2Can Support Portal - About Amino Acid and Nucleotide Codes

Protein Sequences

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

More about amino acids.

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, Thr.
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	.