Amino Acid Sequence Analyzer
Analyze a protein sequence's amino acid composition — the percentage that's hydrophobic, polar, acidic, or basic — and estimate its net charge at physiological pH. Two 3D diagrams compare a hydrophobic-rich sequence to a charged-rich one, and charts show the full amino acid category breakdown for your sequence.
Reviewed by the ToolNestr Editorial Team — July 2026
Hydrophobic-rich vs. charged-rich sequence
1. Hydrophobic-rich
Mostly nonpolar residues (grey) — likely buried in a folded protein's core.
2. Charged-rich
Mostly acidic (red) and basic (blue) residues — likely on the protein's surface.
Composition charts
How it works
The core idea in one line: a protein's amino acid composition alone — how much of it is oily-and-water-avoiding, water-loving, positively charged, or negatively charged — predicts a surprising amount about how it will fold, where it will sit in a cell, and how it will behave in the lab.
Category % = (residues in category / total residues) × 100
nonpolar, polar uncharged, acidic, or basic
Net charge ≈ (count of K+R) − (count of D+E)
simplified estimate at physiological pH; histidine excluded due to its near-neutral pKa
Each of the 20 standard amino acids carries a side chain with a characteristic chemical personality: some are oily and avoid water (hydrophobic), some are polar but electrically neutral, and some carry a genuine positive or negative charge at the cell's normal pH. Tallying what fraction of a sequence falls into each category reveals real, predictable biochemistry — a hydrophobic-heavy sequence likely folds with those residues buried in its core, while a highly charged sequence is more likely to be soluble and to migrate strongly in an electric field. Estimating net charge specifically requires care with histidine, whose side chain sits right at the edge of being charged at physiological pH, unlike lysine and arginine's side chains, which are reliably protonated.
Worked example 1 — composition of a short sequence
Given: The sequence MKVLDEEK (8 residues).
This sequence is roughly split between hydrophobic and charged residues, with slightly more acidic than basic character.
Worked example 2 — estimating net charge
Given: Same sequence, MKVLDEEK: 2 lysines (K), 0 arginines (R), 1 aspartate (D), 2 glutamates (E).
A net negative charge at physiological pH means this peptide would migrate toward the positive electrode in an electrophoresis experiment — a real, testable prediction from this simple estimate.
The four amino acid property categories
Every one of the 20 standard amino acids falls into one of these four groups.
| Category | Example residues | Typical location in folded protein |
|---|---|---|
| Nonpolar/hydrophobic ★ | Leu, Val, Ile, Phe, Ala | Buried in the protein's interior |
| Polar uncharged | Ser, Thr, Asn, Gln, Cys, Tyr | Often on the surface, hydrogen bonding |
| Acidic (negative) | Asp, Glu | Usually on the surface |
| Basic (positive) | Lys, Arg, His | Usually on the surface |
★ Reference row. Hydrophobic residues clustering in the core is one of the primary driving forces behind protein folding.
Where amino acid composition actually matters
⚡ Protein electrophoresis (isoelectric focusing)
Isoelectric focusing separates proteins based on their net charge, which shifts with pH — understanding a protein's charged residue composition predicts how it will migrate and helps interpret separation results.
💊 Drug and protein formulation
Pharmaceutical scientists analyze a therapeutic protein's surface charge and hydrophobicity to predict its solubility, stability, and aggregation risk during formulation and storage.
🧬 Predicting protein structure and function
A sequence's hydrophobicity pattern is one of the primary inputs used by computational tools to predict which regions of a protein are likely to be buried, exposed, or embedded in a cell membrane.
🔬 Antibody and enzyme engineering
Engineers modify specific residues to adjust a protein's charge or hydrophobicity, fine-tuning its solubility, binding affinity, or stability for research and therapeutic applications.
Common misconceptions
"A protein's net charge estimate from its sequence is always exactly right."
This is a simplified estimate based on typical residue pKa values at pH 7.4 — the true charge can shift with the exact local environment inside a folded protein, and post-translational modifications (like phosphorylation) add additional charged groups not captured by the raw sequence alone.
"Histidine should be counted as a full positive charge like lysine and arginine."
Histidine's side chain pKa (~6.0) sits close to physiological pH, so only a modest fraction of histidine residues are actually protonated at pH 7.4 — treating it as a full +1 charge like lysine or arginine (whose pKa values are much higher) would overestimate a protein's true net charge.
"All hydrophobic amino acids are on a protein's surface, since that's where they'd be most stable."
It's the opposite — hydrophobic residues are typically buried in a protein's interior, away from the surrounding water, while polar and charged residues face outward into the aqueous environment, which is the more energetically stable arrangement.
"Amino acid composition alone tells you a protein's exact 3D shape."
Composition strongly influences folding tendencies, but the precise order of residues (not just their overall proportions) and complex interactions between distant parts of the chain are what ultimately determine a protein's exact 3D structure.
Formula sources & further reading
The formulas here are standard, traceable to:
- • OpenStax, Biology 2e — Chapter 3, "Biological Macromolecules" (free, peer-reviewed). openstax.org
- • Alberts et al., Molecular Biology of the Cell — Amino acid properties and protein folding chapter.
- • Lehninger, Principles of Biochemistry — Amino acid classification and pKa reference chapter.
Net charge estimate uses standard side-chain pKa approximations at pH 7.4; histidine excluded from the simple count due to its near-neutral pKa (~6.0). Results are simplified estimates, not exact calculations.
How to use this calculator
Enter a protein sequence
Type the sequence using standard one-letter amino acid codes.
Read composition percentages
Hydrophobic, polar, acidic, and basic residue percentages calculate instantly.
Check net charge estimate
A simplified estimate at physiological pH, from basic and acidic residue counts.
Related tools
Frequently asked questions
How are amino acids categorized by chemical property?
Amino acids are commonly grouped into nonpolar/hydrophobic (like leucine, valine), polar uncharged (like serine, asparagine), acidic/negatively charged (aspartate, glutamate), and basic/positively charged (lysine, arginine, histidine).
How is net charge estimated from a sequence?
As a simplified estimate at physiological pH (~7.4): count each lysine (K) and arginine (R) as +1, each aspartate (D) and glutamate (E) as −1, and sum them — histidine is typically left out of this simple estimate since its side chain is only weakly basic and mostly uncharged at pH 7.4.
Why does hydrophobicity matter for protein structure?
Hydrophobic amino acids tend to cluster in a protein's interior (away from water) while polar and charged ones tend to sit on the surface — this hydrophobic effect is one of the most important forces driving how proteins fold into their functional 3D shape.
Why is histidine treated differently from lysine and arginine?
Histidine's side chain has a pKa of about 6.0, very close to physiological pH — meaning only a modest fraction of histidine residues are actually protonated (charged) at pH 7.4, unlike lysine and arginine, whose side chains are essentially always fully protonated at that pH.
Does amino acid composition affect protein solubility?
Yes — proteins with a higher fraction of charged and polar residues on their surface tend to be more soluble in water, while proteins with a large hydrophobic surface fraction are more likely to aggregate or require detergents to stay in solution.