RING - Residue Interaction Network Generator

They derive from the corresponding file previously described. Edges that identify some interactions where hydrogen bonds exist, salt bridges and π-cation interactions are directed in this type of network.

1. Atoms that Determine the minimum distance.
2. Distance between closest atoms.
3. H-Bonds.
4. Is π-cation interactions.
5. π-π stacks.
6. Salt-bridges.
7. Disulfide bonds.
8. Edge-weight.
9. InteractionSite.
10. Mutual Information.
11. Average Product Correction.

They derive from the corresponding file previously described. The directionality of edges identifying some interactions such as hydrogen bonds, salt bridges and π-cation interactions is maintained in some of the corresponding attributes.

1. Atoms determining the minimum distance contact.
2. Distance between closest atoms (Å).
3. H-Bonds.
4. Donor-atom - acceptor atom.
5. Donor-acceptor distance (Å).
6. Angle between donor and acceptor through H.
7. Salt-bridges.
8. Positively-charged residue - negatively charged residue.
9. Salt-bridge distances (Å).
10. Salt-bridge angles (degrees °).
11. π-π stacks.
12. N distances between two rings.
13. P distances between two rings.
14. Angles between two rings.
15. Orientation between two rings.
16. π-cation interactions.
17. Cation - π ring.
18. Distances cations and rings.
19. Angles between cations and rings.
20. Guanidinium ions.
21. Guanidinium ion-angle.
22. Guanidinium-orientation.
23. Disulfide bonds.
24. Disulfide bonds distances (Å).
25. Disulfide bonds angles (degrees °).
26. Edge weights.
27. InteractionSite.
28. Mutual Information.
29. Average Product Correction.

They derive from the corresponding file previously described. The directionality of edges identifying some interactions such as hydrogen bonds, salt bridges and π-cation interactions is maintained in some of the corresponding attributes.

1. Closest atoms.
2. Distance between closest atoms (Å).
3. H-Bonds.
4. Donor-atom - acceptor atom.
5. Donor-acceptor distance (Å).
6. Angle between donor and acceptor through H.
7. Salt-bridges.
8. Positively-charged residue - negatively charged residue.
9. Salt-bridge distances (Å).
10. Salt-bridge angles (degrees °).
11. π-π stacks.
12. N distances between two rings.
13. P distances between two rings.
14. Angles between two rings.
15. Orientation between two rings.
16. π-cation interactions.
17. Cation - π ring.
18. Distances cations and rings.
19. Angles between cations and rings.
20. Guanidinium ions.
21. Guanidinium ion-angle.
22. Guanidinium-orientation.
23. Disulfide bonds.
24. Disulfide bonds distances (Å).
25. Disulfide bonds angles (degrees °).
26. Edge weights.
27. InteractionSite.
28. Van der Waals contact scores.
29. Mutual Information.
30. Average Product Correction.

Node attributes derive from the corresponding files previously described. They depend on the secondary structure conformation of a certain residue and their solvent accessibility. The information is derived from the φ and ψ torsion angles. The allowed values are "E" for sheet, "H" for helix, "C" for coil and "" for unknown.

DSSP is also used to assign solvent accessibility and secondary structure in three and eight classes. The eight DSSP secondary structure classes are transformed into three as follows as follows: "H" = helix : DSSP's "H" (alpha helix) + "G" (3-10 helix) + "I" (π-helix) classes; "E" = strand : DSSP's "E" (extended strand) + "B" (beta-bridge) classes; "C" = the rest : DSSP's "T" (turn) + "S" (bend) + "." (the rest).

Only those residues for which both DSSP and RING produce and output (same three letter code and same PDB numbering) are included in the derived node attributes files.

1. SS - secondary structure derived from the φ and ψ torsion angles.

2. SS3 - DSSP derived secondary structure in three classes.

3. SS8 - DSSP derived secondary structure in eight classes.

4. SA - DSSP derived solvent accessibility.

5. CON - conservation of each amino acid in the sequence in a multiple sequence alignment.

6. FRST - FRST energy calculation.

7. TAP - TAP Score energy calculation.

8. BF - C&alpha B-factor.

9. OC - C&alpha Occupancy.

10. IDs - Node complete ID

11. degree - Node degree.

12. CMI - Comulative Mutual Information.