By following the instructions on this page, you can view the 3D structure of all of the following amino acids

  1. Install a 3D molecular structure viewer on your machine if you do not already have one.
    Our system supports Cn3D from the NCBI, Rasmol and Kinemage.
  2. If you have installed Cn3D, download this file and place it in the Cn3D data directory. It will replace an older file that is already there.
  3. Now visit the TRADES structure generation page and follow the instructions to generate a structure. You will be able to enter any sequence in FASTA using the normal IUPAC amino acid codes and also the following codes for post translationally modified amino acids.

For example, a peptide containing 4-hydroxyproline would look like: MGLGG[P:hy_g]ASIV.

Amino = N-terminal; Carboxy = C-terminal

Modified Residue

Enter this

At what position?

ACETYLATED

N-acetyl-L-alanine

[A:ac]

Amino

N-acetyl-L-arginine

[R:ac]

Amino

N-acetyl-L-asparagine

[N:ac]

Amino

N-acetyl-L-aspartic acid

[D:ac]

Amino

N-acetyl-L-cysteine

[C:ac]

Amino

N-acetyl-L-glutamine

[Q:ac]

Amino

N-acetyl-L-glutamic acid

[E:ac]

Amino

N-acetylglycine

[G:ac]

Amino

N-acetyl-L-histidine

[H:ac]

Amino

N-acetyl-L-isoleucine

[I:ac]

Amino

N-acetyl-L-leucine

[L:ac]

Amino

N2-acetyl-L-lysine

[K:ac]

Amino

N6-acetyl-L-lysine

[K:N6ac]

Any

N-acetyl-L-methionine

[M:ac]

Amino

N-acetyl-L-phenylalanine

[F:ac]

Amino

N-acetyl-L-proline

[P:ac]

Amino

N-acetyl-L-serine

[S:ac]

Amino

N-acetyl-L-threonine

[T:ac]

Amino

N-acetyl-L-tryptophan

[W:ac]

Amino

N-acetyl-L-tyrosine

[Y:ac]

Amino

N-acetyl-L-valine

[V:ac]

Amino

AMIDATED

L-alanine amide

[A:am]

Carboxy

L-arginine amide

[R:am]

Carboxy

FORMYLATED

N-formyl-L-methionine

[M:form]

Amino

HYDROXYLATED

4-hydroxy-L-proline

[P:hy_g]

Any

LIPID MODIFIED

S-farnesyl-L-cysteine

[C:farn]

Any

S-geranylgeranyl-L-cysteine

[C:ger]

Any

N-palmitoyl-L-cysteine

[C:palm_n]

Amino

S-palmitoyl-L-cysteine

[C:palm_s]

Any

N-myristoyl-glycine

[G:myr]

Amino

N6-myristoyl-L-lysine

[K:myr]

Any

METHYLATED

N-methyl-L-alanine

[A:meth_n]

Amino

N,N,N-trimethyl-L-alanine

[A:meth_n3]

Amino

omega-N,omega-N-dimethyl-L-arginine

[R:meth_n7]

Any

L-beta-methylthioaspartic acid

[D:meth_b]

Any

N5-methyl-L-glutamine

[Q:meth_n5]

Any

L-glutamic acid 5-methyl ester

[E:meth_o5]

Any

3'-methyl-L-histidine

[H:meth_n4]

Any

N6-methyl-L-lysine

[K:meth_1]

Any

N6,N6-dimethyl-L-lysine

[K:meth_2]

Any

N6,N6,N6-trimethyl-L-lysine

[K:meth_3]

Any

N-methyl-L-methionine

[M:meth]

Amino

N-methyl-L-phenylalanine

[F:meth]

Amino

PHOSPHORYLATED

omega-N-phospho-L-arginine

[R:po]

Any

L-aspartic 4-phosphoric anhydride

[D:po]

Any

S-phospho-L-cysteine

[C:po]

Any

1'-phospho-L-histidine

[H:po_e]

Any

3'-phospho-L-histidine

[H:po_d]

Any

O-phospho-L-serine

[S:po]

Any

O-phospho-L-threonine

[T:po]

Any

O4'-phospho-L-tyrosine

[Y:po]

Any

OTHER

L-selenocysteine

[C:sel]

Any

L-selenomethionine

[M:sel]

Any

L-3-oxoalanine

[S:oxal]

Any

2-pyrrolidone-5-carboxylic acid

[E:pyro]

Amino

L-glutamyl 5-glycerylphosphorylethanolamine

[E:gpe]

Any

2'-[3-carboxamido-3-(trimethylammonio)propyl]-L-histidine (diphthamide)

[H:diph]

Any

N6-biotinyl-L-lysine

[K:biotin]

Any

N6-(4-amino-2-hydroxybutyl)-L-lysine (hypusine)

[K:hypu]

Any

N6-retinal-L-lysine

[K:retin]

Any