## 4 Discussion  
The detailed presentation of the proteins discussed in this paper, Ferredoxins I and II, delivers an example of a very high accordance between expectations (3D Gauss function, \(T\) distribution) and observed status--\(O\) distribution. So far, the best fit of this kind was seen in titin [14] and type III antifreeze proteins [12]. Such molecules present very good examples for fuzzy oil drop model to describe the folding process as micelle formation, which in some proteins occurs along high \(T\) vs. \(O\) accordance. Ferredoxins I and II have biological activity in form of electron transfer mediated by an iron-sulfur cluster ligand. The ligand binding cavity, which is located in the same spot in both proteins, is quite large in respect to the length of the chain (64 and 58 residues). Figure 12: 3D presentation of results of FOD-based prediction of P-P interaction in Rad50 (1L8D). Native P-P interface is shown on (**a**), prediction output (class \(D_{3}\) + \(D_{2}\) cluster—orange, class \(B_{2}\) cluster—cyan) on (**b**) and its intersection with native data on (**c**). Violet/blue segments correspond to Pfam coiled-coil zn hook region (residues 423–474). See description of Figure 9 for more information how to interpret this figure. Despite its presence, FdI and FdII monomers exhibit a very well-ordered hydrophobic core--high accordance with 3D Gauss function. The pockets, constructed from hydrophobic cysteines (which also coordinate the ligand and as such have their sidechains turned towards inside of the molecule) are accordant in monomers, but become discordant in the dimers where complex formation positions them towards the lower end of \(T\) distribution range. This causes strong local discordances defining the locus for ligand binding. It means the biological activity should appear after finalization of quaternary structure construction process. The role of cysteine--especially the role of S-S bonds in respect to hydrophobic core formation--is discussed in detail in [61] (the S-S bond system seems to generally be in opposition to FOD model expectations). Ferredoxin I and II seem to fold as an individual unit (monomer) incorporating the ligand as consequence of centric hydrophobic core support. Complex formation causes them to lose the accordance status (\(RD\geq 0.5\)). Given the globular shape of the monomers and only seven residues in the P-P interface, this is an expected phenomenon. Based on FOD model data, both dimers seem to be generated through mostly polar interaction, with support (or guide) by hydrophobic interactions from few specific residues. Such a scenario is in agreement with MIR simulations. In FdI these residues appear to be G23 and G41, which are both P-P interface members and are outstanding on monomer \(T\) vs. \(O\) maps. FdII has V32, but its role becomes visible in the dimer. An antifreeze type III protein, although it has a very low \(RD\) value comparable to the ferredoxins, exhibits vastly different features on the hydrophobicity map. In fact, it can be said that it has no such features at all when one is looking for residues marking a putative P-P or P-L interaction areas (at the significant levels of \(D\) and \(B\) classes). This observation is however completely correct when function of this protein is considered and confirms that \(T\) vs. \(O\) map analysis may be used to differentiate between structures which are similar in terms of overall stability of their hydrophobic core. Clustering of spatial neighbors of residues from ferredoxin monomers which were assigned to \(D\) and \(B\) classes of FOD shows that there are two perceived \"seeds\" of discordance in FdI, located at the opposing ends of the molecule. One of them contains the previously mentioned G41 and G23 (class \(D_{2}\)), while the other has only V56 (also \(D_{2}\)) with significant amount of hydrophobicity exposed on the surface, probably gathered from the nearby ligand binding pocket members.