## 3 Results
### Ligand Binding Site and Protein-Protein Interface Determination in Ferredoxin I and II  
Using algorithm from the previous section, we assigned all residues from FdI and FdII monomers to FOD classes in order to check which of them could hint at the native P-P and P-L interaction sites despite low \(RD\). They are visually presented in Figure 8.  
Because both proteins are strongly accordant with the model (\(RD\) around 0.3), as expected, the number of members of classes \(D_{2}\) and \(B_{2}\) is relatively small, with no class \(D_{3}\) or \(B_{3}\) representatives and a high number of residues in classes C\({}_{3}\) and \(S_{3}\)--those which are located in their anticipated regions (center and surface of the molecule). They are additionally supported by class \(Z\) which also positively contributes to the \(RD\)-measured accordance through a \"hydrophobic inertia\" (by being hydrophobically insignificant but otherwise not counteractive towards the situation in the rest of the molecule). In FdI there are three residues in class \(D_{2}\): G23, G41 and V56 and three in class \(D_{1}\): I12, C14 and A42 (Figure 8a,c). This is not surprising. G23 and G41 were already mentioned previously in the context of being hydrophobic and playing role in stabilization of the complex. They are members of native P-P interface, among five other interacting residues that are scattered mostly (except one) within class \(Z\) square. V56--which is a SMIR--is in contact with the ligand and three other residues from the binding site are in its vicinity in the sequence. I12 and C14 also belong to the binding pocket. A42 on the other hand is in the center of the P-P interface. No residues fall into class \(B_{2}\) zone here, but there are five members of class \(B_{1}\): F4, Q8, E46 (a P-P contact), E48 and E49, with the last three located in the second helix. It can be seen on Figure 8c that residues engaged in P-L and P-P interaction in Fdl gravitate towards the upper fragment of the map. In FdII the situation is flipped: there is only K30 in class \(B_{2}\) accompanied by E3 and E12 in class \(B_{1}\) (Figure 8b,d), engaged in P-P and P-L interaction, respectively. The only representatives of \(D\) classes are M9 and A52 at level 1. They surround the ligand. Here contacts are mostly located below the \(T=O\) line and, with the exception of K30, they stay  
Figure 8: Hydrophobicity density profiles and maps of monomers of Fdl (IFXR) (**a**,**c) and FdII (IFXD) (**b**,**d). Residues belonging to core class are shown as red octagons (\(C_{2}\) and \(C_{3}\)—large and \(C_{1}\)—small), surf class—blue squares (\(S_{3}\)—large and \(S_{1}\)—small), dock class—purple pluses (\(D_{2}\)—large and \(D_{1}\)—small) and bind class—real crosses (\(B_{2}\)—large and \(B_{1}\)—small). Orange and cyan lines on (**a**,**b**) and corresponding orange and cyan circles on (**c**,**d**) mark residue clusters located within the protein body in the spatial neighborhood of members of classes \(D_{2}\) and \(B_{2}\). See description of Figure 4 for more information how to interpret this figure. in the accordance zone (Figure 8d). K30 is not in any native contact, but A31 (P-L) and V32 (P-P)--which is linked to stability of the complex--are close to it. The C18-C42 disulfide bond is also unsurprisingly high on the map (class \(C_{2}\)). With all residues classified by FOD, we performed an in silico experiment to check if they are also spatially close to a larger number of native P-P and P-L contacts. If so, this would mean that FOD algorithm may act as a ligand binding or quaternary structure predictor by itself or when joined by other scoring functions. Because there is only a couple of residues present in the important classes, we checked both \(D_{2}\) and \(B_{2}\) (each class type separately) but also their \(D_{2}+D_{1}\) and \(B_{2}+B_{1}\) unions (residues at level 2 and 1 together, each class type union also, separately).