Amino acids

From OpenWetWare

(Difference between revisions)
Jump to: navigation, search
m (shrink image)
Current revision (12:36, 7 September 2007) (view source)
 
(2 intermediate revisions not shown.)
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]]
----
----
Line 18: Line 21:
</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 30:
</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 36:
</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 48:
</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 55:
</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 86:
</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 103:
</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 124:
</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 130:
</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 139:
\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)

Current revision

Contents

General

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

chem


Properties of the amino acids

Residue masses

See Peptide Mass Spec Data


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

Alanine (Ala, A)

chem


Arginine (Arg, R) ("aRginine")

chem


Asparagine (Asn, N) ("asparagiNe," "aspartic-NH2")

chem


Aspartate (Asp, D) ("asparDic acid")

chem


Cysteine (Cys, C)

chem


Glutamate (Glu, E) ("glutEmic acid")

chem


Glutamine (Gln, Q) ("Qutamine")

chem


Glycine (Gly, G)

chem


Histidine (His, H)

chem


Isoleucine (Ile, I)

chem


Leucine (Leu, L)

chem


Lysine (Lys, K) ("K" next to "L")

chem


Methionine (Met, M)

chem


Phenylalanine (Phe, F) ("Fenylalanine")

chem


Proline (Pro, P)

chem


Serine (Ser, S)

chem


Threonine (Thr, T)

chem


Tryptophan (Trp, W) ("tWiptophan")

chem


Tyrosine (Tyr, Y) ("tYrosine")

chem


Valine (Val, V)

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)

Personal tools