Difference between revisions of "Amino acids"

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===Properties of the amino acids===
 
===Properties of the amino acids===
 
[[image:Aa_properties.gif|500px]]
 
[[image:Aa_properties.gif|500px]]
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===Residue masses===
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See [[Peptide Mass Spec Data]]
  
 
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Latest revision as of 10:36, 7 September 2007

General

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

Failed to parse (unknown function "\tetrahedral"): {\displaystyle \ce{ \tetrahedral{0==C;1==\utrigonal{0==C;1==(yl);3D==O;2==O$^-$};2==$^+$H$_3$N;3==R;4==H} }}

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)

Failed to parse (MathML with SVG or PNG fallback (recommended for modern browsers and accessibility tools): Invalid response ("Math extension cannot connect to Restbase.") from server "https://api.formulasearchengine.com/v1/":): {\displaystyle \ce{ \tetrahedral{0==C;1==\utrigonal{0==C;1==(yl);3D==O;2==O$^-$};2==$^+$H$_3$N;3==CH$_3$;4==H} }}

Arginine (Arg, R) ("aRginine")

Failed to parse (unknown function "\tetrahedral"): {\displaystyle \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} }}

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

Failed to parse (unknown function "\tetrahedral"): {\displaystyle \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} }}

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

Failed to parse (unknown function "\tetrahedral"): {\displaystyle \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} }}

Cysteine (Cys, C)

Failed to parse (unknown function "\tetrahedral"): {\displaystyle \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} }}

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

Failed to parse (unknown function "\tetrahedral"): {\displaystyle \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} }}

Glutamine (Gln, Q) ("Qutamine")

Failed to parse (unknown function "\tetrahedral"): {\displaystyle \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} }}

Glycine (Gly, G)

Failed to parse (unknown function "\tetrahedral"): {\displaystyle \ce{ \tetrahedral{0==C;1==\utrigonal{0==C;1==(yl);3D==O;2==O$^-$};2==$^+$H$_3$N;3==H;4==H} }}

Histidine (His, H)

Failed to parse (unknown function "\tetrahedral"): {\displaystyle \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} }}

Isoleucine (Ile, I)

Failed to parse (unknown function "\tetrahedral"): {\displaystyle \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} }}

Leucine (Leu, L)

Failed to parse (unknown function "\tetrahedral"): {\displaystyle \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} }}

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

Failed to parse (unknown function "\tetrahedral"): {\displaystyle \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} }}

Methionine (Met, M)

Failed to parse (unknown function "\tetrahedral"): {\displaystyle \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} }}

Phenylalanine (Phe, F) ("Fenylalanine")

Failed to parse (unknown function "\tetrahedral"): {\displaystyle \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} }}

Proline (Pro, P)

Failed to parse (unknown function "\utrigonal"): {\displaystyle \ce{ \utrigonal{0==C;2==O$^-$;3D==O; 1==\fiveheterov{4==$^+$H$_2$N}{3Sb==(yl);3Sa==H}} }}

Serine (Ser, S)

Failed to parse (unknown function "\tetrahedral"): {\displaystyle \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} }}

Threonine (Thr, T)

Failed to parse (unknown function "\tetrahedral"): {\displaystyle \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} }}

Tryptophan (Trp, W) ("tWiptophan")

Failed to parse (unknown function "\tetrahedral"): {\displaystyle \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} }}

Tyrosine (Tyr, Y) ("tYrosine")

Failed to parse (unknown function "\tetrahedral"): {\displaystyle \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} }}

Valine (Val, V)

Failed to parse (unknown function "\tetrahedral"): {\displaystyle \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} }}


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)