AMINO ACID PROPERTIES AND CHARACTERISTICS
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Entries have the following form:
Amino Acid (Codes), Frequency
Genetic Codons
Substitution Probabilities
Residue Weight(Mr)
Residue Volume(Vr)
Partial Specific Volume(vr)
Hydration(hr)
R-Group pKa
Extinction Coefficient @ maximum wavelength
Units are:
Substitutions (each > sign = factor of 10> than random chance)
Mr (Daltons),
Vr (cubic Angstroms),
vr (cc/g),
hr (moles/mole)
Sources are:
Frequencies: McCaldon & Argos, Proteins 4, 91-122(1988)
Substitutions: Dayhoff, Swartz & Orcutt, Atlas of Protein Sequence
and Structure, Vol. 5, Supplement 3 (1978)
Residue Weight: Cohn & Edsal, Proteins, Amino Acids and Peptides,
Reinhold, New York (1943)
Residue Volume: Creighton, Proteins Structure and Molecular
Properties, W. H. Freeman & Co., NY (1994), p.4
Specific Volume: Cohn & Edsal, ref. cited
Hydration: Bigelow, J. Theoretical Biology 16, 187-211 (1971)
R-Group pKa's: Tanford, Adv. Protein Chem. 17, 69-165 (1962)
Extinction Coefficients: Bailey, Ph.D. Thesis, London University
(1966) as reported by the Handbook of
Biochemistry
Acidic R-groups
(also strong hydrogen and ionic bonding acceptors):
Aspartate (Asp, D), 5.3%
GAU, GAC
E>N Q>G H
Mr = 114.08
Vr = 91
vr = 0.6
hr = 6
pKa = 4.5
Glutamate (Glu, E), 6.2%
GAA, GAG
D > Q > H N
Mr = 128.11
Vr = 109
vr = 0.66
hr = 7.5
pKa = 4.6
Basic R-groups
(also strong hydrogen and ionic bonding donars):
Lysine (Lys , K), 5.7%
AAA, AAG
R >> N Q
Mr = 129.19
Vr = 135
vr = 0.82
hr = 4.5
pKa = 10.4
Arginine (Arg , R), 5.7%
CGU, CGC, CGA, CGG, AGA, AGG
K > W H > Q
Mr = 157.2
Vr = 148
vr = 0.7
hr = 3
pKa = ~12
Histidine (His , H), 2.3%
CAU, CAC
Q > N R > D E
Mr = 138.16
Vr = 118
vr = 0.67
hr = 4
pKa = 6.2
5860 @ 211.3
Polar, Uncharged
(hydrogen bonding, except glycine):
Glycine (Gly , G), 7.2%
GGU, GGC, GGA, GGG
A D S
Mr = 57.07
Vr = 48
vr = 0.64
hr = 1
Serine (Ser , S), 6.9%
UCU, UCC, UCA, UCG, AGU, AGC
A G N P T
Mr = 87.09
Vr = 73
vr = 0.74
hr = 2
Cysteine (Cys , C), 1.7%
UGU, UGC
none
Mr = 103.15
Vr = 86
vr = 0.61
hr = 1
pKa = 9.1 to 9.5
Tyrosine (Tyr , Y), 3.2%
UAU, UAC
F >>>>>>
Mr = 163.12
Vr = 141
vr = 0.61
hr = 3
pKa = 9.6
1420 @ 274.6
Asparagine (Asn , N), 4.4%
AAU, AAC
D H >K
Mr = 114.1
Vr = 96
vr = 0.62
hr = 2
Glutamine (Gln , Q), 4.0%
CAA, CAG
H >D
Mr = 128.14
Vr = 114
vr = 0.67
hr = 2
Non-Polar:
Alanine (Ala , A), 8.3%
GCU, GCC, GCA, GCG
G S T P
Mr = 71.09
Vr = 67
vr = 0.74
hr = 1
Valine (Val , V), 6.6%
GUU, GUC, GUA, GUG
I >>L M >>
Mr = 99.15
Vr = 105
vr = 0.86
hr = 1
Leucine (Leu , L), 9.0%
UUA, UUG, CUU, CUG, CUA, CUG
M >>F I V >>
Mr = 113.18
Vr = 124
vr = 0.90
hr = 1
Proline (Pro ,P), 5.1%
CCU, CCC, CCA, CCG
A S
Mr = 97.13
Vr = 90
vr = 0.76
hr = 3
Phenylalanine (Phe , F), 3.9%
UUU, UUC
Y>>>>>L> I
Mr = 147.19
Vr = 135
vr = 0.77
hr = 0
197 @ 257.4
Tryptophane (Trp , W), 1.3%
UGG
R >
Mr = 186.23
Vr = 163
vr = 0.74
hr = 2
5600 @ 279.8
Methionine (Met , M), 2.4%
AUG
L>> I V>>
Mr = 131.21
Vr = 124
vr = 0.75
hr = 1
ACU, ACC, ACA, ACG
AUU, AUC, AUA