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CATALOGUE
For each secondary structure element, the following information is given:
1- Id: an identifier (sequential number) corresponding to its rank in the tree representation of the secondary structure.
2- Loop type: the type of the loop (junction, terminal, internal,...).
3- Non canonic labels: a string made of codes corresponding to the names of the non-canonical interactions between nucleotides. The correspondance between the codes and the names of the interactions are summarized in the table below.
4- Descriptor: the detailed list of its nucleotides (given by residue number and base letter) and all interactions between them.
5- VIEW3D: a pdb file that isolates the secondary structure element in the molecule.
LISTING
For each interaction motif, the following information is given:
1- Name: an identifier made of the concatenation of the PDB_ID, Chain_ID and a sequential number.
2- Non canonic labels: a string made of codes corresponding to the names of the non-canonical interactions between nucleotides. The correspondance between the codes and the names of the interactions are summarized in the table below.
3- Descriptor: the detailed list of its nucleotides (given by residue number and base letter), all interactions between them and its interacting interfaces.
4- VIEW3D: a pdb file that isolates the interaction motif and its interacting interfaces.
| Non-canonic label | Notation | Description |
|---|---|---|
| a | --- C/C - --- | Backbone connection |
| b | --- W(w)/W(w) c --- | W/W cis |
| c | --- W(w)/W(w) t --- | W/W trans |
| d | --- H(h)/H(h) c --- | H/H cis |
| e | --- H(h)/H(h) t --- | H/H trans |
| f | --- S(s)/S(s) c --- | S/S cis |
| g | --- S(s)/S(s) t --- | S/S trans |
| h | --- W(w)/H(h) [or H(h)/W(w)] c --- | W/H [or H/W] cis |
| i | --- W(w)/H(h) [or H(h)/W(w)] t --- | W/H [or H/W] trans |
| j | --- W(w)/S(s) [or S(s)/W(w)] c --- | W/S [or S/W] cis |
| k | --- W(w)/S(s) [or S(s)/W(w)] t --- | W/S [or S/W] trans |
| l | --- H(h)/S(s) [or S(s)/H(h)] c --- | H/S [or S/H] cis |
| m | --- H(h)/S(s) [or S(s)/H(h)] t --- | H/S [or S/H] trans |
| n | --- +/+ c --- | WC GC or GU |
| n | --- -/- c --- | WC AU |
| s | --- 3/3 s --- | Stacking s33 |
| s | --- 5/5 s --- | Stacking s55 |
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