Foldit Wiki
Don't have an account?
Register
Register
in: Amino acid, Glossary, Biochemistry

Changes: Amino Acids

Back to page
Edit
No edit summary
(Added still more images, and a little text.)
 
(43 intermediate revisions by 11 users not shown)
Line 1: Line 1:
  +
[[File:Tryptophan.enzdes.png|thumb|200px|Tryptophan, the amino acid with the largest sidechain, seen in [[EnzDes]] coloring.]]
−
Amino acids are the basic building blocks of proteins. They are also the basic units of FoldIt.
  
  +
[[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.
−
(This table comes from Wikipedia, and we can use it to get started on discussing individual amino acids. In the meantime, I'd like to get in touch with anyone who has access to jpegs of these compounds showing how they all look in Fold It. -- Diderot)
  
   
  +
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.
−
{| class="wikitable sortable"
  
−
! Amino Acid
  
−
! 3-Letter
  
−
! 1-Letter
  
−
! Side chain polarity
  
−
! Side chain acidity or basicity of neutral species
  
−
! [[Hydropathy index]]<ref>{{cite journal | author = Kyte J & RF Doolittle | title = A simple method for displaying the hydropathic character of a protein | journal = J. Mol. Biol. | issue = 157 | pages = 105–132 | year = 1982 | pmid=7108955 | doi = 10.1016/0022-2836(82)90515-0 | volume = 157 }}</ref>
  
−
|- align="center"
  
−
| [[Alanine]]
  
−
| Ala
  
−
| A
  
−
| nonpolar
  
−
| neutral
  
−
| 1.8
  
−
|- align="center"
  
−
| [[Arginine]]
  
−
| Arg
  
−
| R
  
−
| polar
  
−
| basic (strongly)
  
−
| -4.5
  
−
|- align="center"
  
−
| [[Asparagine]]
  
−
| Asn
  
−
| N
  
−
| polar
  
−
| neutral
  
−
| -3.5
  
−
|- align="center"
  
−
| [[Aspartic acid]]
  
−
| Asp
  
−
| D
  
−
| polar
  
−
| acidic
  
−
| -3.5
  
−
|- align="center"
  
−
| [[Cysteine]]
  
−
| Cys
  
−
| C
  
−
| polar
  
−
| neutral
  
−
| 2.5
  
−
|- align="center"
  
−
| [[Glutamic acid]]
  
−
| Glu
  
−
| E
  
−
| polar
  
−
| acidic
  
−
| -3.5
  
−
|- align="center"
  
−
| [[Glutamine]]
  
−
| Gln
  
−
| Q
  
−
| polar
  
−
| neutral
  
−
| -3.5
  
−
|- align="center"
  
−
| [[Glycine]]
  
−
| Gly
  
−
| G
  
−
| nonpolar
  
−
| neutral
  
−
| -0.4
  
−
|- align="center"
  
−
| [[Histidine]]
  
−
| His
  
−
| H
  
−
| polar
  
−
| basic (weakly)
  
−
| -3.2
  
−
|- align="center"
  
−
| [[Isoleucine]]
  
−
| Ile
  
−
| I
  
−
| nonpolar
  
−
| neutral
  
−
| 4.5
  
−
|- align="center"
  
−
| [[Leucine]]
  
−
| Leu
  
−
| L
  
−
| nonpolar
  
−
| neutral
  
−
| 3.8
  
−
|- align="center"
  
−
| [[Lysine]]
  
−
| Lys
  
−
| K
  
−
| polar
  
−
| basic
  
−
| -3.9
  
−
|- align="center"
  
−
| [[Methionine]]
  
−
| Met
  
−
| M
  
−
| nonpolar
  
−
| neutral
  
−
| 1.9
  
−
|- align="center"
  
−
| [[Phenylalanine]]
  
−
| Phe
  
−
| F
  
−
| nonpolar
  
−
| neutral
  
−
| 2.8
  
−
|- align="center"
  
−
| [[Proline]]
  
−
| Pro
  
−
| P
  
−
| nonpolar
  
−
| neutral
  
−
| -1.6
  
−
|- align="center"
  
−
| [[Serine]]
  
−
| Ser
  
−
| S
  
−
| polar
  
−
| neutral
  
−
| -0.8
  
−
|- align="center"
  
−
| [[Threonine]]
  
−
| Thr
  
−
| T
  
−
| polar
  
−
| neutral
  
−
| -0.7
  
−
|- align="center"
  
−
| [[Tryptophan]]
  
−
| Trp
  
−
| W
  
−
| nonpolar
  
−
| neutral
  
−
| -0.9
  
−
|- align="center"
  
−
| [[Tyrosine]]
  
−
| Tyr
  
−
| Y
  
−
| polar
  
−
| neutral
  
−
| -1.3
  
−
|- align="center"
  
−
| [[Valine]]
  
−
| Val
  
−
| V
  
−
| nonpolar
  
−
| neutral
  
−
| 4.2
  
−
|}
 
   
  +
{|class="wikitable sortable"
−
In addition to the normal amino acid codes, placeholders were used historically in cases where [[Protein sequencing|chemical]] or [[X-ray crystallography|crystallographic]] analysis of a peptide or protein could not completely establish the identity of a certain residue in a structure. The ones they could not resolve between are these pairs of amino-acids:
  
  +
!Amino Acid
−  
  +
!3-Letter
−
{| class="wikitable"
  
  +
!1-Letter
−
! Ambiguous Amino Acids
  
  +
![[Hydrophobicity]] /
−
! 3-Letter
  
  +
[[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>
−
! 1-Letter
  
  +
!polarity
−
|- align="center"
  
  +
!acidity (pH)
−
| Asparagine or aspartic acid
  
  +
|-align="center"
−
| Asx
  
  +
|[[Alanine]]
−
| B
  
  +
|Ala
−
|- align="center"
  
  +
|A
−
| Glutamine or glutamic acid
  
  +
|<span style="color:orange;">1.8</span>
−
| Glx
  
  +
|nonpolar
−
| Z
  
  +
|neutral
−
|- align="center"
  
  +
|-align="center"
−
| Leucine or Isoleucine
  
  +
|[[Arginine]]
−
| Xle
  
−
| J
 +
|Arg
  +
|R
−
|- align="center"
  
  +
|<span style="color:blue;">-4.5</span>
−
| Unspecified or unknown amino acid
  
  +
|polar
−
| Xaa
  
  +
|basic (strongly)
−
| X
  
  +
|-align="center"
  +
|[[Asparagine]]
  +
|Asn
  +
|N
  +
|<span style="color:blue;">-3.5</span>
  +
|polar
  +
|neutral
  +
|-align="center"
  +
|[[Aspartic acid|Aspartate (aspartic acid)]]
  +
|Asp
  +
|D
  +
|<span style="color:blue;">-3.5</span>
  +
|polar
  +
|acidic
  +
|-align="center"
  +
|[[Cysteine]]
  +
|Cys
  +
|C
  +
|<span style="color:orange;">2.5</span>
  +
|polar
  +
|neutral
  +
|-align="center"
  +
|[[Glutamic acid|Glutamate (glutamic acid)]]
  +
|Glu
  +
|E
  +
|<span style="color:blue;">-3.5</span>
  +
|polar
  +
|acidic
  +
|-align="center"
  +
|[[Glutamine]]
  +
|Gln
  +
|Q
  +
|<span style="color:blue;">-3.5</span>
  +
|polar
  +
|neutral
  +
|-align="center"
  +
|[[Glycine]]
  +
|Gly
  +
|G
  +
|<span style="color:orange;">-0.4</span>
  +
|nonpolar
  +
|neutral
  +
|-align="center"
  +
|[[Histidine]]
  +
|His
  +
|H
  +
|<span style="color:blue;">-3.2</span>
  +
|polar
  +
|basic (weakly)
  +
|-align="center"
  +
|[[Isoleucine]]
  +
|Ile
  +
|I
  +
|<span style="color:orange;">4.5</span>
  +
|nonpolar
  +
|neutral
  +
|-align="center"
  +
|[[Leucine]]
  +
|Leu
  +
|L
  +
|<span style="color:orange;">3.8</span>
  +
|nonpolar
  +
|neutral
  +
|-align="center"
  +
|[[Lysine]]
  +
|Lys
  +
|K
  +
|<span style="color:blue;">-3.9</span>
  +
|polar
  +
|basic
  +
|-align="center"
  +
|[[Methionine]]
  +
|Met
  +
|M
  +
|<span style="color:orange;">1.9</span>
  +
|nonpolar
  +
|neutral
  +
|-align="center"
  +
|[[Phenylalanine]]
  +
|Phe
  +
|F
  +
|<span style="color:orange;">2.8</span>
  +
|nonpolar
  +
|neutral
  +
|-align="center"
  +
|[[Proline]]
  +
|Pro
  +
|P
  +
|<span style="color:orange;">-1.6</span>
  +
|nonpolar
  +
|neutral
  +
|-align="center"
  +
|[[Serine]]
  +
|Ser
  +
|S
  +
|<span style="color:blue;">-0.8</span>
  +
|polar
  +
|neutral
  +
|-align="center"
  +
|[[Threonine]]
  +
|Thr
  +
|T
  +
|<span style="color:blue;">-0.7</span>
  +
|polar
  +
|neutral
  +
|-align="center"
  +
|[[Tryptophan]]
  +
|Trp
  +
|W
  +
|<span style="color:orange;">-0.9</span>
  +
|nonpolar
  +
|neutral
  +
|-align="center"
  +
|[[Tyrosine]]
  +
|Tyr
  +
|Y
  +
|<span style="color:orange;">-1.3</span>
  +
|polar
  +
|neutral
  +
|-align="center"
  +
|[[Valine]]
  +
|Val
  +
|V
  +
|<span style="color:orange;">4.2</span>
  +
|nonpolar
  +
|neutral
 
|}
  
|}
   
  +
See the [[Amino_Acid_Gallery|amino acid gallery]] for examples of what each amino acid looks like in Foldit.
−
'''Unk''' is sometimes used instead of '''Xaa''', but is less standard.
  
  +
  +
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]].
  +
  +
See [[wikipedia:Proteinogenic_amino_acid|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 [[Sidechain|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|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.
  +
===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)===
  +
The sidechain of each amino acid is classified as acidic, basic, or neutral.
  +
  +
==References==
  +
  +
<references/>
  +
__NOTOC__
  +
__NOEDITSECTION__
  +
[[Category:Amino acid]]
  +
[[Category:Glossary]]
  +
[[Category:Biochemistry]]

Latest revision as of 18:33, 17 April 2019

Tryptophan

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

Ani4

Animation of some arginine sidechain positions.

Alanine

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

Histidine

Histidine.

Phenylalanine

Phenylalanine.

Aspartate

Aspartate, or aspartic acid.

Glutamate

Glutamate, or glutamic acid.

Lysine

Lysine.

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

  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
Community content is available under CC-BY-SA unless otherwise noted.