequence context, window size, and known biology.
Reading The Results
The average score gives a global tendency. The residue table shows each contribution. The window chart shows local peaks and valleys. A strong positive region may be hydrophobic. A strong negative region may be hydrophilic. The hydrophobic fraction summarizes composition. Molecular weight and estimated charge add useful biochemical context. Hydrophobic moment helps identify amphipathic segments. High moment can mean one face is nonpolar while another face is polar.
Good Practice
Clean the sequence before analysis. Remove numbers, spaces, and FASTA headers. Use one letter amino acid codes. Start with a window of seven to eleven residues for short peptides. Try nineteen to twenty three residues for membrane helix screening. Adjust the threshold for your organism and protein family. Export the CSV when you need residue level records. Export the PDF when you need a quick report for notes or review. Treat every result as a guide. Confirm important predictions with structural tools, experiments, or curated annotations. Repeat the calculation with nearby window sizes. Stable peaks across settings usually deserve more attention than peaks from one narrow choice during review.
FAQs
1. What does amino acid hydrophobicity mean?
It measures how much an amino acid prefers a nonpolar environment instead of water. Hydrophobic residues often appear inside folded proteins or within membrane regions.
2. What is a GRAVY value?
GRAVY is the average Kyte-Doolittle hydrophobicity score for a sequence. Positive values suggest hydrophobic character. Negative values suggest hydrophilic character.
3. Which hydrophobicity scale should I use?
Use Kyte-Doolittle for general GRAVY and membrane profile checks. Use Eisenberg for amphipathic patterns. Use Hopp-Woods for hydrophilic surface tendency.
4. Why does window size matter?
Small windows show fine local changes. Larger windows smooth the profile and reveal longer hydrophobic regions. Membrane helix screening often needs wider windows.
5. What is a hydrophobic segment?
It is a continuous sequence region where the sliding window score stays above your threshold. It may indicate a buried core, signal peptide, or membrane region.
6. What is hydrophobic moment?
Hydrophobic moment estimates how unevenly hydrophobic residues are arranged around a helix. Higher values can suggest amphipathic structure with polar and nonpolar faces.
7. Can this calculator predict protein structure?
It gives useful sequence-based clues, but it does not replace structural prediction or experiments. Use it as an early screening and comparison tool.
8. What happens to unknown residues?
Unknown letters are shown in the table but excluded from averages, molecular weight, charge, and hydrophobic moment. Use standard one-letter codes for best results.