Protein Aliphatic Index
Calculate protein aliphatic index from Ala, Val, Ile, and Leu fractions.
Description
The aliphatic index combines alanine, valine, isoleucine and leucine proportions with fixed weights.
The aliphatic index combines alanine, valine, isoleucine and leucine proportions with fixed weights. The result is a composition index rather than a bounded percentage.1
Calculate protein aliphatic index from Ala, Val, Ile, and Leu fractions.
When to use Protein Aliphatic Index
Use this tool to calculate protein aliphatic index from Ala, Val, Ile, and Leu fractions.
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 Aliphatic Index 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 using the field table and calculation rules, then run the tool.
- Read aliphaticIndex, alanineFraction, valineFraction, ileLeuFraction. 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 |
Enter a canonical sequence. Return the weighted index and the three contributing fractions in 0–1.
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.
index=100(Afraction+2.9 Vfraction+3.9 (I+L)fraction) Units, indexing, boundary conditions and exceptional cases are defined in the calculation rules above.
| Output field | Meaning | Value type |
|---|---|---|
| aliphaticIndex | Aliphatic index | number |
| alanineFraction | Alanine fraction | number |
| valineFraction | Valine fraction | number |
| ileLeuFraction | Ile leu fraction | number |
{
"input": {
"sequence": "AVL"
},
"output": {
"aliphaticIndex": 259.99999999999994,
"alanineFraction": 0.3333333333333333,
"valineFraction": 0.3333333333333333,
"ileLeuFraction": 0.3333333333333333
}
}Limitations and assumptions
The index can exceed 100. It does not measure thermal stability, folding or solvent exposure.
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 Protein GRAVY: Compute grand average of Kyte–Doolittle hydropathy. For a complementary task, use Amino Acid Composition: Tabulate amino-acid counts and composition percentages.
References
-
Protein Aliphatic Index — tool.io
Similar or alternative tools
- Protein GRAVY
Compute grand average of Kyte–Doolittle hydropathy.
- Amino Acid Composition
Tabulate amino-acid counts and composition percentages.