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For a general introduction to ''amino acids'', please see [http://en.wikipedia.org/wiki/Amino_acids Amino Acids in Wikipedia].
For a general introduction to ''amino acids'', please see [http://en.wikipedia.org/wiki/Amino_acids Amino Acids in Wikipedia].


Here are the names of the twenty standard amino acids, with their three and one-letter abbreviations. Mnemonic names may help you to remember the one-letter codes, but are not the correct names.
==22 Standard Amino Acids and Mnemonics==


Here are the names of the twenty-two standard amino acids, with their three and one-letter<ref>A one-letter notation for amino acid sequences (definitive rules). IUPAC—IUB Commission on Biochemical Nomenclature, pages 639-645, International Union of Pure and Applied Chemistry and International Union of Biochemistry, Butterworths, London, 1971. [https://old.iupac.org/publications/pac/1972/pdf/3104x0639.pdf Full Text].</ref> abbreviations. Mnemonic names are intended to help you to remember the one-letter codes, but are not the correct names.
<center>
<table border=1 cellpadding=5>
<table border=1 cellpadding=5>
<tr>
<tr>
<td><tt>
<td><tt><big>
Ala A <b>A</b>lanine
Ala A <b>A</b>lanine
<br>
<br>
Line 16: Line 19:
Cys C <b>C</b>ysteine
Cys C <b>C</b>ysteine


</tt></td><td><tt>
</big></tt></td><td><tt><big>
Lys K Lysine<br>&nbsp;&nbsp;(mnemonic:&nbsp;li<b>K</b>esine)
<br>
Met M <b>M</b>ethionine
<br>
Phe F Phenylalanine<br>&nbsp;&nbsp;(mnemonic:&nbsp;<b>F</b>enylalanine)
<br>
Pro P <b>P</b>roline
<br>
Pyl O Pyrr<b>o</b>lysine*
 
</big></tt></td><td rowspan="2"><tt><big>
&nbsp;
&nbsp;
&nbsp;
mnemonic:
<br>A Ala
<br>B Asx&dagger;
<br>C Cys
<br>D Asp aspar<b>D</b>ic
<br>E Glu glu<b>E</b>tamine
<br>F Phe <b>F</b>enylalanine
<br>G Gly
<br>H His
<br>I Ile
<br><font color="#808080">J</font>
<br>K Lys li<b>K</b>esine
<br>L Leu
<br>M Met
 
</big></tt></td><td rowspan="2"><tt><big>
 
&nbsp;
&nbsp;
&nbsp;
mnemonic:
<br>N Asn asparagi<b>N</b>e
<br>O Pyl*
<br>P Pro
<br>Q Gln <b>Q</b>uetamine
<br>R Arg a<b>R</b>ginine
<br>S Ser
<br>T Thr
<br>U Sec*
<br>V Val
<br>W Trp t<b>W</b>ptophan
<br>X Unk&dagger;
<br>Y Tyr t<b>Y</b>rosine
<br>Z Glx&dagger;
 
</big></tt></td></tr><tr><td><tt><big>
Gln Q Glutamine<br>&nbsp;&nbsp;(mnemonic:&nbsp;<b>Q</b>uetamine)
Gln Q Glutamine<br>&nbsp;&nbsp;(mnemonic:&nbsp;<b>Q</b>uetamine)
<br>
<br>
Line 26: Line 79:
<br>
<br>
Ile I <b>I</b>soleucine
Ile I <b>I</b>soleucine
</tt></td><td><tt>
<br>
Leu L <b>L</b>eucine
Leu L <b>L</b>eucine
<br>


Lys K Lysine<br>&nbsp;&nbsp;(mnemonic:&nbsp;li<b>K</b>esine)
</big></tt></td><td><tt><big>
<br>
Sec U Selenocysteine*<br>&nbsp;&nbsp;(mnemonic:&nbsp;seleni<b>U</b>m)
Met M <b>M</b>ethionine
<br>
<br>
Phe F Phenylalanine<br>&nbsp;&nbsp;(mnemonic:&nbsp;<b>F</b>enylalanine)
<br>
Pro P <b>P</b>roline
</tt></td><td><tt>
Ser S <b>S</b>erine
Ser S <b>S</b>erine
<br>
<br>
Line 48: Line 94:
<br>
<br>
Val V <b>V</b>aline
Val V <b>V</b>aline
</tt></td>
</big></tt></td>
</tr>
</tr>
<tr><td colspan="4"><center>
<nowiki>*</nowiki>Since the mid-20th century, there were 20 standard amino acids. Early in the 21st Century,
genetically encoded
[[#Unusual_Amino_Acids|Selenocysteine and Pyrrolysine]] have been included as standard by the World Wide Protein Data Bank<ref name="pdb22" />.
<br>
&dagger; Asx: Asn or Asp; Glx: Gln or Glu; Unk: unknown.
<br>
[http://old.iupac.org/publications/pac/1972/pdf/3104x0639.pdf IUPAC/IUB 1971 publication] defining one-letter codes.
</center></td></tr>
</table>
</table>
Click on the image below to see it full size with details on 21 amino acids.
{| align="center"
|-
|
<imagemap>
Image:1000px-Amino Acids.svg.png|200 px|
default [http://proteopedia.org/wiki/images/1/13/1000px-Amino_Acids.svg.png]
</imagemap>
|}
</center>
There is also a [http://pdb101.rcsb.org/learn/guide-to-understanding-pdb-data/primary-sequences-and-the-pdb-format list of standard amino acids] at the Protein Data Bank.
{{Clear}}
==L- and D-Amino Acids==
<table border='1' cellpadding='3' align='right' hspace="8" class="wikitable" style="margin:0px 0px 0px 8px;"><tr><td colspan='2'>
PDB Nomenclature
</td></tr><tr><td>
L-form
</td><td>
D-form
</td></tr><tr><td>
ALA<br>ARG<br>ASN<br>ASP<br>CYS<br>GLN<br>GLU<br>HIS<br>ILE<br>LEU<br>LYS<br>MET<br>
PHE<br>PRO<br>PYL<br>SEC<br>SER<br>THR<br>TRP<br>TYR<br>VAL
</td><td>
DAL<br>DAR<br>DSG<br>DAS<br>DCY<br>DGN<br>DGL<br>DHI<br>DIL<br>DLE<br>DLY<br>MED<br>
DPN<br>DPR<br>?<ref name="ddd">In January, 2022, no D-selenocysteine nor D-pyrrolysine were present in the [[wwPDB]], according to David Armstrong of PDBe.</ref><br>?<ref name="ddd" /><br>DSN<br>DTH<br>DTR<br>DTY<br>DVA
</td></tr></table>
The asymmetric &alpha;-carbon in 21 of the standard amino acids (all except glycine) is a chiral (stereogenic) center<ref name='chirality' />. Thus, each amino acid can exist in either of two optical isomers or enantiomers (mirror images), designated the L-form and D-form. Nearly all naturally-occuring amino acids are L-amino acids, so named because they are analogous to the L-form of glyceraldehyde<ref name='chirality'>See [http://en.wikipedia.org/wiki/Chirality_(chemistry) Chirality in Wikipedia]].</ref>. (Not all L-amino acids are levorotatory; some rotate polarized light clockwise<ref name='chirality' />).
More than 700 entries in the [[PDB]] contain one or more D amino acids. Although D-amino acids are rare in nature, they do occur (see [http://en.wikipedia.org/wiki/Chirality_(chemistry)#D-Amino_Acid_Natural_Abundance natural abundance in Wikipedia]). D-alanine (DAL) occurs in over 100 entries in the [[PDB]], D-leucine (DLE), D-phenylalanine (DPN), D-serine (DSN), and D-valine (DVA) each occur in over 50. Some of these entries are chemically synthesized, not naturally occuring. Gramicidin is a naturally occuring antibiotic containing several D-amino acids, e.g. [[1nrm]]. [[4glu]] is the 102 amino acid chain of VEGF-A synthesized entirely from D-amino acids.
==Unusual Amino Acids==
There are at least two historically &quot;non-standard&quot; amino acids now recognized to be [http://en.wikipedia.org/wiki/Genetic_code genetically encoded], discussed below. In 2014, the [[PDB]] began including these two to make 22 standard amino acids<ref name="pdb22">[https://www.wwpdb.org/news/news?year=2014#5764490799cccf749a90cddf Announcement: Standardization of Amino Acid Nomenclature], World Wide Protein Data Bank News, January 8, 2014.</ref>.
===Selenocysteine: the 21st amino acid===
Rare proteins in all domains of life include '''[[Selenocysteine|selenocysteine (Sec, U)]]''', designated the 21st amino acid<ref name='21st'>PMID: 11028985</ref>. In 2024, over 90 entries in the [[PDB]] include selenocysteine, identified as SEC.
===Pyrrolysine: the 22nd amino acid===
'''[[Pyrrolysine|pyrrolysine (Pyl, O)]]'''<ref>See [http://en.wikipedia.org/wiki/Pyrrolysine Pyrrolysine in Wikipedia].</ref> is a genetically encoded amino acid that occurs naturally in methanogenic archaea, now designated the 22nd amino acid<ref>PMID: 15380192</ref>. It occurs in [http://www.rcsb.org/pdb/ligand/ligandsummary.do?hetId=PYL several entries] in the PDB.
See [[Pyrrolysine|more details]].
<!--
Editor's note: Contributions here by [[User:Andrea Gorrell]] were moved to the page on [[Pyrrolysine]].
-->
===No 23rd amino acid?===
The 21st and 22nd amino acids are specified by the [http://en.wikipedia.org/wiki/Genetic_code stop codons UGA and UAG] respectively, modified with downstream stem-loop structures in the mRNA.
Lobanov ''et al.''<ref name='23rd'>PMID: 16713651</ref> searched "16 archaeal and 130 bacterial genomes for tRNAs with anticodons corresponding to the three stop signals". Their data suggest that "the occurrence of additional amino acids that are widely distributed and genetically encoded is unlikely."
===Selenomethionine===
Please see [[Selenomethionine]].
===Postranslational modifications===
Many unusual amino acids are formed by enzyme-catalyzed reactions that modify a genetically encoded standard amino acid after it has been included in a polypeptide; these are called post-translational modifications. Among them:
* phosphorylation of serine, threonine, or tyrosine
** Example: C kinase [[1bkx]]
* hydroxylation of proline (to yield hydroxyproline, e.g. in [[collagen]])
* acetylation of lysine or the N terminus
** Example of N-terminal acetylation: [[4mdh]]
* methylation of lysine
* carboxylation of aspartate or glutamate
* nitrosylation, e.g. to produce [[nitrotyrosine]]
* acylation with a fatty acid (see N-terminal myristoylation of [[Recoverin]])
* prenylation
* glycosylation of serine, threonine or asparagine (yielding glycoproteins)
** Example of N-linked glycolylation: [[1igy]]
==Structure, Properties, Behaviors in Proteins==
Angel Herráez has provided a [http://biomodel.uah.es/en/model1/prot/aa-intro.htm tutorial introduction to amino acid structure] in which 20 amino acids may be visualized in 3D using JSmol.
Please help to expand the list below to include all 22 amino acids.
===Glycine===
Gly G: Small.
See also [[Glycine|Glycine in Proteopedia]] and [http://en.wikipedia.org/wiki/Glycine Glycine] in Wikipedia, where the structure is shown. Glycine is the smallest amino acid, since its side-chain is nothing  but a single hydrogen. Glycine is frequently found in [[Turns in Proteins|turns]], since the steric clashes of larger amino acids would be problematic. Turns typically occur on the surfaces of proteins, between [[Secondary structure|beta-strands or alpha-helices]]. It is common to find '''[[Conservation, Evolutionary|highly conserved]] glycines in turns on protein surfaces''', since mutation to a bulkier residue would interfere with the fold. Glycine also occurs in  [[Secondary structure|beta-strands and alpha-helices]], although its frequency in alpha helices is low (second lowest, after proline, p. 125 in <ref name="kesselbental">Kessel, Amit, and Nir Ben-Tal. ''Introduction to Proteins: Structure, Function, and Motion''. CRC Press, 2011. 653 pages.</ref>). Glycine is commonly found at the C-terminus of alpha helices, and is considered a ''helix terminator'' (p. 125 in <ref name="kesselbental" />).
===Histidine===
His H:
Charged: <font color="blue"><b>Basic</b></font>, Aromatic, Bulky
See [http://en.wikipedia.org/wiki/Histidine Histidine] in Wikipedia, where the structure is shown.
The sidechain of His can be positively charged (protonated), in which case both of the nitrogens in the sidechain imidazole ring have hydrogens, and the charge is delocalized between them. The pKa for protonation is 6.1. This means that, on average at any moment, half of the His sidechains are protonated when the pH is 6.1. At the pH of blood, 7.4 ±0.05, His sidechains are positively charged less than 10% of the time. Therefore, His is not included in the usual list of positively charged amino acids ([[#Lysine|lysine]] and [[#Arginine|arginine]]).
===Phenylalanine===
Phe F:
Neutral, Aromatic, Bulky
See [http://en.wikipedia.org/wiki/Phenylalanine Phenylalanine] in Wikipedia, where the structure is shown. Phe participates in [[Cation-pi interactions]]. [http://en.wikipedia.org/wiki/Phenylketonuria Phenylketonuria] is a genetic disease in which the enzyme that converts phenylalanine to [[#Tyrosine|tyrosine]] is nonfunctional, leading to toxicity from excess phenylalanine, and tyrosine deficiency.
===Tryptophan===
Trp W:
Neutral, Polar, Aromatic, Bulky
See [http://en.wikipedia.org/wiki/Tryptophan Tryptophan] in Wikipedia, where the structure is shown.
In trans-membrane proteins, tryptophans often lie at the interface between water and lipid. An example is the potassium channel, e.g. [[1bl8]]. To see their positions, use the ''Find'' dialog in FirstGlance in Jmol. Trp participates in [[Cation-pi interactions]].
===Tyrosine===
Tyr Y:
Neutral, Polar, Aromatic, Bulky
See [http://en.wikipedia.org/wiki/Tyrosine Tyrosine] in Wikipedia, where the structure is shown, and [[Nitrotyrosine]]. Tyr participates in [[Cation-pi interactions]].
==See Also==
*[[Non-Standard Residues]].
*[[Standard Residues]]
*[http://en.wikipedia.org/wiki/Amino_acids Amino Acids in Wikipedia]
*[[Basics of Protein Structure]]
==References==
<references />

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

Eric Martz, Andrea Gorrell, Angel Herraez, Joel L. Sussman
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