Changes: Amino Acids

Latest revision as of 18:33, 17 April 2019

Tryptophan, the amino acid with the largest sidechain, seen in EnzDes coloring.

Ani4 — Animation of some arginine sidechain positions.

Alanine, the amino acid with the smallest sidechain, except for glycine, which has no sidechain.

Amino acids (also called segments or residues in Foldit) are the building blocks of proteins. Each amino acid has a unique sidechain, except for glycine.

Each protein is identified by a unique sequence of amino acids, the primary structure of the protein.

The table below shows the 20 amino acids used in Foldit. Clicking on the arrows in the column heads changes the sort order of the table. The table is explained in detail below.

Amino Acid	3-Letter	1-Letter	Hydrophobicity / Hydropathy index^[1]	polarity	acidity (pH)
Alanine	Ala	A	1.8	nonpolar	neutral
Arginine	Arg	R	-4.5	polar	basic (strongly)
Asparagine	Asn	N	-3.5	polar	neutral
Aspartate (aspartic acid)	Asp	D	-3.5	polar	acidic
Cysteine	Cys	C	2.5	polar	neutral
Glutamate (glutamic acid)	Glu	E	-3.5	polar	acidic
Glutamine	Gln	Q	-3.5	polar	neutral
Glycine	Gly	G	-0.4	nonpolar	neutral
Histidine	His	H	-3.2	polar	basic (weakly)
Isoleucine	Ile	I	4.5	nonpolar	neutral
Leucine	Leu	L	3.8	nonpolar	neutral
Lysine	Lys	K	-3.9	polar	basic
Methionine	Met	M	1.9	nonpolar	neutral
Phenylalanine	Phe	F	2.8	nonpolar	neutral
Proline	Pro	P	-1.6	nonpolar	neutral
Serine	Ser	S	-0.8	polar	neutral
Threonine	Thr	T	-0.7	polar	neutral
Tryptophan	Trp	W	-0.9	nonpolar	neutral
Tyrosine	Tyr	Y	-1.3	polar	neutral
Valine	Val	V	4.2	nonpolar	neutral

See the amino acid gallery for examples of what each amino acid looks like in Foldit.

See also spmm's amino acid table, which shows the odds of each amino acid being found in helix, sheet, and loop.

See proteinogenic amino acid on wikipedia for more information about each amino acid.

Detail

The table shows how amino acids are identified and lists the key characteristics of their sidechains.

Amino Acid

The first column shows each amino acid's full name, and links to its detail page.

Two amino acids have two names. Aspartate is also called aspartic acid, and glutamate is also called glutamic acid. This is because both have acid sidechains.

3-letter code

Some sources, such as the PDB, use three-letter codes to represent amino acids.

1-letter code

The primary structure of a protein is often reported one-letter codes, such as in FASTA format. Foldit uses lower case for these codes.

Hydrophobicity/Hydropathy index

One important characteristic of an amino acid is how it interacts with water, also known as hydrophobicity. In Foldit, an amino acid is either hydrophilic, meaning it likes water, or hydrophobic, meaning it tries to avoid water. The hydropathy index is a more refined version of this idea.

The hydropathy index values shown in blue are for amino acids classified as hydrophilic in Foldit. The values shown in orange are for amino acids considered hydrophobic. In general, negative values are hydrophilic in Foldit, and positive values are hydrophobic. There are several exceptions in the middle of the table, however.

Polarity

The amino acids listed as "polar" have sidechains with nitrogen or oxygen atoms that can form hydrogen bonds. See sidechain bonding gallery and sidechain bonding table for details on the bondable atoms

Acidity (pH)

The sidechain of each amino acid is classified as acidic, basic, or neutral.

References

↑ Kyte J & RF Doolittle: A simple method for displaying the hydropathic character of a protein in: Journal of Molecular Biology issue 157, 1982, pages 105–132 PMID 7108955

[1] Kyte J & RF Doolittle: A simple method for displaying the hydropathic character of a protein in: Journal of Molecular Biology issue 157, 1982, pages 105–132 PMID 7108955

[1]

@@ Line 1: / Line 1: @@
+[[File:Tryptophan.enzdes.png|thumb|200px|Tryptophan, the amino acid with the largest sidechain, seen in [[EnzDes]] coloring.]]
-==Overview==
+[[File:Ani4.gif|thumb|Animation of some [[arginine]] sidechain positions.]]
+[[File:Alanine.enzdes.png|thumb|Alanine, the amino acid with the smallest sidechain, except for [[glycine]], which has no sidechain.]]
+[[File:Histidine.enzdes.png|thumb|Histidine.]]
+[[File:Phenylalanine.enzdes.png|thumb|Phenylalanine.]]
+[[File:Aspartate.enzdes.png|thumb|Aspartate, or aspartic acid.]]
+[[File:Glutamate.enzdes.png|thumb|Glutamate, or glutamic acid.]]
+[[File:Lysine.enzdes.png|thumb|Lysine.]]
+Amino acids (also called [[Segment|segments]] or [[Residue|residues]] in Foldit) are the building blocks of [[Protein|proteins]]. Each amino acid has a unique [[sidechain]], except for [[glycine]].
+Each protein is identified by a unique sequence of amino acids, the [[Primary Structure|primary structure]] of the protein.
-[[File:Ani4.gif|frame|Animation of some Arginine side chain positions]]Alpha-amino acids are the building blocks of proteins. They combine in a condensation reaction that releases water and the new "amino acid residue" that is held together by a [[Peptide Bond]]. Proteins are defined by their unique sequence of amino acid residues; this sequence is the [[Primary Structure]] of the protein. Just as the letters of the alphabet can be combined to form an almost endless variety of words, amino acids can be linked in varying sequences to form a vast variety of proteins.
+The table below shows the 20 amino acids used in Foldit. Clicking on the arrows in the column heads changes the sort order of the table. The table is explained in detail below.
-Twenty standard amino acids are used by cells in protein biosynthesis, and these are specified by the general genetic code. These 20 amino acids are biosynthesized from other molecules, but organisms differ in which ones they can synthesize and which ones must be provided in their diet. The ones that cannot be synthesized by an organism are called essential amino acids.
-Amino acids are also the basic units of FoldIt. In the structure of a protein, each amino acid contributes one link in the protein [[Backbone]] and (usually) one [[Sidechain]]. The backbone establishes the basic structural aspects of the protein, and the sidechains determine the details of its biological function.
-Here is a list of the amino acids that are known to be found in FoldIt. It is possible that a few others have been or may eventually be used as well, but these are by far the most common.
 {|class="wikitable sortable"
@@ Line 13: / Line 17: @@
 !3-Letter
 !1-Letter
+![[Hydrophobicity]] /
-!Side chain polarity
+[[Hydropathy index]]<ref>Kyte J & RF Doolittle: ''A simple method for displaying the hydropathic character of a protein'' in: ''Journal of Molecular Biology'' issue 157, 1982, pages 105–132 [//www.ncbi.nlm.nih.gov/pubmed/7108955?dopt=Abstract PMID 7108955]</ref>
-!Side chain acidity or basicity of neutral species
+!polarity
-![[Hydropathy index]]
+!acidity (pH)
-<ref>Kyte J & RF Doolittle: ''A simple method for displaying the hydropathic character of a protein'' in: ''Journal of Molecular Biology'' issue 157, 1982, pages 105–132 [http://www.elsevier.com/framework_products/Chemistry/simple.pdf PDF; 1.9&nbsp;MB]</ref>
 |-align="center"
 |[[Alanine]]
 |Ala
 |A
+|<span style="color:orange;">1.8</span>
 |nonpolar
 |neutral
-|<span style="color:orange;">1.8</span>
 |-align="center"
 |[[Arginine]]
 |Arg
 |R
+|<span style="color:blue;">-4.5</span>
 |polar
 |basic (strongly)
-|<span style="color:blue;">-4.5</span>
 |-align="center"
 |[[Asparagine]]
 |Asn
 |N
+|<span style="color:blue;">-3.5</span>
 |polar
 |neutral
-|<span style="color:blue;">-3.5</span>
 |-align="center"
-|[[Aspartic acid]]
+|[[Aspartic acid|Aspartate (aspartic acid)]]
 |Asp
 |D
+|<span style="color:blue;">-3.5</span>
 |polar
 |acidic
-|<span style="color:blue;">-3.5</span>
 |-align="center"
 |[[Cysteine]]
 |Cys
 |C
+|<span style="color:orange;">2.5</span>
 |polar
 |neutral
-|<span style="color:orange;">2.5</span>
 |-align="center"
-|[[Glutamic acid]]
+|[[Glutamic acid|Glutamate (glutamic acid)]]
 |Glu
 |E
+|<span style="color:blue;">-3.5</span>
 |polar
 |acidic
-|<span style="color:blue;">-3.5</span>
 |-align="center"
 |[[Glutamine]]
 |Gln
 |Q
+|<span style="color:blue;">-3.5</span>
 |polar
 |neutral
-|<span style="color:blue;">-3.5</span>
 |-align="center"
 |[[Glycine]]
 |Gly
 |G
+|<span style="color:orange;">-0.4</span>
 |nonpolar
 |neutral
-|<span style="color:orange;">-0.4</span>
 |-align="center"
 |[[Histidine]]
 |His
 |H
+|<span style="color:blue;">-3.2</span>
 |polar
 |basic (weakly)
-|<span style="color:blue;">-3.2</span>
 |-align="center"
 |[[Isoleucine]]
 |Ile
 |I
+|<span style="color:orange;">4.5</span>
 |nonpolar
 |neutral
-|<span style="color:orange;">4.5</span>
 |-align="center"
 |[[Leucine]]
 |Leu
 |L
+|<span style="color:orange;">3.8</span>
 |nonpolar
 |neutral
-|<span style="color:orange;">3.8</span>
 |-align="center"
 |[[Lysine]]
 |Lys
 |K
+|<span style="color:blue;">-3.9</span>
 |polar
 |basic
-|<span style="color:blue;">-3.9</span>
 |-align="center"
 |[[Methionine]]
 |Met
 |M
+|<span style="color:orange;">1.9</span>
 |nonpolar
 |neutral
-|<span style="color:orange;">1.9</span>
 |-align="center"
 |[[Phenylalanine]]
 |Phe
 |F
+|<span style="color:orange;">2.8</span>
 |nonpolar
 |neutral
-|<span style="color:orange;">2.8</span>
 |-align="center"
 |[[Proline]]
 |Pro
 |P
+|<span style="color:orange;">-1.6</span>
 |nonpolar
 |neutral
-|<span style="color:orange;">-1.6</span>
 |-align="center"
 |[[Serine]]
 |Ser
 |S
+|<span style="color:blue;">-0.8</span>
 |polar
 |neutral
-|<span style="color:blue;">-0.8</span>
 |-align="center"
 |[[Threonine]]
 |Thr
 |T
+|<span style="color:blue;">-0.7</span>
 |polar
 |neutral
-|<span style="color:blue;">-0.7</span>
 |-align="center"
 |[[Tryptophan]]
 |Trp
 |W
+|<span style="color:orange;">-0.9</span>
 |nonpolar
 |neutral
-|<span style="color:orange;">-0.9</span>
 |-align="center"
 |[[Tyrosine]]
 |Tyr
 |Y
+|<span style="color:orange;">-1.3</span>
 |polar
 |neutral
-|<span style="color:orange;">-1.3</span>
 |-align="center"
 |[[Valine]]
 |Val
 |V
+|<span style="color:orange;">4.2</span>
 |nonpolar
 |neutral
-|<span style="color:orange;">4.2</span>
 |}
-This may also be of use [[Foldit-aas|foldit-aas]]
-==Chemistry==
-In chemistry, an [http://en.wikipedia.org/wiki/Amino_acid amino acid] is a molecule containing both amine and carboxyl functional groups. In the alpha amino acids, the amino and carboxylate groups are attached to the same carbon, which is called the α–carbon. The various alpha amino acids differ in which side chain (R group) is attached to their alpha carbon. They can vary in size from just a hydrogen atom in glycine through a methyl group in alanine to a large heterocyclic group in tryptophan.
-Beyond the amino acids that are found in all forms of life, many non-natural amino acids have vital roles in technology and industry. For example, the chelating agents EDTA and nitrilotriacetic acid are alpha amino acids that are important in the chemical industry.
-The only difference between the various amino acids is their different side chains (labeled R) that attach at the middle carbon of each amino acid.
-Thus the basic structure of an amino acid can be represented as H2N-CHR-COOH where 2 atoms of Hydrogen are bound to a Nitrogen which is bound to the middle Carbon with a Hydrogen and the R group then the final COOH Carboxylic Acid group.
-Amino Acids bind together in their primary sequence using peptide bonds where one H from the NH2 reacts with the OH (hydroxyl) group of the next acid releasing an H2O an forming a strong bond that forms the backbone of the protein in the sequence specified by the DNA -&gt; RNA transcription process.
-Sidechain interactions define the 3-dimensional conformation of each protein. Some proteins have more than one different stable conformation; these alternate conformations are called Prions and appear to have a role both in [http://stke.sciencemag.org/cgi/content/abstract/sigtrans;2004/214/tw1 memory] and some [http://www.howstuffworks.com/mad-cow-disease.htm diseases].
-<span class="author-p-10495" style="padding-top: 0px; padding-bottom: 1px; cursor: auto;">In the polypeptide chain, the rotation between alpha carbon and nitrogen in </span><span class="author-p-10405" style="padding-top: 0px; padding-bottom: 1px; cursor: auto;">the </span><span class="author-p-10495" style="padding-top: 0px; padding-bottom: 1px; cursor: auto;">backbone is called Phi Φ, and the rotation between alpha carbon and carbonyl carbon is called psi Ψ.</span>
-<span class="author-p-10495" style="padding-top: 0px; padding-bottom: 1px; cursor: auto;">Stetic hyndrance</span><span class="author-p-10405" style="padding-top: 0px; padding-bottom: 1px; cursor: auto;">, or clashes,</span><span class="author-p-10495" style="padding-top: 0px; padding-bottom: 1px; cursor: auto;"> prevent certain angles</span><span class="author-p-10405" style="padding-top: 0px; padding-bottom: 1px; cursor: auto;">.These</span><span class="author-p-10495" style="padding-top: 0px; padding-bottom: 1px; cursor: auto;"> can be see</span><span class="author-p-10405" style="padding-top: 0px; padding-bottom: 1px; cursor: auto;">n</span><span class="author-p-10495" style="padding-top: 0px; padding-bottom: 1px; cursor: auto;"> on the Ramachandran plot. </span>
+See the [[Amino_Acid_Gallery|amino acid gallery]] for examples of what each amino acid looks like in Foldit.
-The (20) amino acids shown above are classified according to the chemical properties of the R group:
-Acidic[2], Basic[3], Uncharged Polar[5], and Non-Polar[10]. Thus we can rewrite the above table as follows.
-===Class, amino acid(Abbrev, Name), R group===
-====Acidic====
-:D Asp [[Aspartic acid]] -CH2-COOH where both the O and the OH are bonded to the C
-:E Glu [[Glutamic acid]] -CH2-CH2-COOH
+See also [[Foldit-aas|spmm's amino acid table]], which shows the odds of each amino acid being found in [[Helix|helix]], [[Sheet|sheet]], and [[Loop|loop]].
-====Basic====
-:K Lys [[Lysine]] -CH2-CH2-CH2-CH2-NH3+
-:R Arg [[Arginine]] -CH2-CH2-CH2-NH-C-(NH2)2 &nbsp;:where 2 NH2 groups are attached to the final C
-:H His [[Histidine]] -CH2-&lt;C-HN-HC=NH+-HC=&gt; &nbsp;:where &lt; chain &gt; actually forms a pentagonal ring bonded at the C
+See [[wikipedia:Proteinogenic_amino_acid|proteinogenic amino acid]] on wikipedia for more information about each amino acid.
-====Uncharged Polar====
-:S Ser [[Serine]] -CH2-OH
-:T Thr [[Threonine]] -CH-CH3OH &nbsp;:where both the CH3 and the OH attach at the initial CH
-:Y Tyr [[Tyrosine]] -CH2-&lt;CH=CH-CH=COH-CH=CH-&gt; &nbsp;:where &lt; ... &gt; forms a hexagonal ring with the OH at the far end
-:N Asn [[Asparagine]] -CH2-CONH2 &nbsp;:where both the =O and the -NH2 attach to the C
-:O Gln [[Glutamine]] -CH2-CH2-CONH2 &nbsp;:same as Asparagine but with an extra CH2<br />
-C Cys [[Cysteine]] -CH2-S-H
-====Non-Polar====
+==Detail==
+The table shows how amino acids are identified and lists the key characteristics of their [[Sidechain|sidechains]].
-:G Gly [[Glycine]] -H
-:A Ala [[Alanine]] -CH3
-:V Val [[Valine]] -CH-(CH3)2
-:L Leu [[Leucine]] -CH2-CH-(CH3)2
-:I Ile [[Isoleucine]] -CH-(CH3, CH2-CH3)
-:P Pro [[Proline]] -&lt;CH2-CH2-CH2&gt; &nbsp;:where the other end of the ring attaches at the N by replacing an H
-:F Phe [[Phenylalanine]] -CH2-&lt;CH=CH-CH=CH-CH=CH-&gt; &nbsp;:like tyrosine without the OH at the far end of the ring.
-:M Met [[Methionine]] -CH2-CH2-S-CH3
-:W Trp [[Tryptophan]] -CH2-&lt;pentagonal ring with NH&gt;&lt;Hexagonal Phenyl ring&gt;
+===Amino Acid===
-A better sense of the actual amino acid structures can be found [http://en.wikipedia.org/wiki/List_of_standard_amino_acids here].
+The first column shows each amino acid's full name, and links to its detail page.
+Two amino acids have two names. Aspartate is also called aspartic acid, and glutamate is also called glutamic acid. This is because both have acid sidechains.
-==Notes==
+===3-letter code===
-*A strong [[Disulfide Bridge]] (S-S) sometimes can be created between the sulfur in the side chains in two [[Cysteine]] amino acids. This plays a strong role in forming the 3 dimensional protein structure.
+Some sources, such as the [[PDB]], use three-letter codes to represent amino acids.
+===1-letter code===
-*Additional bonds occur between acidic and basic end groups of the side chains.
+The [[Primary Structure|primary structure]] of a protein is often reported one-letter codes, such as in [[wikipedia:FASTA_format|FASTA format]]. Foldit uses lower case for these codes.
+===Hydrophobicity/Hydropathy index===
+One important characteristic of an amino acid is how it interacts with water, also known as [[hydrophobicity]]. In Foldit, an amino acid is either [[hydrophilic]], meaning it likes water, or [[hydrophobic]], meaning it tries to avoid water. The [[hydropathy index]] is a more refined version of this idea.
+The hydropathy index values shown in blue are for amino acids classified as hydrophilic in Foldit. The values shown in orange are for amino acids considered hydrophobic. In general, negative values are hydrophilic in Foldit, and positive values are hydrophobic. There are several exceptions in the middle of the table, however.
-*Polar side groups like to remain in a polar environment such as the water surrounding the protein. See [[Hydrophobicity]].
+===Polarity===
+The amino acids listed as "polar" have sidechains with nitrogen or oxygen atoms that can form [[Hydrogen bond|hydrogen bonds]]. See [[Sidechain Bonding Gallery|sidechain bonding gallery]] and [[Sidechain Bonding Table|sidechain bonding table]] for details on the bondable atoms
+===Acidity (pH)===
-*A protein is most stable when in its lowest energy configuration, somewhat like a valley. Interestingly there can be a lower valley over the next rise that is not detected unless a higher energy configuration is achieved. These local minima have to be determined using previous experience and intuition, and also by developing a good sense of [[Aesthetics]].
+The sidechain of each amino acid is classified as acidic, basic, or neutral.
 ==References==
 <references/>
+__NOTOC__
-[[Category:amino acid]]
+__NOEDITSECTION__
+[[Category:Amino acid]]
+[[Category:Glossary]]
+[[Category:Biochemistry]]