Table 2.
Extended stability score of N1N2Y3 codon-pairs
| Amino acid | Codon pair | Fold | N1:N36 H-bonds | N2:N35 H-bonds | N2 Y/R | C3:G34 H-bonds | U3:G34 H-bonds | N1N2C3 Extended stability score | N1N2U3 Extended stability score |
|---|---|---|---|---|---|---|---|---|---|
| Asn | AAY | 2 | 2 | 2 | 0 | 3 | 2 | 7a | 6 |
| Tyr | UAY | 2 | 2 | 2 | 0 | 3 | 2 | 7a | 6 |
| Ser | AGY | 2 | 2 | 3 | 0 | 3 | 2 | 8a | 7 |
| Ile | AUY | 3 | 2 | 2 | 1 | 3 | 2 | 8a | 7 |
| His | CAY | 2 | 3 | 2 | 0 | 3 | 2 | 8a | 7 |
| Asp | GAY | 2 | 3 | 2 | 0 | 3 | 2 | 8a | 7 |
| Cys | UGY | 2 | 2 | 3 | 0 | 3 | 2 | 8a | 7 |
| Phe | UUY | 2 | 2 | 2 | 1 | 3 | 2 | 8a | 7 |
| Arg | CGYb | 4 | 3 | 3 | 0 | 2(+) | 2(−) | 8(+) | 8(−)a |
| Thr | ACY | 4 | 2 | 3 | 1 | 3 | 2 | 9 | 8a |
| Leu | CUY | 4 | 3 | 2 | 1 | 3 | 2 | 9 | 8 |
| Gly | GGY | 4 | 3 | 3 | 0 | 3 | 2 | 9 | 8a |
| Val | GUY | 4 | 3 | 2 | 1 | 3 | 2 | 9 | 8a |
| Ser | UCY | 4 | 2 | 3 | 1 | 3 | 2 | 9 | 8a |
| Pro | CCY | 4 | 3 | 3 | 1 | 3 | 2 | 10 | 9a |
| Ala | GCY | 4 | 3 | 3 | 1 | 3 | 2 | 10 | 9a |
aMarks the extended stability score of the preferred codon according to the observed fold rule.
bThe Arg-CGY codon-pair is read by the ACG (modified to ICG) tRNA. Since bonds formed within an I:C base pair are stronger than within an I:U pair, the relevant hydrogen bonds and the extended stability scores are marked with (+) and (−), respectively.