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 calculated using a combination of Levitt's and SCOP databases derived by Tobi and Elber and composed of 594 representative structures (the total number of residues is equal to 147129 and the cutoff distances were 2.0 < r < 6.4 Ang) database included in the distribution of LOOPP.


Side chains:

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