Alanine

Atom Label Key

Naming Convention for α-amino acids

The Organic acid carbon is labled the acid.
Each carbon afterwards is labeled in order by the greek alphabet
α, β, γ, δ, ε, etc.
Every atom is labeled by element type and then its position ie. the alpha carbon is CA; the beta carbon is CB

Atom Label	Description

C	Main chain Carbon of amide/acid
CA	Main chain α carbon
N	Main chain nitrogen of amide/amine
O	Main chain Oxygen of amide/acid
H	Main chain hydrogen of amide
HA	Main chain hydrogen of on the α carbon
CB	β Carbon, first carbon of the sidechain
HB?	Hydrogen on the β Carbon. '?' is a number 1,2 or 3
OG	Oxygen on the β Carbon.
CG?	γ Carbon. - the '?' if present is a number 1 or 2

The results are shown. The H from the -OH group on C6 is now on the amino acid side chain. The phosphate group has been transferred to the alcohol carbon of glucose and ADP is the other product.

Alanine

Name

3 Letter

1 Letter

Alanine

ALA

Drawn as if part of protein to emphasize the sidechain properties

The "Sidechain Polarity" button draws an an envelope around the sidechain that is colored by charge according to the scale above.

pK_R= not ionizable under physiological conditions

Free amino acid mass = 89 g/M

Probability of being found in a:

α-Helix

β-Sheet;

β-Turn

90%

50%

30%

Special Attributes

A strong helix forming amino acid. side chain is hydrophobic and not ionizable

Have some tendency to be buried inside water soluble proteins

in the demonstration below The highlighted ALA is in a β-turn and is hidden away from water inside the protein structure

In the demonstration below you may "left click and drag" to rotate the molecule "SHIFT left click and drag (up or down)" to make smaller or bigger
Click on the white squares in succession to turn or/off identifying features. Some text describing the issues is in the lower right text box

	Atom Label Description
	Click an atom to diplay it's identity here
	Messages about the currently highlighted features

Jmol: an open-source Java viewer for chemical structures in 3D. http://www.jmol.org/