Aliphatic Index

How to calculate a protein's aliphatic index

Paste a protein sequence, or several FASTA records, and ProteinIQ calculates one aliphatic index for each sequence. The result measures the sequence share of alanine, valine, isoleucine, and leucine, weighted by side-chain volume. Use it to compare proteins or variants on the same sequence-level scale, then download or copy the results table.

For example, these are the mature human insulin chains:

>insulin-B human insulin B chain
FVNQHLCGSHLVEALYLVCGERGFFYTPKT
>insulin-A human insulin A chain
GIVEQCCTSICSLYQLENYCN

The calculation returns:

The value includes every residue in the sequence length. For example, a residue that is not A, V, I, or L contributes zero to the numerator, but still contributes to the denominator.

Input

Sequence lines are joined, whitespace is ignored, and lowercase amino acid codes are converted to uppercase. At processing time, a sequence containing a non-standard residue is rejected. For FASTA input, use a concise first header field when the identifier matters: >insulin-B human insulin B chain appears as insulin-B in the results table.

The per-job sequence limit follows the account tier: 1 for guests, 5 for Free, 1,000 for Lite, 10,000 for Plus, and 100,000 for Pro. Higher tiers have no configured item cap.

Settings

This calculator has no user-configurable settings. It always uses the Ikai coefficients of 2.9 for valine and 3.9 for isoleucine plus leucine.

Results

The table is copyable and downloadable. Each submitted FASTA record produces one row, in the same order as the input.

What is the aliphatic index?

The aliphatic index estimates the relative volume occupied by the aliphatic side chains in a protein. It was introduced by Ikai as a sequence-derived property for comparing globular proteins, and is often used as one indicator when investigating thermal stability.

The calculation is:

Here, each $X$ is the mole percentage of that residue in the complete sequence. The weights mean that a given percentage of valine contributes 2.9 times as much as alanine, while isoleucine and leucine each contribute 3.9 times as much. A sequence made entirely of valine therefore has an index of 290, whereas one made entirely of isoleucine or leucine has an index of 390.

How should I interpret an aliphatic index?

Use the result as a comparative property, not a temperature prediction. A higher value means the sequence is more enriched in the four weighted aliphatic residues. That can be informative when comparing matched homologs, constructs, or single-site variants, especially when sequence length and protein class are similar.

It does not account for tertiary structure, oligomerization, disulfide bonds, cofactors, solvent conditions, pH, or post-translational modifications. A high index alone does not establish that a protein will express well, remain soluble, or tolerate a particular temperature. For a mutation series, compare the index with measured stability and other sequence properties rather than treating a cutoff as a pass or fail rule.

Which protein property tool should I use?

FAQ

What amino acids are used in the aliphatic index?

Alanine, valine, isoleucine, and leucine. Their mole percentages are weighted as 1.0, 2.9, 3.9, and 3.9, respectively; all other residues affect the sequence length but add no weighted contribution.

Is a higher aliphatic index always better?

No. It only indicates greater representation of the weighted aliphatic residues. Whether that is desirable depends on the protein, target conditions, and trade-offs with folding, solubility, activity, and expression.

Can I calculate the aliphatic index for multiple proteins at once?

Yes. Paste multiple FASTA records or upload a supported file. ProteinIQ preserves their input order and reports one result row per valid submitted sequence.

Why does my FASTA header look different in the output?

The results table uses the first token in the header, stopping at whitespace or |. Name a record >variant-7 description when variant-7 is the identifier you want to compare and export.