The Aliphatic Index is a measure of the relative volume occupied by aliphatic amino acid side chains (alanine, valine, isoleucine, and leucine) in a protein sequence. It serves as a positive factor for predicting the thermostability of globular proteins.
Introduced by Atsushi Ikai in his 1980 paper in The Journal of Biochemistry, this index emerged from statistical analysis showing that proteins from thermophilic bacteria have significantly higher aliphatic indices than ordinary proteins. The aliphatic index has since become a standard protein parameter for assessing thermal stability.
The aliphatic index is calculated by summing the mole percentages of aliphatic amino acids, weighted by their relative side chain volumes:
Where , , , and are the mole percentages (100 × mole fraction) of alanine, valine, isoleucine, and leucine respectively.
The coefficients represent the relative volume of each aliphatic side chain compared to alanine:
| Amino Acid | Coefficient | Rationale |
|---|---|---|
| Alanine (A) | 1.0 | Reference side chain (implicit) |
| Valine (V) | 2.9 | Side chain ~2.9× the volume of alanine |
| Isoleucine (I) | 3.9 | Side chain ~3.9× the volume of alanine |
| Leucine (L) | 3.9 | Side chain ~3.9× the volume of alanine |
These coefficients were derived from the relative volumes of aliphatic side chains as determined by Ikai's analysis of globular protein structures.
Higher aliphatic index values indicate greater thermostability potential. Typical ranges vary by protein type:
Proteins from thermophilic bacteria and archaea consistently show elevated aliphatic indices compared to their mesophilic counterparts. This correlation makes the aliphatic index useful for identifying thermostable variants during protein engineering.
Calculate the molar extinction coefficient of protein sequences at 280 nm. Used for protein concentration determination by UV spectroscopy.
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 Aliphatic Index is a measure of the relative volume occupied by aliphatic amino acid side chains (alanine, valine, isoleucine, and leucine) in a protein sequence. It serves as a positive factor for predicting the thermostability of globular proteins.
Introduced by Atsushi Ikai in his 1980 paper in The Journal of Biochemistry, this index emerged from statistical analysis showing that proteins from thermophilic bacteria have significantly higher aliphatic indices than ordinary proteins. The aliphatic index has since become a standard protein parameter for assessing thermal stability.
The aliphatic index is calculated by summing the mole percentages of aliphatic amino acids, weighted by their relative side chain volumes:
Where , , , and are the mole percentages (100 × mole fraction) of alanine, valine, isoleucine, and leucine respectively.
The coefficients represent the relative volume of each aliphatic side chain compared to alanine:
| Amino Acid | Coefficient | Rationale |
|---|---|---|
| Alanine (A) | 1.0 | Reference side chain (implicit) |
| Valine (V) | 2.9 | Side chain ~2.9× the volume of alanine |
| Isoleucine (I) | 3.9 | Side chain ~3.9× the volume of alanine |
| Leucine (L) | 3.9 | Side chain ~3.9× the volume of alanine |
These coefficients were derived from the relative volumes of aliphatic side chains as determined by Ikai's analysis of globular protein structures.
Higher aliphatic index values indicate greater thermostability potential. Typical ranges vary by protein type:
Proteins from thermophilic bacteria and archaea consistently show elevated aliphatic indices compared to their mesophilic counterparts. This correlation makes the aliphatic index useful for identifying thermostable variants during protein engineering.
Calculate the molar extinction coefficient of protein sequences at 280 nm. Used for protein concentration determination by UV spectroscopy.
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.
