Interactions by ligands
This section provides a summary of the interactions established between each ligand and residue atom.
All data
Shows all interactions, for the whole data set, established between ligand and residue atoms in a table. The first column is PDB id and it contains, for each line, PBD id, chain, ligand and Residue sequence number (a field of HETATM in PDB file format) separated by a colon (:). Users can click on the first column to sort the table by PDB id. Also, users can type a word to search for in the table Search textbox.
The other columns may vary depending on the data set because they are related to the residue atoms. The columns headers are labeled according to a residue atom name and each cell presents the interaction information. The content of a cell is:
- First line: residue name (three letter abbreviation) and residue number (Residue sequence number field in PDB file format).
- Second line: type of interaction.
- Third line: ligand atom and atom number (Atom serial number field in PDB file format).
Graph: by clicking on this icon a panel will pop up in the screen. In this panel, we provide an interactive view of the Protein-ligand interactions in 3D and 2D (graph). It is available to users the following set of features:
Show/Hide cartoon: protein is displayed in cartoon mode.
Show/Hide surface: protein surface is shown.
Show/Hide residue labels: provides labels with the name of residues which interact with a ligand.
Show/Hide atom labels: atom labels from residues which interact with a ligand are displayed.
Also, there are Residue name and Residue Number text boxes, where users can select and color residues in the Protein visualization by their name or number. The buttons Search and Clear show the selected residues and clear the selection respectively.
Show/Hide atoms by their types: there are six types of atoms which can be displayed simultaneously or not: Acceptor, Aromatic, Donor, Hydrophobic, Negative and Positive.
Show/Hide interactions: there are five types of interaction which can be displayed simultaneously or not: Aromatic stacking, Hydrogen bond, Hydrogen bond (water), Hydrophobic, Repulsive and Attractive.
Show/Hide interacting residues: all interacting residues are provided and users can choose among them which should be displayed.
Reset graph: selects all the atoms (nodes) and its interactions on the Graph. Consequently, all interactions will be displayed in the Protein visualization.
Protein screenshot and Graph screenshot: users can save an image from the Protein or Graph visualization.
Mouse interactions: users can filter interactions in the Protein view by clicking over the nodes in the Graph visualization. A double click with the Mouse left button, selects one atom and its interactions and remove all the other selections. On the other hand, if the user press Ctrl and click with the Mouse left button over a node, it will remove/add an atom and its interactions to the current selection.
Node size (%): increase/reduce the size of the graph nodes to fit well in the panel.
Show/Hide nodes label: provides labels to the graph nodes.
By clusters
Provides the same data from All data subsection, but segmented by cluster. Users can enter a PDB id to find in which cluster the ligand is located and then choose such cluster to be shown.