Nonstandard residues produce apparent gaps in Protein
Explorer's sequence display. Residues other
than the 20 standard amino acids are supposed to be designated as
"hetero" atoms. Chime does not report heteroatoms in its "show sequence"
report, which is what Protein Explorer depends upon to construct its
sequence display. Therefore, Protein
Explorer's sequence display will show gaps where hetero residues occur.
A single hetero residue will generally not make a gap in the backbone
trace, but its alpha carbon position will not occupy a bend in the trace
trace since backbone positions
are assigned only to non-hetero residues.
An example is residue 5 in chain B of
Since Protein Explorer shows hetero atoms spacefilled in
its FirstView, this residue is already highlighted in the initial 3D display.
In a different view (e.g. if the entire molecule were shown in stick rendering)
you could use the Seq3D interface to highlight
the flanking residues (4 and 6), allowing you can see
that residue 5 is present in the 3D structure; clicking on it reveals its
group identifier PSG and confirms that it is designated "hetero".
Another example is
an octapeptide that contains three
non-standard "hetero" residues. Use the "How to visualize" method
Note that the middle of the backbone trace bypasses the alpha carbon of
residue 4, and that the trace does not extend to the first and last