Compute theoretically the class of a protein sequence

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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

1
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

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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