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>
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===Properties of the amino acids===
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[[image:Aa_properties.gif|500px]]
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===Residue masses===
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See [[Peptide Mass Spec Data]]
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----
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>
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===Arginine (Arg, R)===
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===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>
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===Asparagine (Asn, N)===
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===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>
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===Aspartate (Asp, D)===
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===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>
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===Glutamate (Glu, E)===
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===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>
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===Glutamine (Gln, Q)===
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===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>
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===Lysine (Lys, K)===
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===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>
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===Phenylalanine (Phe, F)===
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===[[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>
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===Tryptophan (Trp, W)===
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===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>
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===Tyrosine (Tyr, Y)===
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===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>
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==Ambiguity codes and Modification codes==
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===Asx, B ("B" near "D")===
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Either Aspartic acid or Asparagine, uncertainty due to hydrolysis.
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===Xle, J ("J" between "I" and "L")===
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Either Isoleucine or Leucine, ambiguity from Mass spec data
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===Xaa, X===
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Unknown amino acid
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===Glx, Z ("Z" near "X")===
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Either Glutamic acid or Glutamine, uncertainty due to hydrolysis
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===Sec, U===
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Selenocysteine (Uniprot uses C and a feature rather than U)
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===Pyl, O ("pyrrOlysine")===
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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):

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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)

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Arginine (Arg, R) ("aRginine")

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

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

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Cysteine (Cys, C)

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

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Glutamine (Gln, Q) ("Qutamine")

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Glycine (Gly, G)

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Histidine (His, H)

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Isoleucine (Ile, I)

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Leucine (Leu, L)

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

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Methionine (Met, M)

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Phenylalanine (Phe, F) ("Fenylalanine")

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Proline (Pro, P)

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Serine (Ser, S)

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Threonine (Thr, T)

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Tryptophan (Trp, W) ("tWiptophan")

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Tyrosine (Tyr, Y) ("tYrosine")

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Valine (Val, V)

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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)

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