*3.3. Frequency of Binding in DOT and Other Residues*

We also computed the frequency of residues binding in DOT regions over all the binding residues by using Equation (2), an error bar is plotted using the bootstrap method by randomly re-sampling an equal sized data with a replacement 1000 times.

$$\text{Frequency of binding by contact residues} = \frac{N\_{i\bar{i}h\bar{l}}}{N\_{i\bar{l}}} \tag{2}$$

where *Nibd*: number of *i*th residues binding in DOT region; *Nib* is number of *i*th residues binding with RNA in complete protein.

#### *3.4. Propensity of Binding Residues in DOT Region*

The normalization of frequency of residues present in DOT regions by individual residue frequency provides the tendency of a residue in DOT regions. Accordingly, propensity values are calculated using the following equation:

$$\text{Proppersity}(\mathbf{I}) = \frac{N\_{\text{ibd}} / N\_{\text{id}}}{N\_{ip} / N\_p} \tag{3}$$

where Propensity (I): propensity of *i*th residue; *Nibd*: number of *i*th residue binding in DOT region; *Nid*: number of *i*th residue in DOT regions; *Nip*: number of *i*th residue in protein; *Np*: number of residues in protein.

#### *3.5. Boot Strap Sampling*

To obtain the standard error in frequency and propensity calculations, bootstrap sampling is performed. In this technique all the protein–RNA complexes are sampled randomly and each sample contains complexes equal to the number of protein–RNA complexes. Therefore, each sample will have redundancy of some complexes and will be devoid of some complexes. In this manner, we have created 1000 samples on which the calculations are performed.
