Christoph: /* External links */

2012-07-26T19:01:43Z

‎External links

Christoph: /* Reduced (redundant or simplified) alphabets for proteins */

2012-05-16T02:34:55Z

‎Reduced (redundant or simplified) alphabets for proteins

Christoph at 17:22, 8 January 2009

2009-01-08T17:22:49Z

Christoph: /* External links */

2008-09-22T03:57:59Z

‎External links

Christoph at 23:46, 21 April 2007

2007-04-21T23:46:54Z

New page

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]]

← Older revision		Revision as of 17:22, 8 January 2009
Line 1:		Line 1:
	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>		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>
		+
		+	==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==		==Reduced (redundant or simplified) alphabets for proteins==

@@ Line 188: / Line 188: @@
 *[http://www.russell.embl.de/aas/ Amino acid properties]
 *[http://openwetware.org/wiki/Amino_acids Amino acids] &mdash; on OpenWetWare.org
 *[[wikipedia:amino acid]]
 [[Category:Bioinformatics]]

@@ Line 50: / Line 50: @@
   IVLFCMAW => P: Hydrophilic
   GTSYPM   => N: Neutral
-  DNEQKR   =>H: Hydrophobic
+  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>

Amino acid - Revision history

Christoph: /* External links */

Christoph: /* Reduced (redundant or simplified) alphabets for proteins */

Christoph at 17:22, 8 January 2009

Christoph: /* External links */

Christoph at 23:46, 21 April 2007