Calculate molecular weight, elemental composition, extinction coefficient at 280 nm, isoelectric point (pI), and GRAVY hydropathy score from any amino acid sequence.
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Ubiquitin is a small regulatory protein found in all eukaryotic cells. It tags other proteins for degradation by the proteasome.
Protein MW Formulas & Guide
Molecular Weight Calculation
MW = Σ(Residue Masses) + H₂O
Sum the masses of all amino acid residues, then add water (18.015 Da for average, 18.01056 Da for monoisotopic)
Each amino acid residue contributes its residue mass (the mass of the amino acid minus water). After summing all residues, the mass of a water molecule (H₂O) is added because peptide bond formation removes water. Monoisotopic masses use the most abundant isotope of each element for precise mass spectrometry applications. Average masses use the weighted average of all naturally occurring isotopes.
Extinction Coefficient (Edelhoch Method)
ε₂₈₀ = nTrp × 5500 + nTyr × 1490 + nCys × 125
Molar extinction coefficient at 280 nm (M⁻¹ cm⁻¹)
The Edelhoch method estimates the molar extinction coefficient of a protein at 280 nm based on its content of tryptophan (Trp/W), tyrosine (Tyr/Y), and cystine (Cys-C/C). Each Trp contributes ~5,500 M⁻¹ cm⁻¹, each Tyr ~1,490 M⁻¹ cm⁻¹, and each cystine (disulfide-bonded Cys) ~125 M⁻¹ cm⁻¹. This allows estimation of protein concentration from A₂₈₀ readings using Beer's Law: c = A / (ε × l).
Isoelectric Point (pI) Estimation
pI ≈ (pKa of dominant charged group)
Estimated from the balance of positively and negatively charged residues
The isoelectric point (pI) is the pH at which a protein has no net charge. Our calculator estimates pI based on the ratio of acidic residues (Asp, Glu) to basic residues (Arg, Lys, His) and the pKa values of the N-terminus and C-terminus. A protein with more acidic residues has a lower pI; more basic residues yield a higher pI.
GRAVY Score (Kyte-Doolittle Hydropathy)
GRAVY = (Σ Hydropathy Values) / n
Grand average of hydropathy — average of Kyte-Doolittle hydropathy values across all residues
The GRAVY score (Grand Average of HydropathY) summarizes the hydrophobicity of a protein. Positive values indicate hydrophobic (membrane-associated) proteins, while negative values indicate hydrophilic (aqueous soluble) proteins. The Kyte-Doolittle scale assigns each amino acid a hydropathy index from -4.5 (most hydrophilic, arginine) to +4.5 (most hydrophobic, isoleucine).
Amino Acid Reference Table
Code
Amino Acid
3-Letter
Monoisotopic Residue Mass (Da)
Average Residue Mass (Da)
Hydropathy (K-D)
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Molecular Weight
Calculate precise protein molecular weight in Daltons (Da) and kilodaltons (kDa) using monoisotopic or average masses. Includes the mass of terminal water.
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Extinction Coefficient
Compute the molar extinction coefficient at 280 nm using the Edelhoch method based on tryptophan, tyrosine, and cystine content. Also calculate A₂₈₀ for 0.1% solutions.
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pI & Net Charge
Estimate the isoelectric point (pI) and net charge at pH 7 based on the ratio of acidic (Asp, Glu) and basic (Arg, Lys, His) residues.
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GRAVY Hydropathy
Calculate the Grand Average of Hydropathy using the Kyte-Doolittle scale. Positive values indicate hydrophobic proteins; negative values indicate hydrophilic proteins.
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Sequence Builder
Build sequences interactively by clicking amino acid buttons. Includes pre-loaded examples for common proteins like hemoglobin and insulin.
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Elemental Composition
View the complete elemental breakdown (C, H, N, O, S atoms) and molecular formula of your protein. Also see per-amino-acid composition counts.
⚠️ Important Note: This calculator provides estimates based on amino acid sequence alone. Post-translational modifications (glycosylation, phosphorylation, disulfide bonds, etc.) are not accounted for and can significantly alter molecular weight and other properties. The pI estimation is approximate and does not consider local sequence effects on pKa values. For accurate experimental values, use mass spectrometry and other analytical methods.
Frequently Asked Questions
How is protein molecular weight calculated from a sequence?
Protein molecular weight is calculated by summing the residue masses of each amino acid in the sequence, then adding the mass of a water molecule (18.015 Da for average mass, 18.01056 Da for monoisotopic). The residue mass is the mass of the amino acid minus the mass of water (H₂O = 18.015 Da), because a water molecule is eliminated during peptide bond formation. For example, alanine (Ala/A) has a full molecular mass of 89.094 Da, but its residue mass is 71.079 Da (89.094 − 18.015). The terminal water is added back to account for the free N-terminus and C-terminus of the polypeptide chain.
What is the difference between monoisotopic and average mass?
Monoisotopic mass is calculated using the most abundant isotope of each element (e.g., ¹²C, ¹H, ¹⁴N, ¹⁶O, ³²S). This gives the exact mass of a molecule containing only the most common isotopes. It is commonly used in mass spectrometry for precise identification. Average mass uses the weighted average of all naturally occurring isotopes for each element (e.g., carbon's average atomic mass is 12.011 Da, accounting for ¹²C, ¹³C, and ¹⁴C). Average mass is used for general biochemical calculations and approximates the bulk physical mass of a protein sample. Monoisotopic masses are typically 0.5–2 Da lighter than average masses for small peptides, and the difference increases with protein size.
What is the Edelhoch method for extinction coefficient?
The Edelhoch method (1967) estimates the molar extinction coefficient of a protein at 280 nm based on its content of three chromophoric amino acids: tryptophan (Trp/W), tyrosine (Tyr/Y), and cystine (Cys-C) in disulfide bonds. The formula is: ε₂₈₀ = (nTrp × 5,500) + (nTyr × 1,490) + (nCys × 125) M⁻¹ cm⁻¹. This method is widely used because it requires only the amino acid sequence (no experimental measurement needed). The A₂₈₀ (0.1%) value is the absorbance of a 1 g/L (0.1%) protein solution in a 1 cm cuvette, calculated as: A₂₈₀(0.1%) = ε₂₈₀ / (MW × 10). This is convenient for estimating protein concentration using Beer's Law.
What does the GRAVY score tell me about a protein?
The GRAVY score (Grand Average of Hydropathy) indicates the overall hydrophobicity or hydrophilicity of a protein on the Kyte-Doolittle scale. Positive GRAVY values (e.g., +0.5 to +2.0) suggest hydrophobic proteins that are typically membrane-associated or membrane-integral. Negative GRAVY values (e.g., -0.5 to -2.0) indicate hydrophilic proteins that are water-soluble and likely cytoplasmic or extracellular. Most globular proteins have slightly negative GRAVY scores around -0.3 to -0.6. Extremely negative scores are characteristic of highly charged or heavily glycosylated proteins. Membrane proteins often have positive scores due to their hydrophobic transmembrane domains.
How is the isoelectric point (pI) estimated?
The isoelectric point (pI) is the pH at which a protein carries no net electrical charge. Our calculator estimates pI using the ratio of positively charged residues (Arg/R, Lys/K, His/H) to negatively charged residues (Asp/D, Glu/E), along with the N-terminus (pKa ~8.0) and C-terminus (pKa ~3.1). The estimation considers the pKa values of side chains: Arg (~12.5), Lys (~10.5), His (~6.0), Asp (~3.9), Glu (~4.3). A protein with more acidic residues has a lower pI (acidic protein), while more basic residues yield a higher pI (basic protein). For precise pI determination, experimental methods like isoelectric focusing or 2D gel electrophoresis are recommended, as local sequence context can significantly alter pKa values.
What amino acids are included in the 20 standard set?
The 20 standard amino acids encoded by the genetic code are: Alanine (Ala/A), Arginine (Arg/R), Asparagine (Asn/N), Aspartic Acid (Asp/D), Cysteine (Cys/C), Glutamine (Gln/Q), Glutamic Acid (Glu/E), Glycine (Gly/G), Histidine (His/H), Isoleucine (Ile/I), Leucine (Leu/L), Lysine (Lys/K), Methionine (Met/M), Phenylalanine (Phe/F), Proline (Pro/P), Serine (Ser/S), Threonine (Thr/T), Tryptophan (Trp/W), Tyrosine (Tyr/Y), and Valine (Val/V). Two additional non-standard amino acids — Selenocysteine (Sec/U) and Pyrrolysine (Pyl/O) — are occasionally found in proteins but are not included in this calculator.