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

net.

EMB

net - Euro pean Molecular B

iology Netw

ork - is a wor ld w

ide bioinform

atics s upport network . M

ost countrie s have a nation al node w

hich can provi de training cour ses and other fo rms of help for users of

bioinformatics s oftw

are.

You can find in formation about your national node from

the E MB

net site:

http://www.embnet.org/

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