## 5 Conclusions  
The structures of Ferredoxin I and II analyzed in this paper are an exceptional example of highly spherical micelle-like construction with centric concentration of hydrophobicity with the surface covered by polar residues (very low \(RD\) value \(\approx\) 0.3). Presence of ligand binding cavity introduces local discordance of observed vs. expected (theoretical) hydrophobicity distribution in the monomer which is not the case in these proteins despite the cavity being rather large in comparison to the whole chain. The discordance however appears in the functional--americ form. Despite having similar sequences in terms of hydrophobicity and identical ligand binding site locations, FdI and FdII present vastly different dimeric formations. Globular structures with such low differences between theoretical and observed distributions (at the scale of complete monomer and its segments) are not expected by the FOD model to form complexes or bind ligands. However, considering \(T\) vs. \(O\) hydrophobicity map analysis and residue classification protocol presented in this paper it can be seen that even in such highly accordant proteins there are still individual residues that exhibit discordant status, which in this case is enough to constitute a foothold for the search for the native P-P interface and ligand binding cavity, especially the former. While it appears that \(D\) class has higher significance in this process, one should also consider \(B\) class when looking for putative protein-protein interactions. Ferredoxins I and II together with type III antifreeze and coiled coil (Rad50) proteins show that FOD model can be used with promising results in the process of quaternary structure prediction of proteins when their tertiary structure is known by pointing out residues which may be engaged in non-bonded contact between the chains. To answer whether hydrophobicity is the actual driving force in complex formation of these molecules one would need to perform \(RD\) optimization procedure. On the other hand, in order to verify if (and when) hydrophobicity map analysis is useful for the same purpose when working with other types of proteins, one would need to analyze more (and more varied) structures. Such research will be the object of the future work. The following are available online at [[https://www.mdpi.com/article/10.3390/app11188514/s1](https://www.mdpi.com/article/10.3390/app11188514/s1)]([https://www.mdpi.com/article/10.3390/app11188514/s1](https://www.mdpi.com/article/10.3390/app11188514/s1)); Figure S1: Presentation of 3D Gauss capsule fitting; Figure S2: Presentation of binding of theoretical, observed and random hydrophobicity distributions together with \(RD\) value; Figure S3: 3D presentation of superposition of chain A of FdI and chain A of FdII; Figure S4:Comparison of hydrophobicity density profiles of monomers of Fdl and FdII; Figure S5: Comparison of hydrophobicity density profiles of monomers of FdI and FdII seen as parts of dimers; Table S1: Hydrophobicity status of type III AFP and its selected fragments. Table S2: Hydrophobicity status of monomer of Rad50 and its selected fragments; Table S3: Hydrophobicity status of Pfam coiled-coil zn hook region (residues 423-474) of Rad50. Conceptualization, M.B., I.R. and J.C.; methodology, I.R. and M.B. ; software, M.B. and J.C.; validation, M.B., I.R. and J.C.; formal analysis, M.B., I.R. and J.C.; investigation, M.B. and I.R. ; resources, J.C. and M.B. ; data curation, M.B. and J.C.; writing--original draft preparation, M.B., I.R. and J.C.; writing--review and editing, M.B., J.C. and I.R. ; visualization, M.B. ; supervision, J.C.; project administration, I.R. ; funding acquisition, I.R. and J.C. All authors have read and agreed to the published version of the manuscript. This research was funded by Campus France PHC Polonium grant number 405111 TL. Not applicable.