Chlorine, bromine and iodine had the lowest propensity of interactions for cysteine, while fluorine had a lowest propensity for proline.
Fluorine had the highest propensity of interactions for glycine, while chlorine for leucine, bromine for arginine, and iodine for lysine.
High-resolution structural characterization of denatured states of proteins is one way to obtain information about the propensity of interactions among residues in early stages of folding.
There are 6808 predicted protein-binding sites also provided in the database, which were predicted using Support Vector Machine based evaluation of interaction propensities.
The lack of a propensity for interactions with phenotypically essential proteins suggests a selective pressure to minimise virulence in retroviral evolution.
The advantage of using FLIM-FRET is that both the proportion of epitopes that are interacting and the closeness of that interaction can be independently calculated from the same data set [26], allowing us to address both the question of propensity to bind and closeness of interaction, in a well separated fashion.
We see a similar pattern when we consider all polar amino acids forming hydrogen bonds to mainchain atoms in β-hairpins; asparagine has the highest propensity to form this type of interaction followed by aspartate, arginine, serine and threonine (Table 2 and see Additional file 3, Figure S4 - white bars).
We see a different pattern however when we consider all polar amino acids in centre strands that form hydrogen bonds to mainchain atoms - arginine has the highest propensity to form this type of interaction followed by cysteine, tyrosine, threonine and asparagine (Table 2 and see Additional file 3, Figure S2D - white bars).
Electrostatic interactions, including hydrogen bonds, van der Waals interactions, intrinsic propensities of the amino acids to take up certain structures, hydrophobic interactions and conformational entropy contribute to free energy.
The careful annotation of well-described MoRFs in terms of their sequence propensities or interaction interfaces as well as their known binding partners, and integration of these annotations with MoRF predictions, would likely improve the use of these predictions for gaining insight into IDR functionality.
