Amino Acids - codes, properties and chemical formulas

Name
3-let.
1-let.
 h/p/c
Vol
Propensity 
Freq*
Cont*
ALANINE
ALA
A
h
88.6
alpha
 8.5
 3.1
ARGININE
ARG
R
c
173.4
 
4.6
 2.6
ASPARGINE
ASN
N
p
111.1
 
 4.5
 2.3
ASPARTIC ACID 
ASP
D
c
114.1
 
5.9
2.0
CYSTEINE
CYS
C
h
108.5
S-S bond
 1.7
 4.4
GLUTAMIC ACID
GLU
E
c
138.4
alpha
 6.1
 2.0
GLUTAMINE
GLN
Q
p
143.8
 
 3.7
 2.4
GLYCINE
GLY
G
p
60.1
anti-alpha
 8.1
 2.5
HISTIDINE
HIS
H
h/p/c
153.2
 metal bind.
 2.3
 3.1
ISOLUECINE
ILE
I
h
166.7
 
 5.5
 4.5
LEUCINE
LEU
L
h
166.7
alpha
 8.3
 4.6
LYSINE
LYS
K
c
168.6
 
 6.0
 1.9
METHIONINE
MET
M
h
162.9
alpha
 2.1
 4.2
PHENYLALANINE
PHE
F
h
189.9
 
 3.9
 4.5
PROLINE
PRO
P
h
112.7
start alpha
 4.7
 2.4
SERINE
SER
S
p
89.0
anti-alpha
 6.2
 2.4
THREONINE
THR
T
p
116.1
 
 5.9
 2.8
TRYPTOPHAN
TRP
W
h/p
227.8
 
 1.4
 4.0
TYROSINE
TYR
Y
h/p
193.6
anti-alpha
 3.5
 4.0
VALINE
VAL
V
h
140.0
 
 7.1
 4.2

* Frequency of occuring [in %] and the averaged number of contacts in the first solvation shell calcu-
lated using a combination of Levitt's and SCOP databases, composed of 594 representative structu-
res (the total number of residues is equal to 147129 and the cutoff distances are 2.0 < r < 6.4 Ang) -
see Tobi et. al. 1999


Side chains -
hydrophobic in blue, hydrophilic in red, polar or weakly hydrophilic in violet:

Use appropriate width of the browser window to see it without broken lines ...
 

                                                                                                                                  CH==CH
                                                                                                                                  /             \
GLY  --H        ALA  --CH3       VAL  --CH--CH3       PHE  --CH2--C              CH
                                                                            \                                                     \\           //
                                                                            CH3                                               CH--CH
 

 LEU  --CH2 --CH--CH3       ILE  --CH--CH3       MET  --CH2--CH2--S--CH3
                                 \                                         \
                                  CH3                                   CH2--CH3

             |
 PRO   Ca--CH2                              ARG  --CH2--CH2--CH2--NH--C--NH2
             |          \                                                                                                    ||
                    |               /  CH2                                                                                                                                        NH2+
            N --CH2                                              ASP  --CH2--COO-
             |

 LYS  --CH2--CH2--CH2--CH2--NH3+          GLU  --CH2--CH2--COO-

                                                                                                                                          NH+
                                                                                                                                        /         \\
 ASN  --CH2--C==O        GLN  --CH2--CH2--C==O      HIS  --CH2 --C            CH
                                \                                                          \                                           \\           /
                                 NH2                                                                            NH2                                                     CH--NH

 CYS  --CH2--SH            SER --CH2--OH                        THR --CH2--OH
                                                                                                                             \
                                                                                                                              CH3
                                CH==CH                                                       CH
                                /            \                                                      //         \
 TYR  --CH2--C              C--OH        TRP  --CH2--C             NH
                                \\            //                                                   \            /
                                CH--CH                                                   C == C
                                                                                                   /           \
                                                                                                CH         CH
                                                                                                  \\            //
                                                                                                  CH--CH
 


Collection of Rasmol and Molekel images

Trp    Arg                                                                                              more when I have more time ...


Peptide bond

Dipeptide:                                                                        See also a picture with Ala-Gly-His tripeptide

                                       H         O                 R2
                                        |          ||                  |
                        NH3+--Ca -- C -- N -- Ca -- C --O-
                                                            |                               |              |                    \\
                                                        R1                  H        H             O

The equilibrium length of the peptide bond (C -- N) is about 2 Ang. The average Ca - Ca distance
 in a polypeptide chain is about 3.8 Ang. The angle of rotation around N - Ca bond is called phi, and
the angle around the Ca - C bond is called psi. In polypeptide chain these angles define the overall
conformation of the system  - see myoglobin for instance.


Author: Jarek Meller