## 3 Results
### Hydrophobicity Characteristic--Monomers
Blue lines--theoretical (\(T\)) hydrophobicity profile and red lines--observed (\(O\)) hydrophobicity profile. Horizontal bars at the top denote secondary structure motifs: pink--helix, amber--sheet. Purple triangles--P-P interaction, teal triangles--P-L interaction and white diamonds--ligand-coordinating cysteines. Brown dashed curve on (**b**,**c**) is the C18-C42 disulfide bond. RD status is similar for the compared ferredoxins, both for complete molecules and their fragments. It can be seen that each monomer unit expresses a very high similarity between its \(T\) and \(O\) distributions. \(RD\) for FdI is 0.33 and 0.27 for FdII. This means that each monomer, as a whole, exhibits a very strong micelle-like status, highly resembling (also as a whole) a globular protein that has polar residues exposed on the surface which surround a hydrophobic core localized in its central part. Low \(RD\) value for the entire monomer unit (both FdI and FdII) seems to be the effect of all its fragments (except one--see below) having high \(O\) vs. \(T\) similarity. This includes residues engaged in P-P and P-L interactions, which suggests that their location and amino acid composition does not contradict the global trend in the molecule. In fact, values of \(T\) and \(O\) in P-P interface of FdII are very similar (Figure 4b), yielding an extremely low \(RD\) of 0.18. It may be explained by exposition of mostly non-hydrophobic residues. These similarities are lost in FdI but not to the point of causing a discordance (\(RD=0.46<0.5\)). Ligand binding cavities maintain \(RD\) values of 0.4 and 0.45 due to them being cysteine-rich (especially C11-C8 and C17-C14 pairs which pull \(O\) towards \(T\)) and being located somewhere in between the surface and the center of the molecule. Only one fragment, a beta-structural form at 34-36 (in FdI) and 31-33 (in FdII), exhibits observed status highly different from an idealized hydrophobicity distribution. It is however very short (three residues), so such discrepancy from the rest of the molecule is neither surprising nor significant in global scale. Discordance is caused by sidechains of Y35 (in FdII) and V32 (in FdII) being exposed to the water environment. The interpretation of values given in Table 2 suggests presence of highly ordered hydrophobic core in both FdI and FdII monomers. Their \(O\) distribution follows their \(T\) distribution. It means that the synergy is oriented on centric core formation despite the presence of a relatively large ligand binding cavity and that ligand binding itself does not oppose the formation of a centric hydrophobic core. With the exception of G41 and A42 in FdI and V32 in FdII, P-P interface members in both proteins gravitate towards the lower (hydrophilic) end of hydrophobicity profile in terms of both \(T\) and \(O\). This stands in contradiction to what FOD model expects (non-bonded P-P contacts at the regions of high hydrophobicity exposed on protein surface), which suggests that shielding of the hydrophobicity excess from water is not the major driving force in ferredoxin complex formation. In fact, despite having almost completely different protein-protein interfaces, both ferredoxins aim to bind their monomers using mostly non-hydrophobic residues. When \(T\) and \(O\) distributions of FdI and FdII are compared after sequence alignment (\(T\)-FdI vs. \(T\)-FdII and \(O\)-FdI vs. \(O\)-FdII, Figure S4), one can see striking similarities between the \(Ts\), culminating in a correlation coefficient of 0.96. Peaks on \(O\) of FdII happen due to high hydrophobicity of cysteines forming the disulfide bond (\(H\) parameter = 1), which yield an overall lower but still high correlation coefficient of 0.81.