Protein Extinction Coefficient Calculator

Calculate the molar extinction coefficient of proteins based on their amino acid composition for accurate spectrophotometric protein concentration determination.

How to Use This Calculator

Enter the number of tryptophan (W) residues in your protein
Enter the number of tyrosine (Y) residues in your protein
Enter the number of cystine (C) residues in your protein
Enter the molecular weight of your protein in kilodaltons (kDa)
Click Calculate to see the extinction coefficient and related values

Formula Used

ε = (nW × 5500) + (nY × 1490) + (nC × 125)

Where:

ε = Molar extinction coefficient (M⁻¹cm⁻¹)
nW = Number of tryptophan residues
nY = Number of tyrosine residues
nC = Number of cystine residues (disulfide bonds)

Example Calculation

Real-World Scenario:

Calculating the extinction coefficient for Bovine Serum Albumin (BSA), a commonly used protein standard in laboratories.

Given:

Number of tryptophan residues = 2
Number of tyrosine residues = 20
Number of cystine residues = 17
Molecular weight = 66.5 kDa

Calculation:

ε = (2 × 5500) + (20 × 1490) + (17 × 125)

ε = 11000 + 29800 + 2125

ε = 42925 M⁻¹cm⁻¹

Result: The extinction coefficient of BSA is 42925 M⁻¹cm⁻¹, which means a 1 mg/mL solution of BSA would have an absorbance of approximately 0.667 at 280 nm.

Why This Calculation Matters

Practical Applications

Determining protein concentration in solution
Purification monitoring during chromatography
Protein quantification in biochemical assays

Key Benefits

Non-destructive protein quantification
Rapid and accurate concentration determination
Essential for proper experimental design

Common Mistakes & Tips

The formula requires the number of cystine residues (disulfide bonds), not cysteine residues. Each disulfide bond consists of two cysteine residues, so the number of cystine residues is typically half the number of cysteine residues that form disulfide bonds.

Ensure you're using the correct molecular weight for your protein in kilodaltons (kDa), not grams per mole. If you have the molecular weight in g/mol, divide by 1000 to convert to kDa. This value is essential for calculating the absorbance at 1 mg/mL.

Frequently Asked Questions

The extinction coefficient (also called molar absorptivity) is a measure of how strongly a chemical species absorbs light at a particular wavelength. For proteins, it's typically measured at 280 nm, where aromatic amino acids (tryptophan and tyrosine) absorb light.

At 280 nm, primarily tryptophan, tyrosine, and cystine (disulfide bonds) absorb light significantly. Other amino acids have negligible absorption at this wavelength, so they don't contribute substantially to the overall extinction coefficient.

The Gill and von Hippel equation used in this calculator provides a good approximation (typically within 5-10% accuracy) for most proteins in their native state. However, experimental factors like pH, buffer composition, and protein conformation can affect the actual absorbance.

References & Disclaimer

Scientific Disclaimer

This calculator provides an estimate of protein extinction coefficients based on the Gill and von Hippel equation. For precise quantitative work, experimental determination of the extinction coefficient is recommended. Results should be used as a guide and not as a substitute for laboratory measurements.

References

Gill, S.C., & von Hippel, P.H. (1989). Calculation of protein extinction coefficients from amino acid sequence data. - Analytical Biochemistry, 182(2), 319-326.
Aitken, A., & Learmonth, M. (2009). Protein determination by UV absorbance at 280 nm. - Nature Protocols, 4(2), 251-253.
Stoscheck, C.M. (1990). Quantitation of protein. - Methods in Enzymology, 182, 50-68.

Accuracy Notice

The calculated extinction coefficient assumes the protein is in its native conformation and in a standard buffer at pH 7.0. Factors such as denaturation, aggregation, or unusual buffer compositions can affect the actual absorbance values. For critical applications, experimental validation is recommended.

About the Author

Kumaravel Madhavan

Web developer and data researcher creating accurate, easy-to-use calculators across health, finance, education, and construction and more. Works with subject-matter experts to ensure formulas meet trusted standards like WHO, NIH, and ISO.

Connect with LinkedIn

Tags:

science biostatistics protein extinction coefficient chemistry formula

Related Calculators