Peptides (version 0.4)

hmoment: To compute the hydrophobic moment of a protein sequence

Description

Hydriphobic moment is a quantitative measure of the amphiphilicity perpendicular to the axis of any periodic peptide structure, such as the a-helix or b-sheet. It can be calculated for an amino acid sequence of N residues and their associated hydrophobicities Hn. If the secuence length is < 11 AA, the window length is equal to the AA sequence length, if it is > 11, windows of 11 residues are evaluated

Usage

hmoment(seq,structure)

Arguments

seq

AA sequence string in upper case

structure

Three dimentional structure of protein. If it is alpha-helix type "a" or if it is beta-sheet type "b"

Value

• The max hydrophobic moment (uH) as a numerical vector of length one

References

Eisenberg, David. "Three-dimensional structure of membrane and surface proteins." Annual review of biochemistry 53.1 (1984): 595-623.

Examples

# Hydrophobic moment of PDB: 1MP6 M2 protein 

hmoment("SSDPLVVAASIIGILHLILWILDRL","a") 

## Output
# [1] 0.51