[Jmol-users] Non-standard residues: invisible backbone, LINK records

[Eric M. <em...@mi...>]

The discussion of invisible unbonded atoms or single-residue "chains" 
brings up a related issue.

The "backbone" command in RasMol 2.6/Chime connects amino acid alpha 
carbons and nucleotide phosphorus atoms for standard residues ONLY. 
Non-standard amino acids can be part of an amino acid chain but are 
invisible in a backbone rendering.

This can have two undesirable consequences.

1. Backbone rods will be drawn between residues not connected by a peptide 
bond if they are sufficiently close, skipping intervening non-standard 
residues. Thus, the backbone line is incorrect.

2. When a standard residue is flanked by non-standard residues, it behaves 
like a single-residue chain, so becomes invisible in a backbone rendering.

Example: 1AL4 has 12 non-standard residues (D amino acids, e.g. D-leucine 
DLE, D-valine DVA; note MODRES records) among 34 amino acids. The backbone 
lines connect only the standard L residues, hence don't follow the actual 
chemical backbone. Two standard residues are isolated between non-standard 
residues.
http://molvis.sdsc.edu/protexpl/pe.htm?id=1al4

The covalent peptide bonds between standard and non-standard residues are 
designated in 1AL4's PDB file header with LINK records (ignored by RasMol 
2.6/Chime).

In PE, I worked around the single-residue "chain" issue by showing all 
alpha carbons as spheres the same diameter as backbone rods; hence the two 
isolated standard residues are not invisible.

But Chime offers no way that I know about to correct the backbone paths 
(short of modifying the PDB file). Hence in PE, the backbone lines are 
incorrect in FirstView (best seen after going to Features or QuickViews and 
clicking the Ligand button to hide the non-standard residues, which by PDB 
convention must be designated as HETATM). To see the alpha carbons in 
non-standard residues:

select *.ca and not protein
spacefill 0.6

In 1B07 chain C, a nonstandard amino acid is handled a different way. The 
backbone atoms are named GLY (hence its alpha carbon is included in the 
backbone path for chain C), while the sidechain is HETATM and given the 
name PYL. In RasMol 2.6/Chime, this produces (in stick display) a floating 
sidechain unconnected to the main chain. The missing bonds, both for the 
single-residue HIS "chain" (mentioned in my previous email) and for the PYL 
connection to GLY 5 are specified in LINK records.

SUGGESTIONS for Jmol

Perhaps backbone paths should include all alpha carbons and nucleotide P 
atoms, regardless of whether the residues are standard? Perhaps LINK 
records should be obeyed to produce additional covalent bonds?

I have no idea how consistently LINK records have been used when they are 
appropriate. The fact that 26% of PDB entries contain LINK records suggests 
that they may have been enforced since they were introduced apparently in 
1996 (data thanks to Jaim Prilusky's record type searcher,
http://bip.weizmann.ac.il/oca-bin/pdbRecNames).

PDB format (http://www.rcsb.org/pdb/docs/format/pdbguide2.2/part_48.html):
"The LINK records specify connectivity between residues that is not implied 
by the primary structure. Connectivity is expressed in terms of the atom 
names. This record supplements information given in CONECT records and is 
provided here for convenience in searching."

-Eric

----
Eric Martz, Professor Emeritus, Dept Microbiology
University of Massachusetts, Amherst MA US
http://www.umass.edu/molvis/martz