Peptides (version 1.0.1)

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  ARQQNLFINFC -0.01 0.40      Globular
#  2  RQQNLFINFCL  0.03 0.40      Globular
#  3  QQNLFINFCLI  0.39 0.21      Globular
#  4  QNLFINFCLIL  0.56 0.29 Transmembrane
#  5  NLFINFCLILI  0.77 0.29       Surface
#  6  LFINFCLILIF  0.95 0.21       Surface
#  7  FINFCLILIFL  0.95 0.16 Transmembrane
#  8  INFCLILIFLL  0.93 0.15 Transmembrane
#  9  NFCLILIFLLL  0.90 0.15 Transmembrane
#  10 FCLILIFLLLI  1.10 0.16       Surface

membpos("ARQQNLFINFCLILIFLLLI",160)

#             Pep     H   uH       MembPos
#  1  ARQQNLFINFC -0.01 0.53      Globular
#  2  RQQNLFINFCL  0.03 0.44      Globular
#  3  QQNLFINFCLI  0.39 0.33      Globular
#  4  QNLFINFCLIL  0.56 0.33 Transmembrane
#  5  NLFINFCLILI  0.77 0.35       Surface
#  6  LFINFCLILIF  0.95 0.35       Surface
#  7  FINFCLILIFL  0.95 0.39       Surface
#  8  INFCLILIFLL  0.93 0.39       Surface
#  9  NFCLILIFLLL  0.90 0.18 Transmembrane
#  10 FCLILIFLLLI  1.10 0.18       Surface