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Protein Structural Analysis
Amino Acids Reference Chart
Section Overview
1pKa is the negative of the logarithm of the dissociation constant for the -COOH group.
2pKb is the negative of the logarithm of the dissociation constant for the -NH3group.
3pKx is the negative of the logarithm of the dissociation constant for any other group in the molecule.
4pl is the pH at the isoelectric point.
Reference: D.R. Lide,Handbook of Chemistry and Physics,72nd Edition, CRC Press, Boca Raton, FL, 1991.
Amino acids are the compounds or building blocks that make up peptides and proteins. Each amino acid is structured from an amino group and a carboxyl group bound to a tetrahedral carbon. This carbon is designated as the α-carbon (alpha-carbon). Amino acids differ from each other with respect to their side chains, which are referred to as R groups. The R group for each of the amino acids will differ in structure, electrical charge, and polarity. Refer to the charts and structures below to explore amino acid properties, types, applications, and availability.Amino Acids by Side Chain
Amino Acids with Hydrophobic Side Chain – Aliphatic
Alanine, Ala, A
Isoleucine, Ile, I
Methionine, Met, M
Valine, Val, V
Amino Acids with Hydrophobic Side Chain – Aromatic
Phenylalanine, Phe, F
Tryptophan, Trp, W
Tyrosine, Tyr, Y
Amino Acids with Polar Neutral Side Chains
Asparagine, Asn, N
Cysteine, Cys, C
Glutamine, Gln, Q
Serine, Ser, S
Threonine, Thr, T
Amino Acids with Electrically Charged Side Chains – Acidic
Aspartic acid, Asp, D
Glutamic acid, Glu, E
Amino Acids with Electrically Charged Side Chains – Basic
Arginine, Arg, R
Histidine, His, H
Lysine, Lys, K
Unique Amino Acids
Glycine, Gly, G
Proline, Pro, P
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.Hydrophobicity Index for Common Amino Acids
ApH 2 values: Normalized from Sereda et al.,J. Chrom.676: 139-153 (1994).
BpH 7 values: Moneraet al.,J. Protein Sci.1: 319-329 (1995).
References
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Hayman M, Smith K, Cameron N, Przyborski S. 2005. Growth of human stem cell-derived neurons on solid three-dimensional polymers. Journal of Biochemical and Biophysical Methods. 62(3):231-240. https://doi.org/10.1016/j.jbbm.2004.12.001
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Cho IJ, Ahn JY, Kim S, Choi MS, Ha TY. 2008. Resveratrol attenuates the expression of HMG-CoA reductase mRNA in hamsters. Biochemical and Biophysical Research Communications. 367(1):190-194. https://doi.org/10.1016/j.bbrc.2007.12.140
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Polleux F, Ghosh A. 2002. The Slice Overlay Assay: A Versatile Tool to Study the Influence of Extracellular Signals on Neuronal Development. Science Signaling. 2002(136):pl9-pl9. https://doi.org/10.1126/stke.2002.136.pl9
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Rama Rao KV, Reddy PV, Tong X, Norenberg MD. 2010. Brain Edema in Acute Liver Failure. The American Journal of Pathology. 176(3):1400-1408. https://doi.org/10.2353/ajpath.2010.090756
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Marx M, Günter RH, Hucko W, Radnikow G, Feldmeyer D. 2012. Improved biocytin labeling and neuronal 3D reconstruction. Nat Protoc. 7(2):394-407. https://doi.org/10.1038/nprot.2011.449
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