Peptides (version 1.1.2)

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. An 11 residues window is used as default.

Usage

hmoment(seq,angle,window)

Arguments

seq

Amino acid sequence as string

angle

Protein rotational angle

window

Sequence fraction length

Value

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

Source

This function was written by an anonymous referee of the RJournal

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 : 0.52
# BETA-SHEET  ANGLE=160 : 0.271
  
# ALPHA HELIX VALUE
hmoment(seq = "FLPVLAGLTPSIVPKLVCLLTKKC", angle = 100, window = 11)
# [1] 0.5199226
  
# BETA SHEET VALUE
hmoment(seq = "FLPVLAGLTPSIVPKLVCLLTKKC", angle = 160, window = 11)
# [1] 0.2705906