aIndex: Compute the aliphatic index of a protein sequence

In Peptides: Calculate Indices and Theoretical Physicochemical Properties of Protein Sequences

Compute the aliphatic index of a protein sequence

Description

This function calculates the Ikai (1980) aliphatic index of a protein. The aindex is defined as the relative volume occupied by aliphatic side chains (Alanine, Valine, Isoleucine, and Leucine). It may be regarded as a positive factor for the increase of thermostability of globular proteins.

Usage

aIndex(seq)

Arguments

seq	An amino-acids sequence

Details

Aliphatic amino acids (A, I, L and V) are responsible for the thermal stability of proteins. The aliphatic index was proposed by Ikai (1980) and evaluates the thermostability of proteins based on the percentage of each of the aliphatic amino acids that build up proteins.

Value

The computed aliphatic index for a given amino-acids sequence

References

Ikai (1980). Thermostability and aliphatic index of globular proteins. Journal of Biochemistry, 88(6), 1895-1898.

Examples

# COMPARED TO ExPASy ALIPHATIC INDEX
# http://web.expasy.org/protparam/
# SEQUENCE: SDKEVDEVDAALSDLEITLE
# Aliphatic index: 117.00

aIndex(seq = "SDKEVDEVDAALSDLEITLE")
# [1] 117

Peptides documentation built on May 29, 2024, 11:02 a.m.