Intermaps

Predicted intermolecular interaction maps (intermaps) quantify regions in two IDRs we predicted to engage in attractive (purple) or repulsive (green) interactions. If two different sequences are entered, the heterotypic intermap is predicted. If just one sequence is entered, the homotypic intermap is predicted.




The DDX4 N-terminal domain self-interactions via aromatic and charged residues (Nott et al. 2015).

The first 250 residues of the yeast translation termination factor Sup35 are disordered and has historically been divided into two halves (N- and M-).

The C-terminal disordered regions of the transcription factors Nanog and Sox2 have previously been shown to interact directly with one another (Gagliardi et al. 2013).

Options

Customize the intermap generation by adjusting the following options.

Choose the forcefield to use for predicting the interaction map.

Size of the sliding window used to calculate the interaction map.
Smaller values give you finer-grain resolution but make it harder to identify major trends in the prediction.
Default = 31.

31

If checked, folded domains will be removed from the prediction.
Folded domains are predicted with metapredict (V2)

Defines the dynamic range of the intermap. The dynamic range is the difference between the maximum and minimum values of the intermap.
A higher dynamic range will make the intermap more contrasted.
Default and recommended values for Mpipi-GG and CALVADOS2 are set (2.5 and 7.5)

How to read intermaps

Intermaps report on the predicted intermolecular interaction propensity between subregions in an IDR. These make it easy to identify subregions in two proteins that are predicted to interact favorably.

The numbering on the x and y axis reports on the protein-space numbering, but because intermaps are calculated using a sliding window, that numbering starts at (windowsize-1)/2 because the position on the intermap is in the middle of the windows being compared. These sequences associated with the two windows are then displayed and colored under the intermap if you click on the map, and these sequences are also copied for your clipboard. Note that the NUMBERING here corresponds to the first/last residue in the window, not the middle residue.