Each of the views in the next three tables is achieved with one click
When actually using FirstGlance
, the molecular
views are much larger
Initial view (Cartoon plus Ligands+)
of Gal4 transcriptional
regulator (DNA-binding domain only) bound
Each chain is a different color.
view of Gal4 with alpha helices
Compare with another molecule below showing
a beta sheet.
N->C Rainbow view of Gal4:DNA showing
Composition view of Gal4:DNA indicating
Hydrophobic/Polar view of Gal4:DNA indicating
Polar residues on the surface.
Charge view of Gal4:DNA indicating
on the surface.
Atomic detail is available in Vines.. views.
The Slab.. option (not pictured) hides
atoms distant from the point of interest.
Secondary Structure view of Streptococcal
Begin Contacts.. Section
tool of FirstGlance
the following views.
The snapshots below are much smaller than
the actual views when using FirstGlance
Contacts.. enables you to see how the chains
(each a different color) touch each other.
(View obtained with 1 click.)
Optionally, you can select a target (by clicking on chains, groups, or atoms)
in order to display the putative non-covalent bonds to the target.
Clicking on one protein chain (green) marks it as the target
with a black asterisk (magnified in inset) on each atom.
obtained with 2 clicks.)
Only the atoms that contact the green target chain
are now shown.
(View obtained with 3 clicks;
These contacts can be shown in great
detail, in seven subsets of different kinds of
non-covalent bonds, as shown below.
Contacts 1: non-water hydrogen bonds.
target Gal4 protein
atoms (larger balls, bottom, marked with white asterisks)
are shown within hydrogen-bonding
distances of DNA atoms (smaller balls, top).
These hydrogen bonds are to a specific sequence of bases.
The DNA sequence
recognized by Gal4, CGG (in chain E), can be visualized here.
Atoms represented as sticks are too distant from the protein to be
hydrogen-bonded, but are shown for context.
obtained with 6 clicks, plus additional double-clicks
for each distance measurement.)
Double-clicking atoms reports distances or angles.
In this view (and many views below), atoms are colored by element:
Contacts 2 view of 1D66:
putative hydrogen bonds to
Contacts 3 view of 1D66:
bridges, a subset of hydrogen bonds to water.
One putative bridge from 1D66 is shown above.
Clicking on any atom reports its identity to the lower left
of the molecule, as shown above. ("NH2" means Nitrogen, Eta2.
Contacts 4 view of 1D66:
van der Waals (hydrophobic) interactions.
Here, the target chain atoms are spacefilled to van der Waals
radii, while the contacting atoms are small balls.
Contacts 5: protein salt bridges.
Contacts 6 view of 1BL8:
protein cation-pi orbital interactions.
Contacts 7: metal and misc. interactions.
Here the interactions of
in heme are shown (from
Begin Hide.., Find.. Section
This potassium channel
is a homotetramer (four identical chains).
This view is obtained with one click on Contacts...
Here, the Hide.. dialog of FirstGlance has been
used to hide the front two chains (3 more clicks). Now we can see three potassium
ions, and one water molecule.
(View of 1BL8).
Hydrophobic/Polar shows that most of the surface of this
molecule is hydrophobic (gray), consistent with its transmembrane
obtained with 1 click.)
Compare with the
same view for Gal4.
The Find.. dialog of FirstGlance was
used to locate all tryptophan residues (yellow clouds). Clearly,
they sit at the lipid-water boundaries.
obtained with 2 clicks plus typing "TRP".)
Begin Structural Bioinformatics Resources Section
has numerous links to structural bioinformatics
servers and resources.
One of the most important is the link to
Probable Quaternary Structure:
Notice the implausible folding of the left end,
which suggests that some of the chains are missing in this model,
(the asymmetric unit).
(View obtained with 1 click.)
Might this molecule have formed specific oligomers, with more chains,
in the protein crystal? The answer is provided by a visit to
the Probable Quaternary Structure (PQS) server of the European
In FirstGlance, simply click on
Indeed, PQS reports that the molecule existed in the crystal as a hexamer,
rather than a dimer. The hexamer is formed from three dimers by symmetry
operations. A link to FirstGlance at PQS displays the above
What is this amazing molecular machine? To find out,
and click on either
Crystallographic models often have portions missing -- regions where the molecule
was disordered ("blurry") in the crystal.
To find out,
Nearly 50 amino acids are missing from the asymmetric unit (so nearly
150 from the specific hexamer)!
In addition to the structural bioinformatics resources mentioned above,
FirstGlance offers links, under
More Views.., to:
- Assessment of model quality by All Atom Contact Analysis
at the MolProbity server
- List of energetically significant cation-pi orbital interactions
at the CaPTURE server.
- The Jmol console and command language.
- Protein Explorer: more information for beginners, and more power
for advanced users, compared to FirstGlance in Jmol.
- Visualize evolutionary conservation with the ConSurf server.
- And more.
Begin More Views.. Section
Within FirstGlance, More Views.. offers a display of all protein salt bridges
throughout the molecule. Here, all salt bridges in an SH3 domain
are shown. (View obtained with 2 clicks.)
When the same view is colored by chain, it is easy to see
that one of the salt bridges is between two chains.
(View obtained with 1 additional click.)
The same dialog displays all protein cation-pi orbital interactions
throughout the molecule.
(View obtained with 2 clicks.)
More Views.. has a checkbox to
highlight (as ball and stick) non-standard amino acids
or nucleotides. Here, phospho-serine (SEP) is indicated in
(View obtained with 2 clicks.)
More Views.. also offers to
color the molecule by uncertainty (crystallographic "temperature" or "B factor").
The positions of the red atoms in Gal4:DNA model above have the least
obtained with 3 clicks.)
More Views.. also offers to show the atomic coordinate
axes, the unit cell, or the boundbox (in any combination).
Above, all three are shown for Gal4:DNA
(View obtained with 4 clicks.)