The molar extinction coefficient () describes how strongly a protein absorbs light at a given wavelength. At 280 nm, sequence-based protein estimates come mainly from tryptophan, tyrosine, and cystine, the disulfide-bonded form of cysteine.
This calculator uses the protein sequence to estimate , molecular weight, predicted for a 0.1% solution, and optional concentration from a measured absorbance value. It is intended for purified proteins without additional UV-absorbing cofactors, labels, nucleic acids, or other chromophores.
For a broader physicochemical profile, use Protein Parameters, which reports molecular weight, pI, amino acid composition, instability index, GRAVY, and related sequence properties.
The calculation follows the Pace et al. 1995 280 nm coefficients used by common protein-parameter tools:
| Term | Meaning | Contribution |
|---|---|---|
| Number of tryptophan residues (W) | 5,500 | |
| Number of tyrosine residues (Y) | 1,490 | |
| Number of cystine pairs, meaning disulfide bonds | 125 |
Free reduced cysteine contributes 0 at 280 nm. A disulfide-bonded cysteine pair contributes 125, so cystine is counted per disulfide bond rather than per cysteine residue.
Molecular weight is calculated from average residue masses, subtracting peptide-bond water and adding terminal water. The Abs 0.1% value is calculated as:
where is molecular weight in daltons. A 0.1% protein solution is 1 mg/mL, or 1 g/L.
Paste one or more canonical protein sequences as FASTA:
>Protein1
MKWVTFISLLFLFSSAYSRGVFRRDAHKSEVAHRFKDLGE
>Protein2
GIVEQCCTSICSLYQLENYCNPlain one-letter protein sequence input is also accepted for a single sequence. Uploaded files can use .fasta, .fa, .fas, .txt, or .csv.
CSV input is supported when the header includes a recognizable sequence column such as sequence, seq, or protein:
id,sequence
p1,MKWVTFISLLFLFSSAYSRGVFRRDAHKSEVAHRFKDLGE
p2,GIVEQCCTSICSLYQLENYCNOnly the 20 canonical amino acid letters are accepted:
ARNDCQEGHILKMFPSTWYVWhitespace and line numbers are ignored. Punctuation, alignment gaps, stop codons, and noncanonical residue codes such as B, J, O, U, X, and Z are rejected instead of being silently removed.
| Setting | Default | What it does |
|---|---|---|
| Cysteine assumption | Reduced + oxidized | Returns both reduced and oxidized coefficients by default. |
| Disulfide bonds | 0 | Used only when Specified disulfide count is selected. Values above the possible number of cysteine pairs are clamped. |
| A280 | Empty | Optional measured absorbance at 280 nm. When provided, concentration columns are added. |
| Path length | 1 cm | Cuvette or plate path length used in the Beer-Lambert calculation. |
| Dilution factor | 1 | Multiplies the calculated concentration to account for sample dilution before measurement. |
| Concentration basis | Oxidized coefficient | Selects which coefficient is used for the primary concentration columns. |
If Specified disulfide coefficient is selected as the concentration basis without using Specified disulfide count as the cysteine assumption, the calculator falls back to the oxidized coefficient.
The standard result table includes one row per sequence:
| Column | Description |
|---|---|
| Protein ID | FASTA header, CSV ID, or generated sequence name. |
| Amino acids | Sequence length after whitespace and digit cleanup. |
| Molecular weight (Da) | Average molecular weight for the protein sequence. |
| Trp count, Tyr count, Cys count | Residue counts used by the 280 nm calculation. |
| Disulfides assumed | Number of disulfide bonds used for the selected cysteine assumption. |
| Ext. coeff. reduced | with all cysteine residues treated as reduced thiols. |
| Ext. coeff. oxidized | with all possible cysteine pairs treated as disulfide bonds. |
| Abs 0.1% reduced / oxidized | Predicted for 1 mg/mL protein using each coefficient. |
Optional columns are only shown when they have data:
| When | Additional columns |
|---|---|
| Specified disulfide count is selected | Specified-disulfide extinction coefficient and Abs 0.1%. |
| A positive A280 value is entered | Concentration in M, uM, and mg/mL for the selected basis. |
| A positive A280 value is entered | Reduced and oxidized concentration columns for comparison. |
| A positive A280 value is entered with specified disulfides | Specified-disulfide concentration columns. |
The concentration calculation is:
where is molar concentration, is measured absorbance, is the selected extinction coefficient, is path length in cm, and is dilution factor.
Warnings are shown above the result table when a result needs extra context:
| Warning | Meaning |
|---|---|
| No tryptophan residues | The estimate is less reliable because tyrosine and cystine absorb more weakly and are more environment-sensitive. |
| Odd cysteine count | The oxidized coefficient uses only complete disulfide pairs, so one cysteine remains unpaired. |
| Custom disulfide count was clamped | The requested count exceeded floor(Cys / 2), the maximum possible number of cysteine pairs. |
| CSV warnings | Some CSV rows or columns required cleanup or could not be interpreted as sequence records. |
The reduced and oxidized values are theoretical assumptions, not structural predictions. The calculator does not infer real disulfide bonding from a structure or sequence motif.
Sequence-based extinction coefficients work best for purified proteins whose 280 nm absorbance is dominated by Trp and Tyr. Results can differ from experimental values because of folding state, pH, buffer composition, detergents, reducing agents, cofactors, prosthetic groups, nucleic acid contamination, labels, post-translational modifications, aggregation, and light scattering.
For quantitative assays, blank the instrument with the matching buffer, measure within the detector's linear range, and use the same cysteine assumption that matches the sample state. For high-accuracy work, determine the extinction coefficient empirically under the assay conditions.
Calculate the aliphatic index of protein sequences. A measure of the relative volume occupied by aliphatic side chains, indicating thermostability.
Find potential N-linked glycosylation sites (NX[S/T] sequons) in protein sequences. Identifies asparagine residues in the consensus motif for N-glycosylation.
Calculate the GRAVY (Grand Average of Hydropathy) score of protein sequences. Positive values indicate hydrophobic proteins, negative values indicate hydrophilic proteins.
Calculate the instability index of protein sequences. Values above 40 indicate an unstable protein with a short half-life in vitro.
Calculate protein molecular weight (MW) from amino acid sequences in Daltons and kilodaltons. Supports FASTA and CSV sequence input, average or monoisotopic masses, initiator Met removal, and disulfide correction.
Calculate the theoretical isoelectric point (pI) of protein sequences. The pI is the pH at which a protein carries no net electrical charge.
Analyze amino acid composition of protein sequences. The tool accepts FASTA sequences and outputs the percentage of each amino acid in the sequence.
Scan protein sequences for biologically important motifs including glycosylation sites, phosphorylation sites, nuclear localization signals, prenylation motifs, and more.
Download InterPro protein family and domain records as JSON by InterPro ID.
Download QuickGO Gene Ontology term records as JSON by GO ID.
The molar extinction coefficient () describes how strongly a protein absorbs light at a given wavelength. At 280 nm, sequence-based protein estimates come mainly from tryptophan, tyrosine, and cystine, the disulfide-bonded form of cysteine.
This calculator uses the protein sequence to estimate , molecular weight, predicted for a 0.1% solution, and optional concentration from a measured absorbance value. It is intended for purified proteins without additional UV-absorbing cofactors, labels, nucleic acids, or other chromophores.
For a broader physicochemical profile, use Protein Parameters, which reports molecular weight, pI, amino acid composition, instability index, GRAVY, and related sequence properties.
The calculation follows the Pace et al. 1995 280 nm coefficients used by common protein-parameter tools:
| Term | Meaning | Contribution |
|---|---|---|
| Number of tryptophan residues (W) | 5,500 | |
| Number of tyrosine residues (Y) | 1,490 | |
| Number of cystine pairs, meaning disulfide bonds | 125 |
Free reduced cysteine contributes 0 at 280 nm. A disulfide-bonded cysteine pair contributes 125, so cystine is counted per disulfide bond rather than per cysteine residue.
Molecular weight is calculated from average residue masses, subtracting peptide-bond water and adding terminal water. The Abs 0.1% value is calculated as:
where is molecular weight in daltons. A 0.1% protein solution is 1 mg/mL, or 1 g/L.
Paste one or more canonical protein sequences as FASTA:
>Protein1
MKWVTFISLLFLFSSAYSRGVFRRDAHKSEVAHRFKDLGE
>Protein2
GIVEQCCTSICSLYQLENYCNPlain one-letter protein sequence input is also accepted for a single sequence. Uploaded files can use .fasta, .fa, .fas, .txt, or .csv.
CSV input is supported when the header includes a recognizable sequence column such as sequence, seq, or protein:
id,sequence
p1,MKWVTFISLLFLFSSAYSRGVFRRDAHKSEVAHRFKDLGE
p2,GIVEQCCTSICSLYQLENYCNOnly the 20 canonical amino acid letters are accepted:
ARNDCQEGHILKMFPSTWYVWhitespace and line numbers are ignored. Punctuation, alignment gaps, stop codons, and noncanonical residue codes such as B, J, O, U, X, and Z are rejected instead of being silently removed.
| Setting | Default | What it does |
|---|---|---|
| Cysteine assumption | Reduced + oxidized | Returns both reduced and oxidized coefficients by default. |
| Disulfide bonds | 0 | Used only when Specified disulfide count is selected. Values above the possible number of cysteine pairs are clamped. |
| A280 | Empty | Optional measured absorbance at 280 nm. When provided, concentration columns are added. |
| Path length | 1 cm | Cuvette or plate path length used in the Beer-Lambert calculation. |
| Dilution factor | 1 | Multiplies the calculated concentration to account for sample dilution before measurement. |
| Concentration basis | Oxidized coefficient | Selects which coefficient is used for the primary concentration columns. |
If Specified disulfide coefficient is selected as the concentration basis without using Specified disulfide count as the cysteine assumption, the calculator falls back to the oxidized coefficient.
The standard result table includes one row per sequence:
| Column | Description |
|---|---|
| Protein ID | FASTA header, CSV ID, or generated sequence name. |
| Amino acids | Sequence length after whitespace and digit cleanup. |
| Molecular weight (Da) | Average molecular weight for the protein sequence. |
| Trp count, Tyr count, Cys count | Residue counts used by the 280 nm calculation. |
| Disulfides assumed | Number of disulfide bonds used for the selected cysteine assumption. |
| Ext. coeff. reduced | with all cysteine residues treated as reduced thiols. |
| Ext. coeff. oxidized | with all possible cysteine pairs treated as disulfide bonds. |
| Abs 0.1% reduced / oxidized | Predicted for 1 mg/mL protein using each coefficient. |
Optional columns are only shown when they have data:
| When | Additional columns |
|---|---|
| Specified disulfide count is selected | Specified-disulfide extinction coefficient and Abs 0.1%. |
| A positive A280 value is entered | Concentration in M, uM, and mg/mL for the selected basis. |
| A positive A280 value is entered | Reduced and oxidized concentration columns for comparison. |
| A positive A280 value is entered with specified disulfides | Specified-disulfide concentration columns. |
The concentration calculation is:
where is molar concentration, is measured absorbance, is the selected extinction coefficient, is path length in cm, and is dilution factor.
Warnings are shown above the result table when a result needs extra context:
| Warning | Meaning |
|---|---|
| No tryptophan residues | The estimate is less reliable because tyrosine and cystine absorb more weakly and are more environment-sensitive. |
| Odd cysteine count | The oxidized coefficient uses only complete disulfide pairs, so one cysteine remains unpaired. |
| Custom disulfide count was clamped | The requested count exceeded floor(Cys / 2), the maximum possible number of cysteine pairs. |
| CSV warnings | Some CSV rows or columns required cleanup or could not be interpreted as sequence records. |
The reduced and oxidized values are theoretical assumptions, not structural predictions. The calculator does not infer real disulfide bonding from a structure or sequence motif.
Sequence-based extinction coefficients work best for purified proteins whose 280 nm absorbance is dominated by Trp and Tyr. Results can differ from experimental values because of folding state, pH, buffer composition, detergents, reducing agents, cofactors, prosthetic groups, nucleic acid contamination, labels, post-translational modifications, aggregation, and light scattering.
For quantitative assays, blank the instrument with the matching buffer, measure within the detector's linear range, and use the same cysteine assumption that matches the sample state. For high-accuracy work, determine the extinction coefficient empirically under the assay conditions.
Calculate the aliphatic index of protein sequences. A measure of the relative volume occupied by aliphatic side chains, indicating thermostability.
Find potential N-linked glycosylation sites (NX[S/T] sequons) in protein sequences. Identifies asparagine residues in the consensus motif for N-glycosylation.
Calculate the GRAVY (Grand Average of Hydropathy) score of protein sequences. Positive values indicate hydrophobic proteins, negative values indicate hydrophilic proteins.
Calculate the instability index of protein sequences. Values above 40 indicate an unstable protein with a short half-life in vitro.
Calculate protein molecular weight (MW) from amino acid sequences in Daltons and kilodaltons. Supports FASTA and CSV sequence input, average or monoisotopic masses, initiator Met removal, and disulfide correction.
Calculate the theoretical isoelectric point (pI) of protein sequences. The pI is the pH at which a protein carries no net electrical charge.
Analyze amino acid composition of protein sequences. The tool accepts FASTA sequences and outputs the percentage of each amino acid in the sequence.
Scan protein sequences for biologically important motifs including glycosylation sites, phosphorylation sites, nuclear localization signals, prenylation motifs, and more.
Download InterPro protein family and domain records as JSON by InterPro ID.
Download QuickGO Gene Ontology term records as JSON by GO ID.