Protein Extinction 280

Estimate 280-nm molar extinction coefficient from Trp, Tyr, and cystine.

Description

A 280-nm extinction estimate adds tryptophan, tyrosine and disulfide contributions.

A 280-nm extinction estimate adds tryptophan, tyrosine and disulfide contributions. Disulfide count must be supplied because sequence alone does not identify actual cystine pairing.^{[1, 2]}

Estimate 280-nm molar extinction coefficient from Trp, Tyr, and cystine.

When to use Protein Extinction 280

Use this tool to estimate 280-nm molar extinction coefficient from Trp, Tyr, and cystine.

Prepare the canonical sequence, peptide assignments, fitted assay parameters or upstream measurements requested. Keep corresponding entries aligned, use the stated mass and signal units, and remove FASTA headers before entering sequence text.

How to use Protein Extinction 280 and understand its results

Prepare the canonical sequence, peptide assignments, fitted assay parameters or upstream measurements requested. Keep corresponding entries aligned, use the stated mass and signal units, and remove FASTA headers before entering sequence text.
Enter sequence, disulfideBondCount using the field table and calculation rules, then run the tool.
Read extinctionCoefficient, trpCount, tyrCount. The explanation below defines the units, signs, ordering and any flags or placeholder values.
If the tool reports an input issue, correct the values and run it again. Apply the stated assumptions when interpreting a successfully returned result.

Input field	Meaning	Value type; see rules below	Requirement
sequence	Sequence	string	Required
disulfideBondCount	Disulfide bond count	number	Required

Enter a canonical sequence and nonnegative safe-integer disulfide count no greater than floor(Ccount/2). Return the molar extinction estimate in M−1 cm−1 plus W and Y counts.

The shared sequence helper trims outer whitespace and uppercases the sequence. It requires at least one residue from ACDEFGHIKLMNPQRSTVWY. Internal whitespace, FASTA headers, ambiguous letters and modified-residue notation are rejected. Sequence indexes refer to the normalized sequence; individual tools may preserve original strings in their returned lists as explained above.

epsilon280=5500×Wcount+1490×Ycount+125×disulfideCount

Units, indexing, boundary conditions and exceptional cases are defined in the calculation rules above.

Output field	Meaning	Value type
extinctionCoefficient	Extinction coefficient	number
trpCount	Trp count	number
tyrCount	Tyr count	number

json

{
  "input": {
    "sequence": "WYCC",
    "disulfideBondCount": 1
  },
  "output": {
    "extinctionCoefficient": 7115,
    "trpCount": 1,
    "tyrCount": 1
  }
}

Limitations and assumptions

This is a sequence-composition estimate. Other chromophores, measurement conditions and actual disulfide formation are not assessed; the output is not absorbance or protein concentration.

Numeric inputs must be finite. Follow the calculation-specific rules for overflow, underflow and exceptional cases. Extremely large text inputs are rejected. Missing required fields, extra fields, wrong value types and violations of the calculation rules are input errors.

Alternative or Complementary methods

Use Disulfide Bond Capacity: Compute the maximum number of intrachain disulfides from cysteine count. For a complementary task, use Protein Dilution Backcalculation: Back-calculate original protein concentration after dilution.

Further background: ProtParam documentation: extinction coefficient.

References

Protein Extinction 280 — tool.io
ProtParam documentation: extinction coefficient — SIB Swiss Institute of Bioinformatics

Similar or alternative tools

Disulfide Bond Capacity
Compute the maximum number of intrachain disulfides from cysteine count.
Protein Dilution Backcalculation
Back-calculate original protein concentration after dilution.