اسیدهای آمینه - خواص فیزیکی و شیمیایی

1. General information

   Chemical structures

   IUPAC naming convention

   Protecting groups

   Protecting groups (by amino acid)

   Solvent accessibility

   Post-translation modifications

2. Suggested amino acid substitutions

   for solvent exposed residues	for interior residues
   based on the Dayhoff matrix	the PAM250 matrix
   scoring matrix comparison

3. Physico-Chemical properties

   Chemical classifications	Hydrophobicity scales
   Residue volume, area and pKa	Solubility, density and pI

4. Structural properties

   Peptide bond geometry	Chou-Fasman parameters
   Bond angles	Residue hydrogen bonding

5. Genetic properties

   The genetic code	Genetic code (non-cannonical)
   Mutation mass shifts	Nucleotide naming conventions

6. References
7. Authors

Amino Acid Physical Properties

Amino acids are the building blocks of peptides and proteins, and while they all have common elements of an amine group, a carboxyl group and a side chain, the various functional groups that comprise the side chain give each amino acid distinct physical properties that influence protein formation and function. Understanding these physical properties, including charge, solubility and pKa, aid in designing peptide sequences that are optimized for high synthesis yield and purity. To simplify the handling of peptide sequences, each amino acid has a designated single-letter code. The table below includes the single-letter codes and physical properties of the 20 standard amino acids. Amino acid physical properties. Amino Acid Code Hydropathy Charge pKa, NH2 pKa, COOH pK(R) Solubility Arginine R hydrophilic + 9.09 2.18 13.2 71.8 Asparagine N hydrophilic N 8.8 2.02   2.4 Aspartate D hydrophilic - 9.6 1.88 3.65 0.42 Glutamate E hydrophilic - 9.67 2.19 4.25 0.72 Glutamine Q hydrophilic N 9.13 2.17   2.6 Lysine K hydrophilic + 10.28 8.9 2.2   Serine S hydrophilic N 9.15 2.21   36.2 Threonine T hydrophilic N 9.12 2.15   freely Cysteine C moderate N 10.78 1.71 8.33 freely Histidine H moderate + 8.97 1.78 6 4.19 Methionine M moderate N 9.21 2.28   5.14 Alanine A hydrophobic N 9.87 2.35   15.8 Valine V hydrophobic N 9.72 2.29   5.6 Glycine G hydrophobic N 9.6 2.34   22.5 Isoleucine I hydrophobic N 9.76 2.32   3.36 Leucine L hydrophobic N 9.6 2.36   2.37 Phenylalanine F hydrophobic N 9.24 2.58   2.7 Proline P hydrophobic N 10.6 1.99   1.54 Tryptophan W hydrophobic N 9.39 2.38   1.06 Tyrosine Y hydrophobic N 9.11 2.2 10.1 0.038

Hydrophobic - aliphatic Hydrophobic - aromatic Neutral - polar side chains Acidic Basic Unique Properties of Common Amino Acids Hydrophobicity Index   Amino Acids with Hydrophobic Side Chain - Aliphatic   Alanine, Ala, A Isoleucine, Ile, I Leucine, Leu, L Valine, Val, V back to top Amino Acids with Hydrophobic Side Chain - Aromatic   Phenylalanine, Phe, F Tryptophan, Trp, W Tyrosine, Tyr, Y back to top Amino Acids with Polar Neutral Side Chains   Asparagine, Asn, N Cysteine, Cys, C Glutamine, Gln, Q Methionine, Met, M Serine, Ser, S Threonine, Thr, T back to top Amino Acids with Electricaly Charged Side Chains - Acidic   Aspartic acid, Asp, D Glutamic acid, Glu, E back to top Amino Acids with Electricaly Charged Side Chains - Basic   Arginine, Arg, R Histidine, His, H Lysine, Lys, K back to top Unique Amino Acids   Glycine, Gly, G Proline, Pro, P back to top Properties of Common Amino Acids back to top

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.

 Amino acids

• IMGT classes of the 20 common amino acids
• Charge, hydrogen donor and acceptor atoms, and polarity of the amino acid side chains
• Formula of the 20 common amino acids and structural details of the side chains

        Amino acid abbreviations, characteristics, volume and   
        hydropathy index

Click on the 3 letter abbreviations for GIF image (IMB, Jena, Germany).

1. Da: Dalton
2. 1 Da = 1.66x10-24g (1 Dalton is the unit of mass defined as one twelfth of the mass of the carbon atom ¹²C, that is 12/12N gram or 1/N gram).
3. N (Avogadro number) = 6.023 x 1023. N (Avogadro number) = 6.023 x 10²³. A team of the Physikalisch-Technische Bundesanstalt Braunschweig (Office fédéral allemand de métrologie de Brunswick) has determined, in 2003, a new value of the Avogadro number :
   NA ≈ 6,0221353 x 1023 mol-1
4. One Dalton is more or less equivalent to the mass of one hydrogen atom. The molecular mass, in Daltons, of a molecule is the mass of the atoms by reference to hydrogen.
   The mean molecular mass of an amino acid is 136.75 Da.
5. The mean number of atoms per amino acid is 19.20.
6. A polypeptide chain of 1kDa corresponds approximately to 8.42 amino acid residues (118.75 Da, 16.20 atoms) and to 136 atoms.
7. Å3: Angström³

Formula of the 20 common amino acids and structural details of the side chains

• Formula of the 20 common amino acids
• Structural details of the side chains: formula, 3D model and atoms nomenclature

Formula of the 20 common amino acids

The formula of an amino acid comprises, bound to a carbon (alpha carbon):

• a carboxyl group -COOH
• an amine group -NH2
• an atom of hydrogen -H
• a variable radical -R, that is the functional group (in red in the table) of the amino acid.

Chemically speaking, an amino acid is a carboxylic acid which has an amine group attached to it. The general linear formula of an amino acid is R-CH(NH2)-COOH.

The 20 common amino acids are grouped in classes according to their side chains:

Click here for IMGT classes of the 20 common amino acids 'Physicochemical' properties.

Structural formula

Amino acids with uncharged side chains

POLAR SIDE CHAINS		NON POLAR SIDE CHAINS
SERINE		GLYCINE
THREONINE		ALANINE
TYROSINE		CYSTEINE (1)
ASPARAGINE		VALINE
GLUTAMINE		LEUCINE
		ISOLEUCINE
		PROLINE
		METHIONINE
		PHENYLALANINE
		TRYPTOPHAN

Amino acids with charged side chains

Charged side chains are POLAR.

ACIDIC SIDE CHAINS		BASIC SIDE CHAINS
ASPARTIC ACID		LYSINE
GLUTAMIC ACID		ARGININE
		HISTIDINE

1. ⁽¹⁾ Paired cysteines allow disulfide bonds to form in proteins: -CH2-S-S-CH2-

Molecular and linear formulas

The general formula of an amino acid is composed by a carbon alpha atom, a carboxyl group, a side chain group and an amino group.

 لینک واحد اتمی Atomic mass unit

تبدیل واحداتمی به دالتون amu to Dalton units