Amino Acid Properties Table

Introduction

This interactive reference table covers all 20 standard amino acids with searchable, filterable data: residue molecular weight, alpha-carboxyl and alpha-amino pKa values, isoelectric point, Kyte-Doolittle hydrophobicity index, and chemical group. Used by biochemistry students, protein chemists, and structural biologists to quickly look up physicochemical properties without opening a textbook.

About the Tool

The Amino Acid Properties Table is a client-side reference tool: all 20 proteinogenic amino acids and their physicochemical properties are built into the page, and the table renders, searches, and filters entirely in your browser with no data sent to a server. Each row summarizes the core properties used daily in protein chemistry — residue molecular weight, the two backbone pKa values, isoelectric point (pI), and Kyte-Doolittle hydrophobicity — while clicking a row opens a detail panel with the side-chain pKa (where applicable), molecular formula, and a plain-English description of the side chain. It's built for quick bench-side lookups, coursework, and cross-checking values used in other BioToolsKit calculators such as the Isoelectric Point Calculator and Amino Acid MW Calculator.

Input Explanation

Type any amino acid name (e.g. Alanine), three-letter code (e.g. Ala), or one-letter code (e.g. A) into the search box to instantly filter the table. The search matches on all three identifiers simultaneously, so partial input such as "gly" will find Glycine. Use the group filter buttons — Nonpolar, Polar, Charged, Aromatic — to narrow the display to a specific biochemical class. The row count above the table updates automatically to show how many amino acids are currently visible. Clicking any row opens a detail panel below the table with the complete data set for that amino acid.

Formula Explanation

For amino acids with no ionisable side chain, pI is simply the average of the α-carboxyl and α-amino pKa values. For the nine amino acids with an ionisable R group (Asp, Glu, His, Cys, Tyr, Lys, Arg, and the borderline cases Ser/Thr), the pI calculation instead averages the two pKa values that bracket the pH range where the molecule carries zero net charge — which are not always the same two groups used for non-ionisable side chains. All values are for the free amino acid in aqueous solution at 25°C, not for the residue embedded in a folded protein.

Worked Example

Aspartate (Asp, D) — pKa(α-COOH) = 1.88, pKa(R, side-chain carboxyl) = 3.65, pKa(α-NH₃⁺) = 9.60

1. Identify the ionisable groups. Aspartate has three: the α-carboxyl (pKa 1.88), the acidic side chain (pKa 3.65), and the α-amino group (pKa 9.60).
2. Find where the net charge is zero. Below pH 1.88, all three groups are protonated (net charge +1). Between pH 1.88 and 3.65, only the α-carboxyl has deprotonated (net charge 0) — this is the zwitterionic window.
3. Average the two pKa values that bracket that window. Because both bracketing groups are acidic, use pI = (pKa₁ + pKaR) / 2, not the α-amino pKa (9.60), which only becomes relevant far above the zwitterionic range.
4. Calculate: pI = (1.88 + 3.65) / 2 = 5.53 / 2 = 2.765

This matches the pI listed for aspartate in the table (2.77). Because this value is well below physiological pH (7.4), aspartate's side chain is fully deprotonated and negatively charged at physiological pH — this is why aspartate residues contribute negative surface charge to proteins and why aspartate binds strongly to anion-exchange resin at neutral pH.

Result Interpretation

Click any row in the table to open a detailed panel beneath it. The panel displays all data fields including the side chain (R group) pKa — which is only present for amino acids with ionisable side chains. The panel also shows the molecular formula, chemical group classification, and a plain-English description of the side chain's chemical nature and functional significance. A pI far from 7 signals a residue that carries strong charge at physiological pH; a hydrophobicity score above roughly +1.8 (as with isoleucine, valine, leucine, phenylalanine) signals a residue likely to sit buried in a folded protein core or embedded in a membrane, while strongly negative scores (arginine, lysine, aspartate, glutamate) signal residues typically found on a protein's solvent-exposed surface.

Practical Applications

This table is useful in a wide range of practical and academic contexts. Use it when designing ion-exchange chromatography conditions — comparing the pI of your target protein with the pH of the mobile phase determines whether the protein binds to a cation- or anion-exchange column. Use the Kyte-Doolittle hydrophobicity values when predicting transmembrane helices or signal peptides in protein sequences using sliding window plots. Use the residue molecular weights when calculating the theoretical mass of a peptide or protein by summing residue masses and adding 18.02 Da for the terminal water molecule. Use the pKa values when choosing a buffer pH that will maintain the charge state of key active-site residues in an enzyme assay.

Scientific Notes & Limitations

All values shown are for the free amino acid in aqueous solution, not the residue embedded in a folded protein — a residue's local environment (burial, hydrogen bonding, neighboring charges) can shift its effective pKa by one or more pH units. Residue molecular weights already have 18.02 Da subtracted for the water lost during peptide bond formation; add it back for free amino acid mass. The pI values here describe individual amino acids and should not be applied directly to predict a whole protein's isoelectric point, which depends on the full sequence composition and solvent exposure — use a dedicated protein pI calculator for that. Reference values are consistent with standard physical biochemistry sources such as Lehninger Principles of Biochemistry and the CRC Handbook of Chemistry and Physics; minor variation (±0.1–0.2 pH units) between textbooks and software is normal due to differing measurement conditions and ionic strength corrections.

Practical Tips

• Use the group filter buttons instead of scrolling when you only need one biochemical class — for example, filter to "Aromatic" when checking UV-absorbing residues (Trp, Tyr, Phe) for A280 protein quantification.
• When designing an ion-exchange purification, sort candidate proteins by comparing your protein's estimated pI against the target amino acid's pI in this table to anticipate how individual surface residues will behave.
• Cross-check pI and pKa values here against your specific buffer's ionic strength — published pKa values assume standard conditions and can shift with high salt or non-standard temperature.
• Bookmark the detail panel view (click any row) when you need the molecular formula alongside the numeric properties for stoichiometry calculations.

Common Mistakes

• Confusing residue MW with free amino acid MW: The values in this table are residue masses (after losing water during peptide bond formation). The free amino acid mass is approximately 18 Da higher. Use residue masses for protein MW calculations and free amino acid masses only for preparing stock solutions of individual amino acids.
• Misreading the hydrophobicity bar direction: A longer orange bar means more hydrophobic (positive score), while a longer blue bar means more hydrophilic (negative score). Isoleucine (+4.5) and valine (+4.2) are the most hydrophobic; arginine (−4.5) and aspartate (−3.5) are the most hydrophilic.
• Ignoring side chain pKa when predicting protein charge: At physiological pH (7.4), histidine (pKa ≈ 6.0) is largely uncharged, while glutamate (pKa ≈ 4.25) and lysine (pKa ≈ 10.53) are fully charged. Failing to account for side chain ionisation leads to incorrect charge predictions and poor isoelectric point estimates.
• Applying the table pI to a whole protein: The pI values here are for free amino acids in solution. Protein pI depends on the composition and solvent exposure of all ionisable residues, their local electrostatic environment, and any post-translational modifications. Use a dedicated pI calculator for protein-level predictions.

Frequently Asked Questions

What does the isoelectric point (pI) of an amino acid mean?

The isoelectric point (pI) is the pH at which an amino acid carries no net electrical charge — its positive and negative charges are exactly balanced. At pH values below the pI, the amino acid is net positively charged; above the pI it is net negatively charged. The pI is calculated as the average of the two pKa values flanking the zwitterionic form. For amino acids with ionisable side chains, such as aspartate (pI 2.77) or lysine (pI 9.74), the side chain pKa is also factored in. Knowing the pI is essential for predicting protein solubility, designing gel electrophoresis conditions, and selecting isoelectric focusing protocols.

What is the Kyte-Doolittle hydrophobicity scale?

The Kyte-Doolittle scale assigns a hydrophobicity index to each amino acid based on the energetics of transferring its side chain from water into a non-polar organic phase. Values range from +4.5 (most hydrophobic, isoleucine) to −4.5 (most hydrophilic, arginine). Positive values indicate hydrophobic residues that prefer the interior of folded proteins or lipid bilayers, while negative values indicate hydrophilic residues that favour contact with water on protein surfaces. The scale is widely used for predicting transmembrane helices, signal peptides, and exposed surface regions in protein structure prediction.

Why do amino acid molecular weights in this table differ from textbook values?

This table lists residue molecular weights — the mass of each amino acid after losing one water molecule (18.02 Da) during peptide bond formation. The free amino acid mass (e.g. alanine = 89.09 Da) equals the residue mass, while the average residue mass in a polypeptide chain accounts for the shared water lost per bond. When calculating the molecular weight of a protein or peptide, use residue masses and add 18.02 Da for the single water molecule at the termini. Free amino acid masses (for solution preparation or assay calibration) should use the full molecular weight including water.

Which amino acids are considered 'special' and why?

Glycine, cysteine, and proline are classified as special amino acids because their side chains have unique structural or chemical properties that set them apart from the four standard groups. Glycine has no side chain (its R group is just a hydrogen atom), giving it exceptional conformational flexibility and making it the only amino acid that is not optically active. Cysteine contains a reactive thiol (–SH) group capable of forming disulfide bonds, which are critical for protein tertiary structure stability. Proline has its side chain bonded back to the backbone nitrogen, forming a rigid five-membered ring that acts as a helix breaker and is common in beta-turns and collagen triple helices.

How is pKa different from pI, and how do I use pKa values in the lab?

pKa is the pH at which a specific ionisable group is 50% protonated and 50% deprotonated, while pI is the overall pH of net zero charge for the whole molecule. Each amino acid has at least two pKa values: one for the alpha-carboxyl group (typically 1.8–2.4) and one for the alpha-amino group (typically 8.8–10.8). Amino acids with ionisable side chains have a third pKa for the R group. In the lab, pKa values are used to predict charge states at physiological pH, design ion-exchange chromatography conditions, interpret titration curves, and understand enzyme active site chemistry. The Henderson-Hasselbalch equation — pH = pKa + log([A⁻]/[HA]) — links pKa directly to the ionisation state at any given pH.

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