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New 1 letter code for amino acids

New 1 letter code for amino acids - Molecular Biology Articles and Protocols

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Old 08-01-2009, 10:21 AM
Pipette Filler
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Post New 1 letter code for amino acids



New easy-to-memorize 1-letter code for amino acids
by Dr. rer. nat. Peter Erich Keller
Member of the International Union of Crystallography
Member of the European Peptide Society


A new easy-to-memorize 1-letter code for amino acids is proposed. To obtain good readability, additionally Greek letters, the Swedish letter , the Latin combined letter and the @ symbol from the internet are used. This new 1-letter code shows considerable advantages over the old one and might be chosen as new standard coding.

Amino acid 3-letter 1-letter new 1-letter
code [1] code [1] code

Alanine Ala a @ alanine
Arginine Arg r arginine
Asparagine Asn n asparagine
Aspartic acid Asp d a aspartic acid
Cysteine Cys c c cysteine
Glutamic acid Glu e g glutamic acid
Glutamine Gln q q glutamine
Glycine Gly g γ glycine
Histidine His h h histidine
Isoleucine Ile i i isoleucine
Leucine Leu l l leucine
Lysine Lys k λ lysine
Methionine Met m m methionine
Phenylalanine Phe f φ phenylalanine
Proline Pro p p proline
Serine Ser s s serine
Threonine Thr t θ threonine
Tryptophan Trp w τ tryptophan
Tyrosine Tyr y t tyrosine
Valine Val v v valine

Unknown x ξ unknown


An example taken from the NCBI [2] peptide sequence database is given. The proinsulin precursor (Homo sapiens) peptide sequence is translated in the new easy-to-memorize 1-letter code. The readability is greatly enhanced in comparison to the old 1-letter code. Even a secondary structural element, an α-helical region, can be estimated from the new 1-letter code, see amino acids #21 to #25, by usage of the at symbol for the good α-helix builder alanine [3]. For coding phenylalanine, the chemical abbreviation for the phenyl group φ is used. Threonine is coded by the Greek letter θ (.theta.) with first and second letter in coincidence with its name. All amino acids with the first letter A in their names are coded by an a containing 1-letter code: @, , , a.

Example:
NCBI Reference Sequence: NP_000198.1
proinsulin precursor [Homo sapiens]
1 malwmrllpl m@lτmllpl
11 lallalwgpd l@ll@lτγpa
21 paaafvnqhl p@@@φvqhl
31 cgshlvealy cγshlvg@lt
41 lvcgergffy lvcγgγφφt
51 tpktrreaed θpλθg@ga
61 lqvgqvelgg lqvγqvglγγ
71 gpgagslqpl γpγ@γslqpl
81 alegslqkrg @lgγslqλγ
91 iveqcctsic ivgqccθsic
101 slyqlenycn sltqlgtc


References
[1] Cooper, G. M.; Hausman, R. E. (2004). The cell: a molecular approach (3rd ed.). Sinauer. p. 51.
[2] National Center for Biotechnology Information, National Library of Medicine, Bethesda MD, U.S.A.
[3] Quellre, P. (Keller, P.) 2007, Why is alanine such a good α-helix builder, virtual poster presented at the European Crystallographic Meeting ECM24, Morocco, Marrakes
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