Editing SecStrAnnotator:Analysis (section)

==Example case study: Cytochromes P450==

===Data===

For the Cytochrome P450 family, structures of 1855 protein domains are available, located in 1012 PDB entries (updated on 7 July 2020). The analysis was performed on a non-redundant subset containing 183 protein domains.

The data are available [https://doi.org/10.5281/zenodo.3939133 here] (structural files not included because of their size).

===Occurrence of SSEs=== 

The ''occurrence'' describes in what percentage of the structures a particular SSE is present.

<div><ul> 
<li style="display: inline-block;"> [[File:SecStrAnnotator-cyp-sse-occurrence.png | thumb | 500px | Occurrence of particular SSEs in the whole set.]] </li>
<li style="display: inline-block;"> [[File:SecStrAnnotator-cyp-sse-occurrence-Bact-Euka.png | thumb | 500px | Occurrence of particular SSEs – comparison of bacterial and eukaryotic structures.]] </li>
</ul></div>

===Length of SSEs===

The ''length'' of an SSE is measured as the number of residues. The following violin plots show the distribution of length for each SSE.

<div><ul> 
<li style="display: inline-block;"> [[File:SecStrAnnotator-cyp-sse-length.png | thumb | 500px | Length distribution of particular SSEs in the whole set. ]] </li>
<li style="display: inline-block;"> [[File:SecStrAnnotator-cyp-sse-length-Bact-Euka.png | thumb | 500px | Length distribution of particular SSEs – comparison of bacterial and eukaryotic structures. ]] </li>
</ul></div>

===Sequence of SSEs===

The amino acid sequences for each SSE can be aligned and used to produce a sequence logo. Where the sequence conservation is sufficient, we can establish a generic numbering scheme: the most conserved residue in helix X serves as its reference residue and is numbered as @X.50. The remaining residues in the helix are numbered accordingly.

<gallery mode="packed" heights=140px caption="Helices">
File:SecStrAnnotator-cyp-sse-logo-A-.png
File:SecStrAnnotator-cyp-sse-logo-A.png
File:SecStrAnnotator-cyp-sse-logo-B.png
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File:SecStrAnnotator-cyp-sse-logo-B--.png
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File:SecStrAnnotator-cyp-sse-logo-K-.png
File:SecStrAnnotator-cyp-sse-logo-K--.png
File:SecStrAnnotator-cyp-sse-logo-L.png
File:SecStrAnnotator-cyp-sse-logo-L-.png
</gallery>



<gallery mode="packed" heights=140px caption="Beta strands">
File:SecStrAnnotator-cyp-sse-logo-1-0.png
File:SecStrAnnotator-cyp-sse-logo-1-1.png
File:SecStrAnnotator-cyp-sse-logo-1-2.png
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File:SecStrAnnotator-cyp-sse-logo-2-1.png
File:SecStrAnnotator-cyp-sse-logo-2-2.png
File:SecStrAnnotator-cyp-sse-logo-3-1.png
File:SecStrAnnotator-cyp-sse-logo-3-2.png
File:SecStrAnnotator-cyp-sse-logo-3-3.png
File:SecStrAnnotator-cyp-sse-logo-4-1.png
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File:SecStrAnnotator-cyp-sse-logo-5-1.png
File:SecStrAnnotator-cyp-sse-logo-5-2.png
File:SecStrAnnotator-cyp-sse-logo-6-1.png
File:SecStrAnnotator-cyp-sse-logo-6-2.png
</gallery>

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