Amino acids
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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) | ||
Revision as of 14:01, 30 January 2007
General
Amino acids are of the general form (R represents any group):
Properties of the amino acids
The 20 common amino acids are (with 3 letter and 1 letter abbreviations):
Alanine (Ala, A)
Arginine (Arg, R) ("aRginine")
Asparagine (Asn, N) ("asparagiNe," "aspartic-NH2"
Aspartate (Asp, D) ("asparDic acid")
Cysteine (Cys, C)
Glutamate (Glu, E) ("glutEmic acid")
Glutamine (Gln, Q) ("Qutamine")
Glycine (Gly, G)
Histidine (His, H)
Isoleucine (Ile, I)
Leucine (Leu, L)
Lysine (Lys, K) ("K" next to "L")
Methionine (Met, M)
Phenylalanine (Phe, F) ("Fenylalanine")
Proline (Pro, P)
Serine (Ser, S)
Threonine (Thr, T)
Tryptophan (Trp, W) ("tWiptophan")
Tyrosine (Tyr, Y) ("tYrosine")
Valine (Val, V)
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)
