View source for Amino acid

In chemistry, an '''amino acid''' is a molecule that contains both amine and carboxyl functional groups. In biochemistry, this term refers to alpha-amino acids with the general formula NH<sub>2</sub>CHRCOOH.<ref>Proline is an exception to this general formula. It lacks the NH<sub>2</sub> group because of the cyclization of the side chain.</ref>

==Reduced (redundant or simplified) alphabets for proteins==
*Two letters alphabet<ref name="Chan1989">Chan HS, Dill KA (1989). "Compact polymers". ''Macromolecules, 22:4559-4573''.</ref><ref name="Lau1989">Lau KF, Dill KA (1989). "A lattice statistical mechanics model of the conformational and sequence spaces of proteins". ''Macromolecules, 22:3986-3997''.</ref>
 AGTSNQDEHRKP => P: Hydrophilic
 CMFILVWY     => H: Hydrophobic

*Five letters alphabet: Chemical / structural properties<ref name="Betts">Betts MJ, Russell RB (2003). "[http://www.russell.embl-heidelberg.de/aas/aas.html Amino acid properties and consequences of subsitutions]". ''Bioinformatics for Geneticists, M.R. Barnes, I.C. Gray eds, Wiley''.</ref>
 IVL   => A: Aliphatic
 FYWH  => R: Aromatic
 KRDE  => C: Charged
 GACS  => T: Tiny
 TMQNP => D: Diverse

*Six letters alphabet: Chemical / structural properties #2<ref name="Betts">Betts MJ, Russell RB (2003). "[http://www.russell.embl-heidelberg.de/aas/aas.html Amino acid properties and consequences of subsitutions]". ''Bioinformatics for Geneticists, M.R. Barnes, I.C. Gray eds, Wiley''.</ref>
 IVL   => A: Aliphatic
 FYWH  => R: Aromatic
 KR    => C: Pos. charged
 DE    => C: Neg. charged
 GACS  => T: Tiny
 TMQNP => D: Diverse

*3 IMGT amino acid hydropathy alphabet<ref name="Pommie2004">Pommié C, Levadoux S, Sabatier R, Lefranc G & Lefranc MP (2004). "IMGT standardized criteria for statistical analysis of immunoglobulin V-REGION amino acid properties". ''Journal of Molecular Recognition, 17:17-32''. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=14872534&dopt=Abstract PMID: 14872534]</ref>
 IVLFCMAW => P: Hydrophilic
 GTSYPM   => N: Neutral
 DNEQKR   =>H: Hydrophobic

*Five letters alphabet: Chemical / structural properties<ref name="Pommie2004">Pommié C, Levadoux S, Sabatier R, Lefranc G & Lefranc MP (2004). "IMGT standardized criteria for statistical analysis of immunoglobulin V-REGION amino acid properties". ''Journal of Molecular Recognition, 17:17-32''. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=14872534&dopt=Abstract PMID: 14872534]</ref>
 IVL   => A: Aliphatic
 FYWH  => R: Aromatic
 KRDE  => C: Charged
 GACS  => T: Tiny
 TMQNP => D: Diverse5 IMGT amino acid volume alphabet
 GAS   => G: 60-90
 CDPNT => C: 108-117
 EVQH  => E: 138-154
 MILKR => M: 162-174
 FYW   => F: 189-228

*11 IMGT amino acid chemical characteristics alphabet<ref name="Pommie2004">Pommié C, Levadoux S, Sabatier R, Lefranc G & Lefranc MP (2004). "IMGT standardized criteria for statistical analysis of immunoglobulin V-REGION amino acid properties". ''Journal of Molecular Recognition, 17:17-32''. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=14872534&dopt=Abstract PMID: 14872534]</ref>
 AVIL => A: Aliphatic
 F    => F: Phenylalanine
 CM   => C: Sulfur
 G    => G: Glycine
 ST   => S: Hydroxyl
 W    => W: Tryptophan
 Y    => Y: Tyrosine
 P    => P: Proline
 DE   => A: Acidic
 NQ   => N: Amide
 HKR  => H: Basic

*Murphy ''et al.'', 2000; 15 letters alphabet<ref name="Murphy2000">Murphy LR, Wallqvist A, Levy RM (2000). "Simplified amino acid alphabets for protein fold recognition and implications for folding". ''Protein Eng, 13:149-152''. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=10775656&dopt=Abstract PMID: 10775656]</ref>
 LVIM => L: Large hydrophobic
 C    => C
 A    => A
 G    => G
 S    => S
 T    => T
 P    => P
 FY   => F: Hydrophobic/aromatic sidechains
 W    => W
 E    => E
 D    => D
 N    => N
 Q    => Q
 KR   => K: Long-chain positively charged
 H    => H

*Murphy ''et al.'', 2000; 10 letters alphabet<ref name="Murphy2000">Murphy LR, Wallqvist A, Levy RM (2000). "Simplified amino acid alphabets for protein fold recognition and implications for folding". ''Protein Eng, 13:149-152''. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=10775656&dopt=Abstract PMID: 10775656]</ref>
 LVIM => L: Large hydrophobic
 C    => C
 A    => A
 G    => G
 ST   => S: Polar
 P    => P
 FYW  => F:Hydrophobic/aromatic sidechains
 EDNQ => E: Charged / polar
 KR   => K: Long-chain positively charged
 H    => H

*Murphy ''et al.'', 2000; 8 letters alphabet<ref name="Murphy2000">Murphy LR, Wallqvist A, Levy RM (2000). "Simplified amino acid alphabets for protein fold recognition and implications for folding". ''Protein Eng, 13:149-152''. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=10775656&dopt=Abstract PMID: 10775656]</ref>
 LVIMC => L: Hydrophobic
 AG    => A
 ST    => S: Polar
 P     => P
 FYW   => F: Hydrophobic/aromatic sidechains
 EDNQ  => E
 KR    => K: Long-chain positively charged
 H     => H

*Murphy ''et al.'', 2000; 4 letters alphabet<ref name="Murphy2000">Murphy LR, Wallqvist A, Levy RM (2000). "Simplified amino acid alphabets for protein fold recognition and implications for folding". ''Protein Eng, 13:149-152''. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=10775656&dopt=Abstract PMID: 10775656]</ref>
 LVIMC   => L: Hydrophobic
 AGSTP   => A
 FYW     => F: Hydrophobic/aromatic sidechains
 EDNQKRH => E

*Murphy ''et al.'', 2000; 2 letters alphabet<ref name="Murphy2000">Murphy LR, Wallqvist A, Levy RM (2000). "Simplified amino acid alphabets for protein fold recognition and implications for folding". ''Protein Eng, 13:149-152''. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=10775656&dopt=Abstract PMID: 10775656]</ref>
 LVIMCAGSTPFYW => P: Hydrophobic
 EDNQKRH       => E: Hydrophilic

*Wang & Wang, 1999; 5 letters alphabet<ref name="Wang1999">Wang J, Wang W (1999). "A computational approach to simplifying the protein folding alphabet". ''Nat Struct Biol, 11:1033-1038''. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=10542095&dopt=Abstract PMID: 10542095]</ref>
 CMFILVWY => I
 ATH      => A
 GP       => G
 DE       => E
 SNQRK    => K

*Wang & Wang, 1999; 5 letters variant alphabet<ref name="Wang1999">Wang J, Wang W (1999). "A computational approach to simplifying the protein folding alphabet". ''Nat Struct Biol, 11:1033-1038''. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=10542095&dopt=Abstract PMID: 10542095]</ref>
 CMFI => I
 LVWY => L
 ATGS => A
 NQDE => E
 HPRK => K

*Wang & Wang, 1999; 3 letters alphabet<ref name="Wang1999">Wang J, Wang W (1999). "A computational approach to simplifying the protein folding alphabet". ''Nat Struct Biol, 11:1033-1038''. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=10542095&dopt=Abstract PMID: 10542095]</ref>
 CMFILVWY => I
 ATHGPR   => A
 DESNQK   => E

*Wang & Wang, 1999; 2 letters alphabet<ref name="Wang1999">Wang J, Wang W (1999). "A computational approach to simplifying the protein folding alphabet". ''Nat Struct Biol, 11:1033-1038''. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=10542095&dopt=Abstract PMID: 10542095]</ref>
 CMFILVWY     => I
 ATHGPRDESNQK => A

*Li ''et al.'', 2003; 10 letters alphabet<ref name="Li2003">Li T, Fan K, Wang J, Wang W (2003). "Reduction of protein sequence complexity by residue grouping". ''Protein Eng, 5:323-330''. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12826723&dopt=Abstract PMID: 12826723]</ref>
 C   => C
 FYW => Y
 ML  => L
 IV  => V
 G   => G
 P   => P
 ATS => S
 NH  => N
 QED => E
 RK  => K

*Li ''et al.'', 2003; 5 letters alphabet<ref name="Li2003">Li T, Fan K, Wang J, Wang W (2003). "Reduction of protein sequence complexity by residue grouping". ''Protein Eng, 5:323-330''. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12826723&dopt=Abstract PMID: 12826723]</ref>
 CFYW    => Y
 MLIV    => I
 G       => G
 PATS    => S
 NHQEDRK => E

*Li ''et al.'', 2003; 4 letters alphabet<ref name="Li2003">Li T, Fan K, Wang J, Wang W (2003). "Reduction of protein sequence complexity by residue grouping". ''Protein Eng, 5:323-330''. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12826723&dopt=Abstract PMID: 12826723]</ref>
 CFYW    => Y
 MLIV    => I
 GPATS   => S
 NHQEDRK => E

*Li ''et al.'', 2003; 3 letters alphabet<ref name="Li2003">Li T, Fan K, Wang J, Wang W (2003). "Reduction of protein sequence complexity by residue grouping". ''Protein Eng, 5:323-330''. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12826723&dopt=Abstract PMID: 12826723]</ref>
 CFYWMLIV => I
 GPATS    => S
 NHQEDRK  => E

==References==
<references/>
===Further reading===
*Spitzer M, Fuellen G, Cullen P, Lorkowski S (2004). "VisCoSe: visualization and comparison of consensus sequences". ''Bioinformatics, 20:433-435''. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=14960475&dopt=Abstract PMID: 14960475].
*Livingstone CD, Barton GJ (1993). "Protein sequence alignments: a strategy for the hierarchical analysis of residue conservation". ''Comput Appl Biosci, 9(6):745-56''. PMID: 8143162.

==External links==
*[http://www.russell.embl.de/aas/ Amino acid properties]
*[[wikipedia:amino acid]]

[[Category:Bioinformatics]]