Amino acids - Revision history

Austin J. Che at 17:36, 7 September 2007

2007-09-07T17:36:21Z

←Older revision		Revision as of 17:36, 7 September 2007
Line 8:		Line 8:
	===Properties of the amino acids===		===Properties of the amino acids===
	[[image:Aa_properties.gif\|500px]]		[[image:Aa_properties.gif\|500px]]
		+
		+	===Residue masses===
		+	See [[Peptide Mass Spec Data]]

	----		----

Austin J. Che at 16:12, 6 September 2007

2007-09-06T16:12:44Z

←Older revision		Revision as of 16:12, 6 September 2007
Line 27:		Line 27:
	</chem>		</chem>

-	===Asparagine (Asn, N) ("asparagiNe," "aspartic-NH<sub>2</sub>"===	+	===Asparagine (Asn, N) ("asparagiNe," "aspartic-NH<sub>2</sub>")===
	<chem>		<chem>
	\tetrahedral{0==C;1==\utrigonal{0==C;1==(yl);3D==O;2==O$^-$};2==$^+$H$_3$N;3==\tetrahedral{0==C;1==(yl);2==H;4==H;		\tetrahedral{0==C;1==\utrigonal{0==C;1==(yl);3D==O;2==O$^-$};2==$^+$H$_3$N;3==\tetrahedral{0==C;1==(yl);2==H;4==H;
Line 100:		Line 100:
	</chem>		</chem>

-	===Phenylalanine (Phe, F) ("Fenylalanine")===	+	===[[Phenylalanine]] (Phe, F) ("Fenylalanine")===
	<chem>		<chem>
	\tetrahedral{0==C;1==\utrigonal{0==C;1==(yl);3D==O;2==O$^-$};2==$^+$H$_3$N;3==\tetrahedral{0==C;1==(yl);2==H;4==H;3==\bzdrv{1==(yl)}};4==H}		\tetrahedral{0==C;1==\utrigonal{0==C;1==(yl);3D==O;2==O$^-$};2==$^+$H$_3$N;3==\tetrahedral{0==C;1==(yl);2==H;4==H;3==\bzdrv{1==(yl)}};4==H}

Tk at 18:01, 30 January 2007

2007-01-30T18:01:55Z

←Older revision		Revision as of 18:01, 30 January 2007
Line 18:		Line 18:
	</chem>		</chem>

-	===Arginine (Arg, R)===	+	===Arginine (Arg, R) ("aRginine")===
	<chem>		<chem>
	\tetrahedral{0==C;1==\utrigonal{0==C;1==(yl);3D==O;2==O$^-$};2==$^+$H$_3$N;3==\tetrahedral{0==C;1==(yl);2==H;4==H;		\tetrahedral{0==C;1==\utrigonal{0==C;1==(yl);3D==O;2==O$^-$};2==$^+$H$_3$N;3==\tetrahedral{0==C;1==(yl);2==H;4==H;
Line 27:		Line 27:
	</chem>		</chem>

-	===Asparagine (Asn, N)===	+	===Asparagine (Asn, N) ("asparagiNe," "aspartic-NH<sub>2</sub>"===
	<chem>		<chem>
	\tetrahedral{0==C;1==\utrigonal{0==C;1==(yl);3D==O;2==O$^-$};2==$^+$H$_3$N;3==\tetrahedral{0==C;1==(yl);2==H;4==H;		\tetrahedral{0==C;1==\utrigonal{0==C;1==(yl);3D==O;2==O$^-$};2==$^+$H$_3$N;3==\tetrahedral{0==C;1==(yl);2==H;4==H;
Line 33:		Line 33:
	</chem>		</chem>

-	===Aspartate (Asp, D)===	+	===Aspartate (Asp, D) ("asparDic acid")===
	<chem>		<chem>
	\tetrahedral{0==C;1==\utrigonal{0==C;1==(yl);3D==O;2==O$^-$};2==$^+$H$_3$N;3==\tetrahedral{0==C;1==(yl);2==H;4==H;		\tetrahedral{0==C;1==\utrigonal{0==C;1==(yl);3D==O;2==O$^-$};2==$^+$H$_3$N;3==\tetrahedral{0==C;1==(yl);2==H;4==H;
Line 45:		Line 45:
	</chem>		</chem>

-	===Glutamate (Glu, E)===	+	===Glutamate (Glu, E) ("glutEmic acid")===
	<chem>		<chem>
	\tetrahedral{0==C;1==\utrigonal{0==C;1==(yl);3D==O;2==O$^-$};2==$^+$H$_3$N;3==\tetrahedral{0==C;1==(yl);2==H;4==H;		\tetrahedral{0==C;1==\utrigonal{0==C;1==(yl);3D==O;2==O$^-$};2==$^+$H$_3$N;3==\tetrahedral{0==C;1==(yl);2==H;4==H;
Line 52:		Line 52:
	</chem>		</chem>

-	===Glutamine (Gln, Q)===	+	===Glutamine (Gln, Q) ("Qutamine")===
	<chem>		<chem>
	\tetrahedral{0==C;1==\utrigonal{0==C;1==(yl);3D==O;2==O$^-$};2==$^+$H$_3$N;3==\tetrahedral{0==C;1==(yl);2==H;4==H;		\tetrahedral{0==C;1==\utrigonal{0==C;1==(yl);3D==O;2==O$^-$};2==$^+$H$_3$N;3==\tetrahedral{0==C;1==(yl);2==H;4==H;
Line 83:		Line 83:
	</chem>		</chem>

-	===Lysine (Lys, K)===	+	===Lysine (Lys, K) ("K" next to "L")===
	<chem>		<chem>
	\tetrahedral{0==C;1==\utrigonal{0==C;1==(yl);3D==O;2==O$^-$};2==$^+$H$_3$N;3==\tetrahedral{0==C;1==(yl);2==H;4==H;		\tetrahedral{0==C;1==\utrigonal{0==C;1==(yl);3D==O;2==O$^-$};2==$^+$H$_3$N;3==\tetrahedral{0==C;1==(yl);2==H;4==H;
Line 100:		Line 100:
	</chem>		</chem>

-	===Phenylalanine (Phe, F)===	+	===Phenylalanine (Phe, F) ("Fenylalanine")===
	<chem>		<chem>
	\tetrahedral{0==C;1==\utrigonal{0==C;1==(yl);3D==O;2==O$^-$};2==$^+$H$_3$N;3==\tetrahedral{0==C;1==(yl);2==H;4==H;3==\bzdrv{1==(yl)}};4==H}		\tetrahedral{0==C;1==\utrigonal{0==C;1==(yl);3D==O;2==O$^-$};2==$^+$H$_3$N;3==\tetrahedral{0==C;1==(yl);2==H;4==H;3==\bzdrv{1==(yl)}};4==H}
Line 121:		Line 121:
	</chem>		</chem>

-	===Tryptophan (Trp, W)===	+	===Tryptophan (Trp, W) ("tWiptophan")===
	<chem>		<chem>
	\tetrahedral{0==C;1==\utrigonal{0==C;1==(yl);3D==O;2==O$^-$};2==$^+$H$_3$N;3==\tetrahedral{0==C;1==(yl);2==H;4==H;		\tetrahedral{0==C;1==\utrigonal{0==C;1==(yl);3D==O;2==O$^-$};2==$^+$H$_3$N;3==\tetrahedral{0==C;1==(yl);2==H;4==H;
Line 127:		Line 127:
	</chem>		</chem>

-	===Tyrosine (Tyr, Y)===	+	===Tyrosine (Tyr, Y) ("tYrosine")===
	<chem>		<chem>
	\tetrahedral{0==C;1==\utrigonal{0==C;1==(yl);3D==O;2==O$^-$};2==$^+$H$_3$N;3==\tetrahedral{0==C;1==(yl);2==H;4==H;3==\bzdrv{1==(yl);4==OH}};4==H}		\tetrahedral{0==C;1==\utrigonal{0==C;1==(yl);3D==O;2==O$^-$};2==$^+$H$_3$N;3==\tetrahedral{0==C;1==(yl);2==H;4==H;3==\bzdrv{1==(yl);4==OH}};4==H}
Line 136:		Line 136:
	\tetrahedral{0==C;1==\utrigonal{0==C;1==(yl);3D==O;2==O$^-$};2==$^+$H$_3$N;3==\dtrigonal{0==CH;1==(yl);2==CH$_3$;3==H$_3$C};4==H}		\tetrahedral{0==C;1==\utrigonal{0==C;1==(yl);3D==O;2==O$^-$};2==$^+$H$_3$N;3==\dtrigonal{0==CH;1==(yl);2==CH$_3$;3==H$_3$C};4==H}
	</chem>		</chem>
		+
		+
		+	==Ambiguity codes and Modification codes==
		+
		+	===Asx, B ("B" near "D")===
		+	Either Aspartic acid or Asparagine, uncertainty due to hydrolysis.
		+
		+
		+	===Xle, J ("J" between "I" and "L")===
		+	Either Isoleucine or Leucine, ambiguity from Mass spec data
		+
		+	===Xaa, X===
		+	Unknown amino acid
		+
		+	===Glx, Z ("Z" near "X")===
		+	Either Glutamic acid or Glutamine, uncertainty due to hydrolysis
		+
		+	===Sec, U===
		+	Selenocysteine (Uniprot uses C and a feature rather than U)
		+
		+	===Pyl, O ("pyrrOlysine")===
		+	Pyrrolysine (Uniprot uses K and a feature rather than O)

Austin J. Che: shrink image

2006-08-09T01:28:14Z

shrink image

←Older revision		Revision as of 01:28, 9 August 2006
Line 7:		Line 7:

	===Properties of the amino acids===		===Properties of the amino acids===
-	[[image:Aa_properties.gif]]	+	[[image:Aa_properties.gif\|500px]]

	----		----

Tk at 00:38, 9 August 2006

2006-08-09T00:38:15Z

←Older revision		Revision as of 00:38, 9 August 2006
Line 5:		Line 5:
	\tetrahedral{0==C;1==\utrigonal{0==C;1==(yl);3D==O;2==O$^-$};2==$^+$H$_3$N;3==R;4==H}		\tetrahedral{0==C;1==\utrigonal{0==C;1==(yl);3D==O;2==O$^-$};2==$^+$H$_3$N;3==R;4==H}
	</chem>		</chem>
		+
		+	===Properties of the amino acids===
		+	[[image:Aa_properties.gif]]
		+
		+	----

	The 20 common amino acids are (with 3 letter and 1 letter abbreviations):		The 20 common amino acids are (with 3 letter and 1 letter abbreviations):

Austin J. Che at 17:01, 20 July 2006

2006-07-20T17:01:48Z

New page

===General===
Amino acids are of the general form (R represents any group):

<chem>
\tetrahedral{0==C;1==\utrigonal{0==C;1==(yl);3D==O;2==O$^-$};2==$^+$H$_3$N;3==R;4==H}
</chem>

The 20 common amino acids are (with 3 letter and 1 letter abbreviations):

===Alanine (Ala, A)===
<chem>
\tetrahedral{0==C;1==\utrigonal{0==C;1==(yl);3D==O;2==O$^-$};2==$^+$H$_3$N;3==CH$_3$;4==H}
</chem>

===Arginine (Arg, R)===
<chem>
\tetrahedral{0==C;1==\utrigonal{0==C;1==(yl);3D==O;2==O$^-$};2==$^+$H$_3$N;3==\tetrahedral{0==C;1==(yl);2==H;4==H;
3==\tetrahedral{0==C;1==(yl);2==H;4==H;
3==\tetrahedral{0==C;1==(yl);2==H;4==H;
3==\tetrahedral{0==N;1==(yl);2==H;
3==\dtrigonal{0==C;1==(yl);2==NH$_2$;3D==$^+$NH$_2$}}}}};4==H}
</chem>

===Asparagine (Asn, N)===
<chem>
\tetrahedral{0==C;1==\utrigonal{0==C;1==(yl);3D==O;2==O$^-$};2==$^+$H$_3$N;3==\tetrahedral{0==C;1==(yl);2==H;4==H;
3==\dtrigonal{0==C;1==(yl);2==NH$_2$;3D==O}};4==H}
</chem>

===Aspartate (Asp, D)===
<chem>
\tetrahedral{0==C;1==\utrigonal{0==C;1==(yl);3D==O;2==O$^-$};2==$^+$H$_3$N;3==\tetrahedral{0==C;1==(yl);2==H;4==H;
3==\dtrigonal{0==C;1==(yl);2==O$^-$;3D==O}};4==H}
</chem>

===Cysteine (Cys, C)===
<chem>
\tetrahedral{0==C;1==\utrigonal{0==C;1==(yl);3D==O;2==O$^-$};2==$^+$H$_3$N;3==\tetrahedral{0==C;1==(yl);2==H;4==H;
3==SH};4==H}
</chem>

===Glutamate (Glu, E)===
<chem>
\tetrahedral{0==C;1==\utrigonal{0==C;1==(yl);3D==O;2==O$^-$};2==$^+$H$_3$N;3==\tetrahedral{0==C;1==(yl);2==H;4==H;
3==\tetrahedral{0==C;1==(yl);2==H;4==H;
3==\dtrigonal{0==C;1==(yl);2==O$^-$;3D==O}}};4==H}
</chem>

===Glutamine (Gln, Q)===
<chem>
\tetrahedral{0==C;1==\utrigonal{0==C;1==(yl);3D==O;2==O$^-$};2==$^+$H$_3$N;3==\tetrahedral{0==C;1==(yl);2==H;4==H;
3==\tetrahedral{0==C;1==(yl);2==H;4==H;
3==\dtrigonal{0==C;1==(yl);2==NH$_2$;3D==O}}};4==H}
</chem>

===Glycine (Gly, G)===
<chem>
\tetrahedral{0==C;1==\utrigonal{0==C;1==(yl);3D==O;2==O$^-$};2==$^+$H$_3$N;3==H;4==H}
</chem>

===Histidine (His, H)===
<chem>
\tetrahedral{0==C;1==\utrigonal{0==C;1==(yl);3D==O;2==O$^-$};2==$^+$H$_3$N;3==\tetrahedral{0==C;1==(yl);2==H;4==H;
3==\fiveheteroh[ac]{1==CH;2==NH$^+$;3==C;4==HC;5==NH}{3==(yl)}};4==H}
</chem>

===Isoleucine (Ile, I)===
<chem>
\tetrahedral{0==C;1==\utrigonal{0==C;1==(yl);3D==O;2==O$^-$};2==$^+$H$_3$N;3==\tetrahedral{0==C;1==(yl);4==CH$_3$;2==H;
3==\tetrahedral{0==C;1==(yl);2==H;4==H;
3==CH$_3$}};4==H}
</chem>

===Leucine (Leu, L)===
<chem>
\tetrahedral{0==C;1==\utrigonal{0==C;1==(yl);3D==O;2==O$^-$};2==$^+$H$_3$N;3==\tetrahedral{0==C;1==(yl);2==H;4==H;
3==\dtrigonal{0==CH;1==(yl);2==CH$_3$;3==H$_3$C}};4==H}
</chem>

===Lysine (Lys, K)===
<chem>
\tetrahedral{0==C;1==\utrigonal{0==C;1==(yl);3D==O;2==O$^-$};2==$^+$H$_3$N;3==\tetrahedral{0==C;1==(yl);2==H;4==H;
3==\tetrahedral{0==C;1==(yl);2==H;4==H;
3==\tetrahedral{0==C;1==(yl);2==H;4==H;
3==\tetrahedral{0==C;1==(yl);2==H;4==H;
3==NH$_3^+$}}}};4==H}
</chem>

===Methionine (Met, M)===
<chem>
\tetrahedral{0==C;1==\utrigonal{0==C;1==(yl);3D==O;2==O$^-$};2==$^+$H$_3$N;3==\tetrahedral{0==C;1==(yl);2==H;4==H;
3==\tetrahedral{0==C;1==(yl);2==H;4==H;
3==\tetrahedral{0==S;1==(yl);
3==CH$_3$}}};4==H}
</chem>

===Phenylalanine (Phe, F)===
<chem>
\tetrahedral{0==C;1==\utrigonal{0==C;1==(yl);3D==O;2==O$^-$};2==$^+$H$_3$N;3==\tetrahedral{0==C;1==(yl);2==H;4==H;3==\bzdrv{1==(yl)}};4==H}
</chem>

===Proline (Pro, P)===
<chem>
\utrigonal{0==C;2==O$^-$;3D==O;
1==\fiveheterov{4==$^+$H$_2$N}{3Sb==(yl);3Sa==H}}
</chem>

===Serine (Ser, S)===
<chem>
\tetrahedral{0==C;1==\utrigonal{0==C;1==(yl);3D==O;2==O$^-$};2==$^+$H$_3$N;3==\tetrahedral{0==C;1==(yl);2==H;4==H;3==OH};4==H}
</chem>

===Threonine (Thr, T)===
<chem>
\tetrahedral{0==C;1==\utrigonal{0==C;1==(yl);3D==O;2==O$^-$};2==$^+$H$_3$N;3==\tetrahedral{0==C;1==(yl);2==H;3==CH$_3$;4==OH};4==H}
</chem>

===Tryptophan (Trp, W)===
<chem>
\tetrahedral{0==C;1==\utrigonal{0==C;1==(yl);3D==O;2==O$^-$};2==$^+$H$_3$N;3==\tetrahedral{0==C;1==(yl);2==H;4==H;
3==\nonaheteroh[bjge]{1==N}{1==H;2Sb==H;3==(yl)}};4==H}
</chem>

===Tyrosine (Tyr, Y)===
<chem>
\tetrahedral{0==C;1==\utrigonal{0==C;1==(yl);3D==O;2==O$^-$};2==$^+$H$_3$N;3==\tetrahedral{0==C;1==(yl);2==H;4==H;3==\bzdrv{1==(yl);4==OH}};4==H}
</chem>

===Valine (Val, V)===
<chem>
\tetrahedral{0==C;1==\utrigonal{0==C;1==(yl);3D==O;2==O$^-$};2==$^+$H$_3$N;3==\dtrigonal{0==CH;1==(yl);2==CH$_3$;3==H$_3$C};4==H}
</chem>