Help - About Amino Acid and Nucleotide Codes
- Protein Sequences
- Amino Acid Properties and Substitutions
- Nucleotide Sequences
- Nucleotide codes assigned by IUB
The one-letter and three-letter abbreviation codes for amino acids for example, used in UniProtKB/Swiss-Prot are those adopted by the commission on Biochemical Nomenclature of the IUPAC-IUB and are as follows:
-
One-letter code Three-letter code Amino-acid name A Ala Alanine R Arg Arginine N Asn Asparagine D Asp Aspartic acid C Cys Cysteine Q Gln Glutamine E Glu Glutamic acid G Gly Glycine H His Histidine J Xle Leucine or Isoleucine L Leu Leucine I ILe Isoleucine K Lys Lysine M Met Methionine F Phe Phenylalanine P Pro Proline O Pyl Pyrrolysine U Sec Selenocysteine S Ser Serine T Thr Threonine W Trp Tryptophan Y Tyr Tyrosine V Val Valine B Asx Aspartic acid or Asparagine Z Glx Glutamic acid or Glutamine X Xaa Any amino acid
Amino Acid Properties and Substitutions
A substitution is more likely to occur between amino acids with similar biochemical properties. For example the hydrophobic amino acids Isoleucine(I) and valine(V) are more likely to substitute for one another than the hydrophilic amino acid cystine would with one of these. Amino acids come in the following types.
-
Type of Amino Acid Properties Amino Acids Amino acids with aliphatic hydrophobic side chains
The hydrophobic side chains of these amino acids will not form hydrogen bonds or ionic bonds with other groups. These hydrophobic amino acids tend to be buried in the centre of proteins away from the surrounding aqueous environment.
Ala, Val, Leu, lle, Met, Pro, Phe, Trp. Amino acids with uncharged but polar side chains
The side chains of these amino acids are uncharged at physiological pH.
Ser, Tyr, Asn, Gln, Cys. Amino acids with acidic side chains
These have a carboxylic acid group in their side chain and are very hydrophilic.
Asp, Glu. Amino acids with basic side chains
The positive charge on these side chains makes them hydrophilic and they are likely to be found at the protein surface
Lys, Arg, His. Neutral side chain The single hydrogen atom side chain has no strong hydrophobic or hydrophilic properties. Gly
Nucleotide Sequences
Nucleotide bases fall into two categories depending on the ring structure of the base. Purines (Adenine and Guanine) are two ring bases, pyrimidines (Cytosine and Thymine) are single ring bases. Mutations in DNA are changes in which one base is replaced by another. A mutation that conserves the ring number is called a transition (e.g., A -> G or C -> T) a mutation that changes the ring number are called transversions. (e.g. A -> C or A -> T and so on).
-
One-letter code Name Location A Adenine DNA/RNA G Guanine
DNA/RNA C Cytosine
DNA/RNA T Thymine
DNA U Uracil RNA
Nucleotide codes assigned by IUB
-
IUB Meaning Complement A A T C C G G G C T/U T A M A/C K R A/G Y W A/T W S C/G S Y C/T R K G/T M V A/C/G B H A/C/T D D A/G/T H B C/G/T V X/N A/C/G/T X . None .