Properties of relations involving a O3'-P covalent bond:
| stack | $$ | Stacking | ||
| nostack | $$ | No stacking (deprecated, use !stack) | ||
| reverse | $$ | Reverse stacking | ||
| connect | $$ | Any covalently bonded relation (stack+!stack) (deprecated, use adjacent) | ||
| helix | $$ | Standard A-Form double helical stacking |
Properties of relations for paired residues:
| pairing | $$ | All pairing interaction | ||
| <I to XXVIII> | $$ | Pairing described by Saenger | ||
| saenger | $$ | All of the above | ||
| <29 to 137> | $$ | One-H-bond pairings described by Gautheret | ||
| one_hbond | $$ | All of the above One-H-bond | ||
| theo | $$ | Only theoretical (planar) pairing | ||
| cis | $$ | Glycosyl bonds are in the same orientation relative to the mean orientation of H-bonds | ||
| trans | $$ | Glycosyl bonds are in opposite orientation relative to the mean orientation of H-bonds | ||
| wct | $$ | Watson-Crick pairing used to build standard A-form helix |
Properties of residues in paired relations:
| any | $$ | any of the residue faces involved | ||
| W | $$ | Watson-Crick face involved: (Ww |
||
| Ww | $$ | center of the Watson-Crick face involved | ||
| Wh | $$ | Watson-Crick face involved, near the Hoogsteen face | ||
| Ws | $$ | Watson-Crick face involved, near the Sugar face | ||
| H | $$ | Hoogsteen face involved: (Hw |
||
| Hh | $$ | center of the Hoogsteen face involved | ||
| Hw | $$ | Hoogsteen face involved, near the Watson-Crick face | ||
| C8 | $$ | Hoogsteen face involved, near the C8 atom | ||
| S | $$ | Sugar face involved: (Sw |
||
| Sw | $$ | Sugar face involved, near the Watson-Crick face | ||
| Ss | $$ | center of the Sugar face involved | ||
| B | $$ | Bifurcated face involved | ||
| Bs | $$ | Bifurcated face involved, near the Sugar face | ||
| Bh | $$ | Bifurcated face involved, near the Hoogsteen face |