In Foldit, there are 20 different amino acids.
Each protein has a unique sequence of amino acids. This sequence is called the "primary structure" of the protein. It's common to see the sequence listed as a string of one-character lowercase amino acid codes, for example:
The table below lists the amino acids and their one- and three-character abbreviations.
When it comes to protein folding, one important characteristic of an amino acid is how it interacts with water. In Foldit, an amino acid is either hydrophilic, meaning it likes water, or hydrophobic, meaning it tries to avoid water. The "hydropathy index" column of the table is a more refined version of this idea.
The other main characteristic of an amino acid is it's sidechain. All amino acids have the same backbone. It's the sidechain, projecting off the backbone, which makes each amino acid different. See the amino acid gallery for examples of what each amino acid looks like in Foldit.
All the amino acids in Foldit are left-handed, meaning the sidechain is always in the same position relative the other parts of the protein backbone, which are the amino group, the alpha carbon, and the carboxyl group.
Table of amino acids Edit
The table below shows the amino acids used in Foldit. It includes the three-letter abbreviation and one-character code for each amino acid. Two amino acids have two names. Aspartate is also called aspartic acid, and glumate is also called glutamic acid. This is because both have acid sidechains.
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.
The table shows whether the sidechain is acidic or basic. Finally, the table shows the hydropathy index.
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 hyrdophobic. In general, negative values are hydrophilic in Foldit, and positive values are hydrophobic. There are several exceptions in the middle of the table, however. (Click on the arrows at the top of the hydropathy index column to sort the table by hydropathy.)
|Amino Acid||3-Letter||1-Letter||Side chain polarity||Side chain acid or base||Hydropathy index|
|Aspartate (aspartic acid)||Asp||D||polar||acidic||-3.5|
|Glutamate (glutamic acid)||Glu||E||polar||acidic||-3.5|
The wikipedia article proteinogenic amino acid has much more information about each amino acid