Metabolomics

Amino Acids Reference Chart

Amino Acids with Hydrophobic Side Chain – Aliphatic

Alanine, Ala, A

Alanine
, Ala, A

Isoleucine, Ile, I

Isoleucine
, Ile, I

Leucine, Leu, L

Leucine
, Leu, L

Methionine, Met, M

Methionine
, Met, M
 

Valine, Val, V

Valine
, Val, V

Amino Acids with Hydrophobic Side Chain – Aromatic

Phenylalanine, Phe, F

Phenylalanine
, Phe, F
 

Tryptophan, Trp, W

Tryptophan
, Trp, W

 

Tyrosine, Tyr, Y

Tyrosine
, Tyr, Y
 

Amino Acids with Polar Neutral Side Chains

Asparagine, Asn, N

Asparagine
, Asn, N
 

Cysteine, Cys, C

Cysteine
, Cys, C
 

Glutamine, Gln, Q

Glutamine
, Gln, Q
 

Serine, Ser, S

Serine
, Ser, S
 

Threonine, Thr, T

Threonine
, Thr, T
 

Amino Acids with Electrically Charged Side Chains – Acidic

Aspartic acid, Asp, D

Aspartic acid
, Asp, D
 

Glutamic acid, Glu, E

Glutamic acid
, Glu, E
 

Amino Acids with Electrically Charged Side Chains – Basic

Arginine, Arg, R

Arginine
, Arg, R
 

Histidine, His, H

Histidine
, His, H
 

Lysine, Lys, K

Lysine
, Lys, K
 

Unique Amino Acids

Glycine, Gly, G

Glycine
, Gly, G
 

Proline, Pro, P

Proline
, Pro, P
 

Properties of Common Amino Acids

 

Name 3-Letter
Symbol
1-Letter
Symbol
Molecular
Weight
Molecular
Formula
Residue
Formula
Residue Weight
(-H2O)
pKa1 pKb2 pKx3 pl4
Alanine Ala A 89.10 C3H7NO2 C3H5NO 71.08 2.34 9.69 6.00
Arginine Arg R 174.20 C6H14N4O2 C6H12N4O 156.19 2.17 9.04 12.48 10.76
Asparagine Asn N 132.12 C4H8N2O3 C4H6N2O2 114.11 2.02 8.80 5.41
Aspartic acid Asp D 133.11 C4H7NO4 C4H5NO3 115.09 1.88 9.60 3.65 2.77
Cysteine Cys C 121.16 C3H7NO2S C3H5NOS 103.15 1.96 10.28 8.18 5.07
Glutamic acid Glu E 147.13 C5H9NO4 C5H7NO3 129.12 2.19 9.67 4.25 3.22
Glutamine Gln Q 146.15 C5H10N2O3 C5H8N2O2 128.13 2.17 9.13 5.65
Glycine Gly G 75.07 C2H5NO2 C2H3NO 57.05 2.34 9.60 5.97
Histidine His H 155.16 C6H9N3O2 C6H7N3O 137.14 1.82 9.17 6.00 7.59
Hydroxyproline Hyp O 131.13 C5H9NO3 C5H7NO2 113.11 1.82 9.65
Isoleucine Ile I 131.18 C6H13NO2 C6H11NO 113.16 2.36 9.60 6.02
Leucine Leu L 131.18 C6H13NO2 C6H11NO 113.16 2.36 9.60 5.98
Lysine Lys
K 146.19 C6H14N2O2 C6H12N2O 128.18 2.18 8.95 10.53 9.74
Methionine Met M 149.21 C5H11NO2S C5H9NOS 131.20 2.28 9.21 5.74
Phenylalanine Phe F 165.19 C9H11NO2 C9H9NO 147.18 1.83 9.13 5.48
Proline Pro P 115.13 C5H9NO2 C5H7NO 97.12 1.99 10.60 6.30
Pyroglutamatic Glp U 139.11 C5H7NO3 C5H5NO2 121.09 5.68
Serine Ser S 105.09 C3H7NO3 C3H5NO2 87.08 2.21 9.15 5.68
Threonine Thr T 119.12 C4H9NO3 C4H7NO2 101.11 2.09 9.10 5.60
Tryptophan Trp W 204.23 C11H12N2O2 C11H10N2O 186.22 2.83 9.39
5.89
Tyrosine Tyr Y 181.19 C9H11NO3 C9H9NO2 163.18 2.20 9.11 10.07 5.66
Valine Val V 117.15 C5H11NO2 C5H9NO 99.13 2.32 9.62 5.96
1 pKa is the negative of the logarithm of the dissociation constant for the -COOH group.
2 pKb is the negative of the logarithm of the dissociation constant for the -NH3 group.
3 pKx is the negative of the logarithm of the dissociation constant for any other group in the molecule.
4 pl is the pH at the isoelectric point.
Reference: D.R. Lide, Handbook of Chemistry and Physics, 72nd Edition, CRC Press, Boca Raton, FL, 1991.

 

Hydrophobicity Index for Common Amino Acids

The hydrophobicity index is a measure of the relative hydrophobicity, or how soluble an amino acid is in water. In a protein, hydrophobic amino acids are likely to be found in the interior, whereas hydrophilic amino acids are likely to be in contact with the aqueous environment.

The values in the table below are normalized so that the most hydrophobic residue is given a value of 100 relative to glycine, which is considered neutral (0 value). The scales were extrapolated to residues which are more hydrophilic than glycine.
 

At pH 2A At pH 7B
Very Hydrophobic
Leu 100 Phe 100
Ile 100 Ile 99
Phe 92 Trp 97
Trp 84 Leu 97
Val 79 Val 76
Met 74 Met 74
Hydrophobic
Cys 52 Tyr 63
Tyr 49 Cys 49
Ala 47 Ala 41
Neutral
Thr 13 Thr 13
Glu 8 His 8
Gly 0 Gly 0
Ser -7 Ser -5
Gln -18 Gln -10
Asp -18    
Hydrophilic
Arg -26 Arg -14
Lys -37 Lys -23
Asn -41 Asn -28
His -42 Glu -31
Pro -46 Pro -46 (used pH 2)
    Asp -55
ApH 2 values: Normalized from Sereda et al., J. Chrom. 676: 139-153 (1994).
BpH 7 values: Monera et al., J. Protein Sci. 1: 319-329 (1995).

Amino Acids Technical Articles

Hayman MW1, Smith KH, Cameron NR, Przyborski SA.
2005 Mar 31;62(3):231-40. Epub 2004 Dec 30.
Understanding neural differentiation and the development of complex neurite networks in three-dimensional matrices is critical for neural tissue engineering in vitro. In this study we describe for the first time the growth of human stem cell-derived neurons on solid polystyrene matrices coated with bioactive molecules. Highly poRead More
Cho IJ1, Ahn JY, Kim S, Choi MS, Ha TY.
2008 Feb 29;367(1):190-4. doi: 10.1016/j.bbrc.2007.12.140. Epub 2007 Dec 31.
We investigated the hypolipidemic effect of resveratrol focused on the mRNA expression and hepatic HMG-CoA reductase (HMGR) activity in hamsters fed a high-fat diet. Male Syrian Golden hamsters were fed a high-fat diet containing 0.025% fenofibrate or 0.025% resveratrol for 8 weeks. The concentrations of serum total cholesterol Read More
Polleux F1, Ghosh A.
2002 Jun 11;2002(136):pl9.
We have developed a technique that allows characterization and identification of extracellular signals that regulate various aspects of neuronal differentiation. In this in vitro assay, dissociated cells isolated from the developing cerebral wall are labeled and cultured over organotypic cortical slices. We have used this slice Read More
Rama Rao KV1, Reddy PV, Tong X, Norenberg MD.
2010 Mar;176(3):1400-8. doi: 10.2353/ajpath.2010.090756. Epub 2010 Jan 14.
Brain edema and the associated increase in intracranial pressure are potentially lethal complications of acute liver failure (ALF). Astrocyte swelling (cytotoxic edema) represents a significant component of the brain edema in ALF, and elevated blood and brain ammonia levels have been strongly implicated in its formation. We earlRead More
Marx M1, Günter RH, Hucko W, Radnikow G, Feldmeyer D.
2012 Feb 2;7(2):394-407. doi: 10.1038/nprot.2011.449.
In this report, we describe a reliable protocol for biocytin labeling of neuronal tissue and diaminobenzidine (DAB)-based processing of brain slices. We describe how to embed tissues in different media and how to subsequently histochemically label the tissues for light or electron microscopic examination. We provide a detailed dRead More