Amino acids
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
Residue masses
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)
