- _ f

p1(, values
Abbreviation/
Amino acid symbol
Ph IKz
M,* (-C00H) (-N$)
Hydropathy 0ccu:rencein
indexr proteins (%)*
PKn
(R group) pI
Nonpolar, aliphatic
R groups
Glycine
Alanine
Proline
Valine
Leucine
Isoleucine
Methionine
Aromatic
R groups
Phenylalanine
$'rosine
TYylgtophan
Polar, uncharged
R groups
Serine
Threonine
Cysteines
Asparagine
Glutamine
Gly G
Ala A
Pro P
Vai V
Leu L
Ile I
Met M
Phe F
lyr Y
Tlp W
Ser S
Thr T
Cys C
Asn N
Gln
Q
Lys K
His H
Arg R
Asp D
GIu E
10. 53
6. 00
12.48
, J. Oi )
4.25
75
89
115
IT7
131
131
149
l 0D
181
204
105
119
1.21.
B2
r46
\ 46
155
\74
133
1 4 . 7
2. 34
2. 34
1. 99
2. 32
2. 36
236
2. 28
1. 83
2. 20
2. 38
2. 21
2. TI
1. 96
2.02
2. 17
2. r 8
L. 82
2. t 7
1. 88
2. r 9
9. 60
9. 69
10. 96
9.62
9. 60
9.68
9. 2\
9. 13
9. 1 1
9. 39
9. 15
962
r0.28
880
9. r 3
8. 95
Lr 7
904
960
967
5. 97
6. 01
6.48
5. 97
5. 98
6. 02
D . t +
-0.4
1. 8
1. 6
4.2
3. 8
4. 5
1 q
2. 8
-
1. 3
- 0. 9
-0. 8
-0.7
9 t r ,
- 3. 5
7. 2
7. 8
5. 2
6. 6
9. 1
i ). . 1
2. 3
3. 9
o- a
) . 4
6. 8
5. 9
1. 9
+. o
4. 2
Z . J
5. 1
K A
o..t
5. 48
D. 00
5.89
Positively charged
R groups
I rrqi n e
Histidine
Arginine
10. 07
818
D. Od
5. 87
5.07
5. 4r
5.65
9.74
7.59
10. 76
2. 77
3. 22
_ a o
_
J . L
Negatively charged
R groups
Aspartate
Glutamate
+M/val ues
refl ect the structures as shown i n Fi gure 3-5.The el ements of water (M,78) arc del eted when the ami no aci d i s
i ncorporated i nto a pol ypepti de.
tA
scal e combi ni ng hydrophobi ci ty and hydrophi l i ci ty of R groups. The val ues refl ect the free energy (AG) of transfer of the ami no
aci d si de chai n from a hydrophobi c sol vent to water. Thi s transfer i s favorabl e (AG < 0; negati ve val ue i n the i ndex) for charged
or pol ar ami no aci d si de charns, and unfavorabl e (AG > 0; posi ti ve val ue i n the i ndex) for ami no aci ds wi th nonpol ar or more
hydr ophobi csi dechai ns SeeChapt er l l . Fr omKyt e, J &Dool i t t l e, R. E( 1982) Asi mpl emet hodf or di spl ayi ngt hehydr opat hi c
character of a protei n. J. Mol . Bi ol . 157, 105- 132.
fAverage
occunence i n more than 1,150 protei ns. From Dool i ttl e, R.E (1989) Redundanci es i n protei n sequences.l n Predi cti on
of Protein Structure and the Pilnciples of Protein Confornation (Fasman, G.D., ed
),
pp 599-623, Plenum Press, NewYork.
Scystei ne
i s general l y cl assi fi ed as pol ar despi te havi ng a posi ti ve hydropathy i ndex. Thi s refl ects the abi l i ty of the sul fhydryl
group t0 act as a weak aci d and to form a weak hydrogen bond wi th oxygen or ni trogen
(see Fig. 1-19). All molecules
"r/ith
a chiral center are
also optically active-that is, they rotate plane-
polarized light (see Box 1-2).
KEY C0NVENTI0N: I\.vo conventi ons are used to i denti fy
the carbons in an amino acid-a Dractice that can be
confusing. The additional carbons in an R group are
commonly designated
B , 7,6,
E, and so forth, proceeding
out from the a carbon. For most other organic mole-
cules, carbon atoms are simply numbered from one end,
giving highest priority (C-1) to the carbon with the sub-
stituent containing the atom of highest atomic number.