| 1-Letter | 3-Letter | Name | Free MW (Da) | Residue MW (Da) | Monoisotopic (Da) | pKa (side chain) | Group |
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Introduction
The Amino Acid MW Calculator is a complete reference tool for the molecular weights and physicochemical properties of all 20 standard amino acids. Search by name or code, filter by physicochemical group, or use Sequence Mode to sum molecular weights across an entire peptide or protein sequence. Every lookup returns free-form mass, residue mass, monoisotopic mass, pKₐ, hydropathy index, molecular formula, and codon usage — everything needed at the bench or in a bioinformatics workflow.
About the Tool
This tool combines a full amino acid reference with a sequence mass calculator. Browse Mode lets you search or filter through all 20 standard amino acids and open a detail panel showing five core mass values plus a full properties table covering molecular formula, net charge, polarity, essential-amino-acid status, and mRNA codon usage. Sequence Mode extends this to whole peptides: paste a sequence in single-letter code and the tool sums either residue or free-form molecular weights across every position, reporting the total mass and sequence length instantly. The Complete Reference Table below both tools lists all 20 amino acids side by side, sorted alphabetically, for quick comparison.
Input Explanation
Search Amino Acid accepts a full name, one-letter code, or three-letter code — for example Alanine, A, or Ala — and narrows results as you type. The filter chips (Hydrophobic, Polar, Positive, Negative, Special) restrict the list to a single physicochemical group at a time. Quick Select shows all 20 one-letter codes for instant lookup without typing.
In Sequence Mode, paste or type a peptide or protein sequence using standard single-letter amino acid codes into the sequence field. Choose Residue MW (peptide) for the mass as it appears in an intact chain, or Free Form MW (solution) for the mass as separate, dissolved amino acids. Any character that is not one of the 20 standard single-letter codes is excluded from the total and listed separately in the result.
Formula Explanation
Free form MW is the molecular weight of an amino acid as an isolated chemical compound, with both its free amino group (−NH₂) and carboxyl group (−COOH) intact. This is the value listed in chemical catalogues and used when working with amino acids in solution, such as when preparing standards for HPLC amino acid analysis or supplementing cell culture media.
Residue MW is the mass contribution of an amino acid once it is incorporated into a polypeptide chain. During peptide bond formation, the −OH from the carboxyl group of one amino acid condenses with the −H from the amino group of the next, eliminating one water molecule (18.015 Da).
Peptide/Protein MW = Σ(Residue MW of each amino acid) + 18.015 Da
Variables and units: Free Form MW is the isolated amino acid mass in daltons (Da). 18.015 Da is the mass of one water molecule, lost per peptide bond formed and added back once for the free N- and C-termini. Σ(Residue MW) is the sum of every residue mass across the sequence, also in daltons.
Worked Example
Sample Input
Peptide sequence MTEYK, synthesized in the lab and due for HPLC-MS analysis to confirm successful synthesis. Mass type: Residue MW (peptide).
Step-by-Step Calculation
Sum the residue masses of each amino acid in the sequence: Met (131.193) + Thr (101.105) + Glu (129.115) + Tyr (163.176) + Lys (128.175) = 652.764 Da. Add one water molecule to account for the free N- and C-termini: 652.764 + 18.015 = 670.779 Da.
Final Result
670.779 Da
Interpretation
This theoretical mass is what you would compare against the observed [M+H]⁺ peak from mass spectrometry — 671.79 Da for the singly protonated ion — to confirm the peptide was synthesized correctly.
Result Interpretation
Free Form MW tells you the mass of the amino acid as an isolated, dissolved molecule — use it when weighing out standards or supplementing media. Residue MW tells you its contribution once bonded into a chain — use it, plus one water molecule, whenever you sum a sequence to a peptide or protein mass. Monoisotopic mass is the figure to compare against a mass spectrometer's isotope-resolved peak for small peptides, while the average mass in the main cards and reference table is the figure to compare against SDS-PAGE or bulk chromatography results. A non-null pKa value flags an ionisable side chain relevant to net charge and buffer selection; the hydropathy index score indicates how strongly that residue favours a hydrophobic (positive) or aqueous (negative) environment.
Practical Applications
Common laboratory scenarios where this tool is valuable include: calculating the expected MW of a synthetic peptide before HPLC-MS analysis; verifying the theoretical mass of a recombinant protein fragment; estimating the molar extinction coefficient contribution of Trp and Tyr residues, which requires knowing their residue MWs; selecting buffer components when working with charged amino acids near their pKa values; and predicting membrane-spanning segments by scanning hydropathy scores. The codon usage data in the detail panel is also useful when designing site-directed mutagenesis experiments, as it shows which codons encode each amino acid and can guide codon selection for optimal expression in a target organism.
Scientific Notes & Limitations
The MW values shown in the main cards and reference table are average masses, calculated using the weighted average atomic weights of all naturally occurring isotopes of each element. This reflects the actual isotope distribution in a bulk sample and is the value most relevant to protein biochemistry, column chromatography, and SDS-PAGE molecular weight estimation. Monoisotopic mass, listed in the detail panel, uses only the most abundant isotope of each element — ¹H, ¹²C, ¹⁴N, ¹⁶O, and ³²S — and is used in mass spectrometry of small peptides where individual isotope peaks are resolved. For peptides and proteins larger than roughly 2 kDa, the monoisotopic peak is no longer the tallest peak in the distribution, so average mass becomes the more appropriate figure.
The hydropathy index values are from the Kyte-Doolittle scale (1982), scoring each amino acid from −4.5 (most hydrophilic) to +4.5 (most hydrophobic). The side-chain pKa values listed represent the intrinsic pKa of each ionisable group in a model peptide context; in a folded protein these values can shift by 2–5 pH units due to local electrostatic environment and burial in the hydrophobic core, which is why catalytic residues such as His in serine proteases can function at pH optima different from their free amino acid pKa. All masses given here are for unmodified amino acids: post-translational modifications are not included, and would need to be added separately — phosphorylation adds +79.966 Da, glycosylation adds a variable mass, and disulfide bond formation subtracts 2.016 Da per pair.
Practical Tips
- Use residue MWs and add 18.015 Da when calculating a peptide or protein MW from sequence; use free-form MWs only for a mixture of separate, dissolved amino acids.
- Use average mass for SDS-PAGE and most spectrophotometric work; switch to monoisotopic mass for mass spectrometry of peptides below roughly 2 kDa.
- When estimating a protein's molar extinction coefficient, note that Trp and Tyr residue MWs are also needed for the parallel mass calculation.
- Account for post-translational modifications separately — this reference lists unmodified residue masses only.
- Consider the six ionisable residues (Asp, Glu, His, Cys, Tyr, Lys, Arg) when choosing a buffer pH for HPLC or ion-exchange work.
Common Mistakes
A very common error is summing free-form MWs to calculate a peptide MW without subtracting water for each peptide bond. For a peptide of n amino acids, (n−1) water molecules are lost during synthesis, and the free terminus adds back one — always use residue MWs and add one water molecule at the end instead. Another frequent mistake is using monoisotopic masses when average masses are needed, or vice versa, which produces MW predictions that do not match measured values: use average masses for SDS-PAGE and most spectrophotometric work, and monoisotopic masses for MS of peptides below 2 kDa.
Frequently Asked Questions
What is the difference between free form MW and residue MW?
Free form MW is the molecular weight of an amino acid as a standalone molecule with intact amino and carboxyl groups. Residue MW is the mass when the amino acid is incorporated into a peptide chain; during peptide bond formation a water molecule (18.015 Da) is lost, so Residue MW = Free MW − 18.015 Da. When calculating protein MW from sequence, sum residue MWs then add 18.015 Da for the free termini.
What is the difference between average mass and monoisotopic mass?
Average mass uses weighted average atomic weights reflecting natural isotope abundances and is the standard for most biochemical work and SDS-PAGE estimation. Monoisotopic mass uses only the most abundant isotope of each element (¹H, ¹²C, ¹⁴N, ¹⁶O, ³²S) and is used in mass spectrometry of small peptides. For proteins above approximately 2 kDa, average mass is more relevant for MS interpretation because the monoisotopic peak is no longer the tallest peak in the isotope envelope.
How do I calculate the molecular weight of a peptide from sequence?
Sum the residue MWs of each amino acid in the sequence, then add 18.015 Da for the single water molecule needed to cap the N- and C-termini. The Sequence Mode on this page does this automatically. For a free amino acid mixture rather than a peptide, sum the free-form MWs without adding water.
Which amino acids have ionisable side chains at physiological pH?
Six amino acids have ionisable side chains: Aspartic acid (pKa 3.9) and Glutamic acid (pKa 4.1) are negatively charged at pH 7; Histidine (pKa 6.5) is partially charged near physiological pH; Cysteine (pKa 8.3), Tyrosine (pKa 10.1), Lysine (pKa 10.5), and Arginine (pKa 12.5) are uncharged at neutral pH but titrate at higher values. These pKa values can shift significantly when residues are buried inside a folded protein.
What is the Kyte-Doolittle hydropathy index used for?
The Kyte-Doolittle hydropathy index assigns each amino acid a score from −4.5 (most hydrophilic) to +4.5 (most hydrophobic). Positive values indicate residues that prefer non-aqueous environments such as membrane bilayers or protein cores; negative values indicate water-favouring residues typically found on protein surfaces. Sliding-window plots of hydropathy along a protein sequence are widely used to predict transmembrane helices, signal peptides, and surface-exposed regions.