Difference between revisions of "Amino acids"

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\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|500px]]
 +
 +
===Residue masses===
 +
See [[Peptide Mass Spec Data]]
 +
 +
----
  
 
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):
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</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;
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</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;
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</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;
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</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;
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</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;
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</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;
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</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}
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</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;
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</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}
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\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)

Latest revision as of 09:36, 7 September 2007

General

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

[math]\ce{ \tetrahedral{0==C;1==\utrigonal{0==C;1==(yl);3D==O;2==O$^-$};2==$^+$H$_3$N;3==R;4==H} }[/math]

Properties of the amino acids

Aa properties.gif

Residue masses

See Peptide Mass Spec Data


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

Alanine (Ala, A)

[math]\ce{ \tetrahedral{0==C;1==\utrigonal{0==C;1==(yl);3D==O;2==O$^-$};2==$^+$H$_3$N;3==CH$_3$;4==H} }[/math]

Arginine (Arg, R) ("aRginine")

[math]\ce{ \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} }[/math]

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

[math]\ce{ \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} }[/math]

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

[math]\ce{ \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} }[/math]

Cysteine (Cys, C)

[math]\ce{ \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} }[/math]

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

[math]\ce{ \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} }[/math]

Glutamine (Gln, Q) ("Qutamine")

[math]\ce{ \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} }[/math]

Glycine (Gly, G)

[math]\ce{ \tetrahedral{0==C;1==\utrigonal{0==C;1==(yl);3D==O;2==O$^-$};2==$^+$H$_3$N;3==H;4==H} }[/math]

Histidine (His, H)

[math]\ce{ \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} }[/math]

Isoleucine (Ile, I)

[math]\ce{ \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} }[/math]

Leucine (Leu, L)

[math]\ce{ \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} }[/math]

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

[math]\ce{ \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} }[/math]

Methionine (Met, M)

[math]\ce{ \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} }[/math]

Phenylalanine (Phe, F) ("Fenylalanine")

[math]\ce{ \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} }[/math]

Proline (Pro, P)

[math]\ce{ \utrigonal{0==C;2==O$^-$;3D==O; 1==\fiveheterov{4==$^+$H$_2$N}{3Sb==(yl);3Sa==H}} }[/math]

Serine (Ser, S)

[math]\ce{ \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} }[/math]

Threonine (Thr, T)

[math]\ce{ \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} }[/math]

Tryptophan (Trp, W) ("tWiptophan")

[math]\ce{ \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} }[/math]

Tyrosine (Tyr, Y) ("tYrosine")

[math]\ce{ \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} }[/math]

Valine (Val, V)

[math]\ce{ \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} }[/math]


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)