*2.6. Secondary Structure of DOT and RNA-Interacting DOT Residues*

The secondary structures of DOT residues are quantified to study the bias of residues to have a specific secondary structure in binding and non-binding regions and data are presented in Table 1 and Table S1 for NR3.5 and NR6 datasets, respectively. In the NR3.5 dataset, all the DOT residues have lower and higher preference in sheet (15%) and other structure class (8%), respectively. Interestingly, in DOT residues, binding with RNA molecules, strand-forming residues have a higher preference (15.2%) as compared to helical (8.6%) and other regions (8.9%).

**Table 1.** Secondary structure of all DOT residues and residues binding with RNA in DOT regions in the NR3.5 dataset.


Percentage is mentioned in the parenthesis. Relative binding in DOT regions are calculated by *Nidt*/*Nd* × 100.

#### *2.7. Relative Solvent Accessibility of DOT Residues*

The spatial arrangement of DOT residues is further explored by solvent accessibility calculation and the result is shown in Table 2. Comparison of RASA of DOT regions and complete protein–RNA complex revealed that in DOT regions, solvent accessibility of every amino acid is more than that of other amino acids of a protein. As expected, charged residues have low fold difference (1.18 to 1.28) in RASA in DOT regions and the complete protein. However, most hydrophobic residues (Ala, Cys, Ile, Leu, Met, Phe, Tyr, and Val) have about 1.8 to 2 folds higher RASA in DOT regions than the complete protein, Met has the highest difference. On the other hand, the mean solvent accessibility of DOT regions of proteins is 44 Å2, which is similar to the average RASA of binding DOT regions (43 Å2) of protein–protein complexes [17].

**Table 2.** Relative average solvent accessibility (RASA) of DOT residues and all residues in non-ribosomal protein–RNA complexes.

