Welcome to Heligeom Webserver
Relating interfaces to supramolecular architectures
About
Heligeom aims at characterizing, manipulating and assembling structural units with a screw organization, in which the structural units may be individual proteins or protein hetero-multimers.
Heligeom relies on the structures of monomer-monomer interfaces both for deriving the transformations and for filament construction.
Screw organization
A regularly organized oligomer is uniquely defined by the geometry of interaction between
neighboring subunits (where the subunit can be a peptide, a protein or a protein assembly).
A regular oligomeric assembly necessarily follows a screw organization, and includes helical,
ring, or linear arrangements along the axis.
The helix is the general case, consisting of a rotation around an axis coupled to a translation along that axis,
and can be characterized using parameters such as the pitch, the
number of monomers per turn and the handedness. A cyclic oligomer, or ring, is a special case of a screw
assembly in which the pitch is null. The linear (straight) assembly is another special case
in which the rotation around the axis is null.
Interfaces
A binding geometry may be characterized by a set of pairs of amino-acid in contact across the
interface. Thus different oligomers may be considered to be members of the same family if they
share a sufficient fraction of contact pairs.
This ratio is called fNAT (fraction of NATive contacts) due to its historical definition
in protein folding and docking studies, but it can be used more generally to characterize the similarity
of alternative interfaces.
References
Santuz H, Laurent B, Robert CH, and Prévost C (2025) Heligeom: A web resource to generate, analyze, and visualize filament architectures based on pairwise association geometries of biological macromolecules. Journal of Molecular Biology. https://doi.org/10.1016/j.jmb.2025.169019
[1] Boyer B, Ezelin J, Poulain P, Saladin A, Zacharias M, Robert C H, and Prévost C (2015) An Integrative Approach to the Study of Filamentous Oligomeric Assemblies, with Application to RecA. PLOS ONE 10(3): e0116414. https://doi.org/10.1371/journal.pone.0116414