PVTL.TW... .NSGSLSSG

How to visualize whether a gap is physical or not: In the Seq3D display, select "Scrutinize range". The "CPK, AlphaC Green" color scheme works well for proteins, as does "Ball and Stick". Then click the residues flanking the gap. (If the highlighted range disappears when you rotate, zoom out. More information on this problem is available.)

1. Disorder leading to inadequate resolution in the electron density map may preclude the assignment of positions of some residues known to be present. If large enough, the gap will be apparent in the backbone trace. (This kind of gap occurs only in X-ray diffraction results; NMR studies typically model all residues.)
   An example is 1fod where a 24-residue gap occurs in chain 4.

   The ends of chains may be disordered in crystals, so it is common for the leading or trailing residues in a chain to be missing in the 3D structure. When a chain is numbered according to the complete chain sequence, and the leading residues are missing, Protein Explorer will show a leading gap. Examples may be seen in chains 2 and 4 of 1fod. Protein Explorer's sequence display will not show trailing gaps, due to limitations in the sequence reporting mechanism of Chime.

2. Numbering the sequence to align with a reference sequence may require gaps. In such a case, the backbone trace will not have a physical gap.
   An example is chain B of 1igt, which contains 23 gaps due to alignment with a reference sequence. It has no physical gaps.

3. This problem will be fixed before the next release of Protein Explorer! 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 1b07. 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 2soc, an octapeptide which contains three non-standard "hetero" residues. Use the "How to visualize" method above. 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 residues.

Multiple residues assigned one sequence number.

1. If the numbering of the sequence is according to alignment with a reference sequence, and if certain residues do not occur in the reference sequence, these may be treated as "inserted" residues and given the same sequence number. An example is 1igt, which contains three such blocks.
2. In some cases the protein may have been heterogeneous, having alternative residues at one or more positions. Since the alternatives occur at a single position, they are given the same sequence number.
   1CBN has two blocks of sequence microheterogeneity noted in REMARK 4 (thanks to Torsten Schwede).