Amino acid
From Christoph's Personal Wiki
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 NH2CHRCOOH.[1]
Contents
Amino acid atoms
The following atoms are expected for a given amino acid:
aa 1 2 3 4 5 6 7 8 9 10 11 12 13 14 A: N CA C O CB : Alanine V: N CA C O CB CG1 CG2 : Valine L: N CA C O CB CG CD1 CD2 : Leucine I: N CA C O CB CG1 CG2 CD1 : Isoleucine P: N CA C O CB CG CD : Proline M: N CA C O CB CG SD CE : Methionine F: N CA C O CB CG CD1 CD2 CE1 CE2 CZ : Phenylalanine W: N CA C O CB CG CD1 CD2 NE1 CE2 CE3 CZ2 CZ3 CH2 : Tryptophan G: N CA C O : Glycine S: N CA C O CB OG : Serine T: N CA C O CB OG1 CG2 : Threonine C: N CA C O CB SG : Cysteine Y: N CA C O CB CG CD1 CD2 CE1 CE2 CZ OH : Tyrosine N: N CA C O CB CG OD1 ND2 : Asparagine Q: N CA C O CB CG CD OE1 NE2 : Glutamine D: N CA C O CB CG OD1 OD2 : Aspartic acid E: N CA C O CB CG CD OE1 OE2 : Glutamic acid K: N CA C O CB CG CD CE NZ : Lysine R: N CA C O CB CG CD NE CZ NH1 NH2 : Arginine H: N CA C O CB CG ND1 CD2 CE1 NE2 : Histidine X: N CA C O CB : Nonstandard (ATOM or HETATM records) #: N CA C O : Unknown (ATOM records)
Reduced (redundant or simplified) alphabets for proteins
AGTSNQDEHRKP => P: Hydrophilic CMFILVWY => H: Hydrophobic
- Five letters alphabet: Chemical / structural properties[4]
IVL => A: Aliphatic FYWH => R: Aromatic KRDE => C: Charged GACS => T: Tiny TMQNP => D: Diverse
- Six letters alphabet: Chemical / structural properties #2[4]
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[5]
IVLFCMAW => P: Hydrophilic GTSYPM => N: Neutral DNEQKR => H: Hydrophobic
- Five letters alphabet: Chemical / structural properties[5]
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[5]
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[6]
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[6]
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[6]
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[6]
LVIMC => L: Hydrophobic AGSTP => A FYW => F: Hydrophobic/aromatic sidechains EDNQKRH => E
- Murphy et al., 2000; 2 letters alphabet[6]
LVIMCAGSTPFYW => P: Hydrophobic EDNQKRH => E: Hydrophilic
- Wang & Wang, 1999; 5 letters alphabet[7]
CMFILVWY => I ATH => A GP => G DE => E SNQRK => K
- Wang & Wang, 1999; 5 letters variant alphabet[7]
CMFI => I LVWY => L ATGS => A NQDE => E HPRK => K
- Wang & Wang, 1999; 3 letters alphabet[7]
CMFILVWY => I ATHGPR => A DESNQK => E
- Wang & Wang, 1999; 2 letters alphabet[7]
CMFILVWY => I ATHGPRDESNQK => A
- Li et al., 2003; 10 letters alphabet[8]
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[8]
CFYW => Y MLIV => I G => G PATS => S NHQEDRK => E
- Li et al., 2003; 4 letters alphabet[8]
CFYW => Y MLIV => I GPATS => S NHQEDRK => E
- Li et al., 2003; 3 letters alphabet[8]
CFYWMLIV => I GPATS => S NHQEDRK => E
References
- ↑ Proline is an exception to this general formula. It lacks the NH2 group because of the cyclization of the side chain.
- ↑ Chan HS, Dill KA (1989). "Compact polymers". Macromolecules, 22:4559-4573.
- ↑ Lau KF, Dill KA (1989). "A lattice statistical mechanics model of the conformational and sequence spaces of proteins". Macromolecules, 22:3986-3997.
- ↑ 4.0 4.1 Betts MJ, Russell RB (2003). "Amino acid properties and consequences of subsitutions". Bioinformatics for Geneticists, M.R. Barnes, I.C. Gray eds, Wiley.
- ↑ 5.0 5.1 5.2 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. PMID: 14872534
- ↑ 6.0 6.1 6.2 6.3 6.4 Murphy LR, Wallqvist A, Levy RM (2000). "Simplified amino acid alphabets for protein fold recognition and implications for folding". Protein Eng, 13:149-152. PMID: 10775656
- ↑ 7.0 7.1 7.2 7.3 Wang J, Wang W (1999). "A computational approach to simplifying the protein folding alphabet". Nat Struct Biol, 11:1033-1038. PMID: 10542095
- ↑ 8.0 8.1 8.2 8.3 Li T, Fan K, Wang J, Wang W (2003). "Reduction of protein sequence complexity by residue grouping". Protein Eng, 5:323-330. PMID: 12826723
Further reading
- Spitzer M, Fuellen G, Cullen P, Lorkowski S (2004). "VisCoSe: visualization and comparison of consensus sequences". Bioinformatics, 20:433-435. 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
- Amino acid properties
- Amino acids — on OpenWetWare.org
- 'amino' bash script — a quick amino acid and DNA lookup table, by Christian Steinruecken.
- wikipedia:amino acid