Peptides (version 1.0.1)

hmoment: Compute the hydrophobic moment of a protein sequence

Description

This function compute the hmoment based on Eisenberg, D., Weiss, R. M., & Terwilliger, T. C. (1984). 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,angle)

Arguments

seq

amino acid sequence as string

angle

Protein rotational angle

Value

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

References

Eisenberg, D., Weiss, R. M., & Terwilliger, T. C. (1984). The hydrophobic moment detects periodicity in protein hydrophobicity. Proceedings of the National Academy of Sciences, 81(1), 140-144.

Examples

# COMPARED TO EMBOSS:HMOMENT
# http://emboss.bioinformatics.nl/cgi-bin/emboss/hmoment
# SEQUENCE: FLPVLAGLTPSIVPKLVCLLTKKC
# ALPHA-HELIX ANGLE=100 : 0.56
# BETA-SHEET  ANGLE=160 : 0.25
  
# ALPHA HELIX VALUE
hmoment("FLPVLAGLTPSIVPKLVCLLTKKC",100)
# [1] 0.56
  
# BETA SHEET VALUE
hmoment("FLPVLAGLTPSIVPKLVCLLTKKC",160)
# [1] 0.25