Table 6.
KUGGUM cluster analysis (Figure 3E).
| Interaction | Percentage of KUGGUM sequence-representative structures with interaction (n = 2)a, b, c | Percentage of all KUGGUM structures in cluster with interaction (x = 9)d | Percentage of all other tetraloop sequence-representative structures with interaction |
|---|---|---|---|
| All nts have an anti glycosidic angle | nt 1 – 100% anti | nt 1 – 100% anti | nt 1 – 100% anti |
| nt 2 – 100% anti | nt 2 – 100% anti | nt 2 – 99% anti | |
| nt 3 – 100% anti | nt 3 – 100% anti | nt 3 – 93% anti | |
| nt 4 – 100% anti | nt 4 – 100% anti | nt 4 – 93% anti | |
| nt 5 – 100% anti | nt 5 – 100% anti | nt 5 – 87% anti | |
| nt 6 – 100% anti | nt 6 – 100% anti | nt 6 – 100% anti | |
| Base pairing between nt 1 and nt 6 | 100% | 100% | 99% |
| Base pairing between nt 4 and nt 5 | 100% | 100% | 0% |
| Hydrogen bond between O2’ (hydroxyl) of nt 2 and OP1 of nt 4 | 100% | 100% | 1% |
| Hydrogen bond between OP1 of nt 5 and O2’ (hydroxyl) of nt 6 | 100% | 78% | 0% |
| Hydrogen bond between N2 (amino) of nt 4 and O4 (carbonyl) of nt 5 | 100% | 100% | 0% |
| Hydrogen bond between O2’ (hydroxyl) of nt 4 and OP2 of nt 5 | 50% | 78% | 0% |
| nt 1, nt 2, an nt 6 have C3’-endo sugar pucker conformation; nt 3 and nt 5 have C2’-endo sugar pucker conformation | nt 1 – 100% C3’-endo | nt 1 – 100% C3’-endo | nt 1 – 96% C3’-endo |
| nt 2 – 100% C3’-endo | nt 2 – 100% C3’-endo | nt 2 – 81% C3’-endo | |
| nt 3 – 100% C2’-endo | nt 3 – 89% C2’-endo | nt 3 – 30% C2’-endo | |
| nt 5 – 100% C2’-endo | nt 5 – 100% C2’-endo | nt 5 – 26% C2’-endo | |
| nt 6 – 100% C3’-endo | nt 6 – 100% C3’-endo | nt 6 – 91% C3’-endo | |
| Stacking between nt 1 and nt 2 | 100% | 100% | 75% |
a
n = number of sequence-representative structures in this cluster.
b
Red values indicate interactions that are found among ≥75% of sequence-representative structures in this cluster and <75% of structures among all other tetraloops.
c
Blue values indicate interactions found in <75% of sequence-representative structures (n = 2) but found in ≥75% of the total number of structures represented by the sequences in this cluster (x = 9).
d
x = total number of structures represented by the sequences in this cluster.