aa123: Convert Between 1-letter and 3-letter Aminoacid Codes

In bio3d: Biological Structure Analysis

Convert Between 1-letter and 3-letter Aminoacid Codes

Description

Convert between one-letter IUPAC aminoacid codes and three-letter PDB style aminoacid codes.

Usage

aa123(aa)
aa321(aa)

Arguments

aa	a character vector of individual aminoacid codes.

Details

Standard conversions will map ‘A’ to ‘ALA’, ‘G’ to ‘GLY’, etc. Non-standard codes in aa will generate a warning and return ‘UNK’ or ‘X’.

Value

A character vector of aminoacid codes.

Author(s)

Barry Grant

References

Grant, B.J. et al. (2006) Bioinformatics 22, 2695–2696.

For a description of IUPAC one-letter codes see:
https://www.insdc.org/documents/feature_table.html#7.4.3

For more information on PDB residue codes see:
http://ligand-expo.rcsb.org/ld-search.html

See Also

read.pdb, read.fasta, pdbseq

Examples

# Simple conversion
aa123(c("D","L","A","G","S","H"))
aa321(c("ASP", "LEU", "ALA", "GLY", "SER", "HIS"))

## Not run: 
# Extract sequence from a PDB file's ATOM and SEQRES cards
pdb <- read.pdb("1BG2") 
s <- aa321(pdb$seqres)                   # SEQRES
a <- aa321(pdb$atom[pdb$calpha,"resid"]) # ATOM

# Write both sequences to a fasta file
write.fasta(alignment=seqbind(s,a), id=c("seqres","atom"), file="eg2.fa")

# Alternative approach for ATOM sequence extraction
pdbseq(pdb)
pdbseq(pdb, aa1=FALSE )

## End(Not run)

bio3d documentation built on Oct. 30, 2024, 1:08 a.m.