Rotamers
is an interface for showing amino acid sidechain rotamers and
optionally replacing the original sidechain,
also implemented as the
swapaa command.
The rotamers can be shown all at once, as in the figure, or individually
by choosing rows in the dialog.
The figure shows binding-site residues of the thyroid hormone receptor β
with hormone bound,
PDB 3gws.
Rotamers for the hormone-resistance mutations N331H and L346R
are shown as partially transparent sticks, with H-bonds (light blue dashed
line) and clashes (light purple dashed lines) calculated for the histidine
rotamers at position 331. The rotamer-list dialog for this position is also
shown. Command script rotamers.cxc
contains the initial, noninteractive part of the setup.
These mutations are described in
Cardoso et al., Endocrine (2020).
Although one histidine rotamer may be able to form the same pocket-stabilizing
H-bond as the wild-type asparagine, it also clashes with several atoms
(third row in the dialog). H-bonds and clashes are not shown for
the arginine rotamers at 346, but they all clash significantly
with the hormone and/or other pocket atoms.
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