Ala (A)Alanine
HA
CA
CB
HB1
HB2
HB3
Arg (R)Arginine
HACA
CB HB1HB2
CGHG1HG2
CD HD1HD2
NEHE
CZ NH1
NH2
HH11
HH12HH22
HH21+
Asn (N)Asparagine
CAHA
CB HB1
HB2CG
OD1
ND2HD21
HD22
Asp (D)Aspartic
Cys (C) Gln (Q)Glu (E) Gly (G)Cysteine GlutamineGlutamic Glycine
His (H)Histidine
+
CAHA
CBHB1HB2
CG
OD1
OD2
CAHAHB2
HB1CB
SG
HG
CAHA
CBHB1HB2
CGHG1HG2
CD OE1NE2
HE21 HE22
CAHA
CB HB1HB2
CGHG1HG2
CDOE1
OE2
CA
HA1HA2
HE1
CE1
HD1NE2
HE2
CD2
HD2CG
CB HB1HB2HA
CA
pKa=2.33 pKa=9.71
pKa=2.03 pKa=9.00
pKa=12.10
pKa=1.95pKa=9.66
pKa=3.71
pKa=2.16
pKa=9.58
pKa=4.15
pKa=2.16 pKa=8.76
pKa=2.18 pKa=9.00pKa=1.91
pKa=10.28
pKa=8.14
pKa=2.34 pKa=9.58
pIE=6.11Pol=0.00OIS=0.33ASA=239.0
pIE=10.76Pol=52.00OIS=1.00ASA=384.1
pIE=10.76Pol=3.38OIS=0.43ASA=293.2
pIE=2.987Pol=49.70OIS=2.41ASA=282.4
pIE=5.02Pol=1.48OIS=0.22ASA=270.2
pIE=5.65Pol=3.53OIS=0.19ASA=320.2
pIE=3.08Pol=49.90OIS=1.61ASA=333.9
pIE=6.06Pol=0.00OIS=1.14ASA=209.6
pIE=7.64Pol=51.60OIS=0.06ASA=333.5
pKa=6.04
H:H
H:H
H:H
H:H
H:H
H:H
H:H
Essential hydrophilic hydrophobic basic acid dipolar neutral aromatic aliphaticionizable
SS
Ile (I)Isoleucine
Leu (L)Leucine
Lys (K)+
CA
CBCG2
CG1
CD
HA
HD1HD2HD3HG12
HG11HG21
HG22HG23
CAHA
CBHB1
HB2
CGHG
CD1
CD2HD11
HD12
HD13
HD21
HD22HD23
Lysine
CAHA
CBHB1
HB2
CGHG1HG2
CDHD1
HD2
CEHE1HE2
NZ
HZ1HZ2
HZ3
pKa=2.15 pKa=9.16
pKa=10.67
pKa=2.26pKa=9.60
pKa=2.32 pKa=9.58
pIE=6.04Pol=0.13OIS=0.81ASA=312.5
pIE=6.06Pol=0.13OIS=0.69ASA=317.7
pIE=9.47Pol=49.50OIS=1.81ASA=358.2
Met (M) Phe (F) Pro (P) Ser (S)
CAHA
CBHB1
HB2
CGHG1HG2
SD
CE
HE1
HE2
HE3
CAHA
CBHB1
HB2
CG
CD1
CD2
HD1
HD2
CE1
CE2
HE1
HE2
CZ
HZ
CA
HA
CB CG
CD
N
HB1
HB2 HG1HG2
HD1
HD2
Methionine Phenylalanine Proline Serine
CA
HA
CB
OG
HG
HB1HB2
pKa=2.13 pKa=9.05
pKa=1.95
pKa=10.47
pKa=2.16 pKa=9.08pKa=2.18
pKa=9.09
pIE=5.74Pol=1.43OIS=0.44ASA=335.1
pIE=5.91Pol=0.35OIS=0.58ASA=359.2
pIE=6.30Pol=1.58OIS=0.31ASA=269.1
pIE=5.68Pol=1.67OIS=0.33ASA=250.1H:H
α
α
γγ
γ
βα
αβ
γ γ
José R. Valverde, 2013
Thr (T) Trp (W) Tyr (Y) Val (V)ValineTyrosineTryptophanThreonine
HE2
CA
HA
CB
HB OGHG1
CG2
HG21
HG22 HG23
pKa=2.20 pKa=8.96CA
HA
CBHB1HB2
CG
CD1
CD2
NE1
CE2
CE3
HD1
CZ2
CZ3
CH2HH2
HZ2
HE1
HZ3 HE3pKa=2.38
pKa=9.34
pKa=2.27
CA
HACB
HB
CG1
CG2
HG11
HG12HG13
HG21
HG22
HG23
pKa=9.52
CA
HA
CB HB1HB2CG
CD1
HD1
CD2
HD2
CE1
HE1
CE2
CZ
OH
HH
pKa=2.24
pKa=9.04
pKa=10.10
pIE=5.60Pol=1.66OIS=0.11ASA=274.9
pIE=5.88Pol=2.10OIS=0.24ASA=414.4
pIE=5.63Pol=1.61OIS=0.23ASA=371.6
pIE=6.02Pol=0.13OIS=0.53ASA=286.3
H:H
H:H
H:H
α: alpha forming
β: beta phorming
γ: turn (gýros) forming
References:
CF78: Chou, Fasman. Adv. Enzym. 47:45
148(1978).
pKa: CRC Handbook of Chemistry, v2010
Pol: Polarity scale. J. Theor. Biol. 21: 170
OIS: (OctanolInterface wholeresidue
hydrophobicity scale) Annu. Rev. Biophys 28:
319
http://blanco.biomol.uci.edu/hydrophobicity_sca
les.html
ASA: Solvent Accessible Surface Area.
http://www.cbi.cnptia.embrapa.br/SMS/STINGm/hel
p/solvent_accessible_area.html
Structural calculations: Electronic density and
properties computed using Semiempirical
Quantum Mechanics with PM6 using MOPAC2009,
James J. P. Stewart, Stewart Computational
Chemistry, vers. 9.069L http://OpenMOPAC.net
Structural graphics: Gabedit. J Comput Chem, 32
(2011) 174
More info
http://sci.cnb.csic.es
This document w
as written and designed by José R
. Valverde
from the Spanish EM
Bnet node (C
NB
/CSIC
) and is being distributed by the P&
PR Project C
omm
ittee of EMB
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A Quick G
uide T o Am
ino Acids
First edition © 2013
License: CCBYNC 3.0
http://creativecommons.org/licenses/bync/
Acknowledgements:
CYTED network 510RT0391
http://cyted.org
http://www.freebit.org
Thanks for comments: EMBnet, G Neshich, G
Vriend, G Bottu
Amino Acids
β βββ