Lysine

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.

Lysine

Name

3 Letter

1 Letter

Lysine

LYS

Unprotonated (base form - neutral)
lysine

Protonated (acid form - positively charged)
dominant in water

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 in H₂O= 9

Free amino acid Mass = 146 g/M

Probability of being found in a:

α-Helix

β-Sheet

β-Turn

75%

50%

60%

Special Attributes

This amino acid sidechain ends with a primary amine which is generally protonated and ionized (positively) at physiological pH.

The charge means that it is usually on the surface of a water soluble protein where it is exposed to water

In the demonstration below the lysine is at the beginning of an α-helix and interestingly the terminal amine group in this particular case does not appear to be sticking out into water - but rather looks to be buried in the protein... such is the way

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/