Peptides (version 1.1.2)

membpos: Compute theoretically the class of a protein sequence

Description

This function calculates the theoretical class of a protein sequence based on the relationship between the hydrophobic moment and hydrophobicity scale proposed by Eisenberg (1984).

Usage

membpos(seq,angle)

Arguments

seq

amino acid sequence string

angle

Protein rotational angle

References

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

Examples

membpos("ARQQNLFINFCLILIFLLLI",100)

#             Pep     H   uH       MembPos
# 1 ARQQNLFINFCL 0.083 0.353      Globular
# 2 RQQNLFINFCLI 0.147 0.317      Globular
# 3 QQNLFINFCLIL 0.446 0.274      Globular
# 4 QNLFINFCLILI 0.632 0.274 Transmembrane
# 5 NLFINFCLILIF 0.802 0.253       Surface
# 6 LFINFCLILIFL 0.955 0.113 Transmembrane
# 7 FINFCLILIFLL 0.955 0.113 Transmembrane
# 8 INFCLILIFLLL 0.944 0.108 Transmembrane
# 9 NFCLILIFLLLI 0.944 0.132 Transmembrane

membpos("ARQQNLFINFCLILIFLLLI",160)

#             Pep     H   uH       MembPos
# 1 ARQQNLFINFCL 0.083 0.467  Globular
# 2 RQQNLFINFCLI 0.147 0.467  Globular
# 3 QQNLFINFCLIL 0.446 0.285  Globular
# 4 QNLFINFCLILI 0.632 0.358  Surface
# 5 NLFINFCLILIF 0.802 0.358  Surface
# 6 LFINFCLILIFL 0.955 0.269  Surface
# 7 FINFCLILIFLL 0.955 0.269  Surface
# 8 INFCLILIFLLL 0.944 0.257  Surface
# 9 NFCLILIFLLLI 0.944 0.229  Surface