Documentation

Examples

Here, you can find a set of pre-computed results to explore Heligeom outputs, taken from the Heligeom webserver paper.

  • 2GLS: It is an oligomeric ring. By choosing the first 2 chains (i.e 'A' and 'B') and construct an oligomer of 6 elements, you can retrieve the first layer of ring present in the PDB file.
    This is the example used when clicking on the Example button on the Run page.
  • 4ESV and core regions: This example showcases the need for defining a core region in the case of flexible monomers.
    For the 1st oligomer, the whole chains B and C are used. In the 2nd one, the same chains are used but a core region is defined (residues 184 to 365).
    Heligeom analysis produces different results due to the N-domain (excluced by selecting the core region) which interact differently.
  • 3ICE and alternative interfaces: This example showcases different interfaces within a same structure (an hexameric ring structure of the Rho transcription termination factor).
    Depending of the pair of chains chosen (here A & B and E & F), the fNAT values differs: 0.43 for AB/EF and 0.85 for AB/BC.

Run Page

1 - First Oligomeric form

The form is organised in 2 parts: the Input data and the Selection.

In the Input data, you can either:

From this input PDB, in the Selection section, you'll need to define the 2 monomers whose the interface and the Screw parameters will be computed from.
For each monomer you can specify either the chain, the residue range or both.
priority_highOnly the Carbon-α of the monomers will be used for the Helical parameters computation. Both monomers needs to have the same number.priority_high

Core Region: A core region is a specific region of the monomer which will be used to compute the helical parameters and the residue at the interface.
priority_highCareful, during the construction of an oligomer, the whole monomer will be used, not just the core region.priority_high

Missing Residues

Heligeom can handle missing residues in one monomer compared to the other:

  • if only the chain is provided: only missing residues inside the chain are handled.
  • if the residue range is provided: missing residues at the begining or at the end are also handled assuming the residue range is filled with the same gap for both monomers (i.e 1-300 and 301-600).

2 - 2nd Oligomeric form (Optional)

Helligeom allows you also to compare 2 interfaces by defining a second interface in the form.
To do that, you will need to click on the text 2nd oligomeric form? and the same form as for the first oligomer will appear.

3 - Run

You can hit the Analyze button to start the computation and get the results.

Result Page with 1 Oligomer

Contacts at the interface

On the left, Heligeom displays a summary of the input parameters.
For each monomer, you will have the chains, the residues range and the core regions. If one is not specified, the word "Unspecified" is displayed instead.
On the right, there is a Mol* visualisation depicting:

  • the 2 monomers selected by the user represented as Cartoon and whose colors matches their respecting title on the left.
  • the residues in contact at the interface, represented as ball and stick

List of contacts: The whole list of contacts can be downloaded by clicking on the button Download list of contacts.
A contact is defined when 2 heavy atoms have a distance < 5Å.

Helical parameters

Heligeom displays the helical parameters computed from the 2 monomers given. It refers to the screw calculation.
priority_highThis calculation is based solely on the C-α of the monomers.priority_high

On the left part:
  • The pitch is the distance of one helix turn along the helix axis.
  • The monomer per turn is the number of monomers needed for 1 turn of the helix.
  • The Handedness is the direction of rotation around the axis.
  • The 2 distances (IntR and ExtR) are the minimal and maximal distances between the screw axis and the atoms of oligomer.

On the right part:

  • The parameters of the Screw axis with a picture above explaining the values. Those will be used to construct the oligomer at the next step.

RMSD: The RMSD value of the superposition between the Carbon-α of the 2 monomers is displayed.
Heligeom provides an hint with a color depending of the value:

  • RMSD <= 2Å:TODO
  • 2 < RMSD <= 5Å:TODO
  • RMSD > 5Å:TODO

Construction Details

Once the helical parameters are computed, Heligeom can construct an oligomer based on those.
The protocol is

  • to take the entire Monomer 1 selection (not only the core regions)
  • create copies of this monomers based on the screw parameters
  • repeat the above step to match the number of monomers given by the form.
There is also the option to align the oligomer to the Z-axis by checking the corresponding checkbox.



Once the construction is finished, a interactive view (thanks to Mol*) of the oligomer is displayed below the form.

By default, the coloration is made by monomers. Each monomers will have a different chain, starting by A.
A set of precomputed visualization buttons is available above the view.
You can download the PDB file of the oligomer with the orange button.

Flatten the oligomer?
There is also the option to flatten the oligomer by checking the corresponding checkbox.
The method is described in the about page.
This computation can take up to several minutes due to the Monte-Carlo algorithm.
Once finished, below the visualisation section, Heligeom displays some parameters resulted from the algorithm.

Result Page with 2 Oligomers

Results

For a couple of oligmers, Heligeom displays the same content that for 1 Oligomer with a side by side view.

Comparison of the interface

On the Result page, Heligeom displays some analyzis of the comparison of the 2 interfaces.
FNAT
The Fnat is the fraction of residue pairs of the 1st interface present in the 2nd interface, as defined here.
Value of 1.0: All of the residue pairs of the 1st interface are present in the 2nd one.
Value of 0.0: None of the residue pairs of the 1st interface are present in the 2nd one.