Table 1.
Accumulated Affinity between Codons
| CF | 1 | 1 | 2 | 2 | 2 | 2 | 2 | 2 | 2 | 2 | 2 | 3 | 3 | 4 | 4 | 4 | 4 | 4 | 6 | 6 | 6 | |
| AA | Met | Trp | Lys | Glu | Phe | Asn | Gln | His | Tyr | Asp | Cys | End | Ile | Pro | Gly | Thr | Ala | Val | Leu | Arg | Ser | |
| 1 | Met | 2.8 | 2.6 | 0.0 | 0.0 | 3.2 | 3.2 | 3.3 | 3.6 | 3.1 | 2.9 | 3.1 | 3.2 | 3.7 | 3.4 | 2.8 | 3.4 | 3.2 | 3.6 | 3.7 | 3.4 | 3.9 |
| 1 | Trp | 2.6 | 1.0 | 0.0 | 0.0 | 3.1 | 3.2 | 3.3 | 3.7 | 3.6 | 3.2 | 3.4 | 2.9 | 3.5 | 3.9 | 3.0 | 3.9 | 3.8 | 3.0 | 4.0 | 3.7 | 3.7 |
| 2 | Lys | 0.0 | 0.0 | 0.0 | 0.0 | 3.8 | 0.0 | 0.0 | 3.1 | 3.3 | 0.0 | 3.3 | 0.0 | 3.4 | 3.1 | 0.0 | 2.9 | 2.9 | 3.4 | 3.9 | 3.1 | 3.9 |
| 2 | Glu | 0.0 | 0.0 | 0.0 | 0.0 | 3.9 | 0.0 | 0.0 | 3.6 | 3.4 | 0.0 | 3.4 | 0.0 | 3.5 | 3.9 | 0.0 | 3.5 | 3.5 | 3.5 | 4.2 | 3.6 | 4.2 |
| 2 | Phe | 3.2 | 3.1 | 3.8 | 3.9 | 0.0 | 3.4 | 3.3 | 0.0 | 0.0 | 3.5 | 0.0 | 3.6 | 3.1 | 0.0 | 4.0 | 3.5 | 3.3 | 3.3 | 0.0 | 4.0 | 3.2 |
| 2 | Asn | 3.2 | 3.2 | 0.0 | 0.0 | 3.4 | 2.9 | 0.0 | 2.8 | 3.5 | 3.2 | 3.7 | 3.6 | 3.6 | 0.0 | 3.2 | 2.9 | 3.0 | 3.9 | 4.0 | 3.2 | 3.8 |
| 2 | Gln | 3.3 | 3.3 | 0.0 | 0.0 | 3.3 | 0.0 | 3.2 | 0.0 | 3.2 | 3.3 | 4.0 | 3.6 | 2.8 | 3.3 | 3.5 | 2.9 | 3.9 | 4.0 | 4.1 | 3.7 | 3.9 |
| 2 | His | 3.6 | 3.7 | 3.1 | 3.6 | 0.0 | 2.8 | 0.0 | 2.7 | 2.7 | 3.7 | 3.6 | 3.8 | 3.2 | 0.0 | 4.0 | 3.1 | 3.6 | 4.0 | 3.7 | 3.9 | 3.7 |
| 2 | Tyr | 3.1 | 3.6 | 3.3 | 3.4 | 0.0 | 3.5 | 3.2 | 2.7 | 3.5 | 3.2 | 3.2 | 3.9 | 3.7 | 0.0 | 3.9 | 3.4 | 3.3 | 4.0 | 3.7 | 3.8 | 4.0 |
| 2 | Asp | 2.9 | 3.2 | 0.0 | 0.0 | 3.5 | 3.2 | 3.3 | 3.7 | 3.2 | 3.2 | 3.5 | 3.4 | 3.8 | 3.7 | 3.4 | 3.5 | 3.5 | 4.0 | 4.0 | 3.9 | 4.2 |
| 2 | Cys | 3.1 | 3.4 | 3.3 | 3.4 | 0.0 | 3.7 | 4.0 | 3.6 | 3.2 | 3.5 | 3.5 | 3.7 | 3.6 | 3.6 | 4.0 | 3.9 | 4.2 | 3.8 | 3.7 | 4.1 | 3.9 |
| 3 | End | 3.2 | 2.9 | 0.0 | 0.0 | 3.6 | 3.6 | 3.6 | 3.8 | 3.9 | 3.4 | 3.7 | 3.8 | 4.0 | 3.7 | 3.3 | 3.9 | 3.8 | 3.9 | 4.3 | 3.8 | 4.2 |
| 3 | Ile | 3.7 | 3.5 | 3.4 | 3.5 | 3.1 | 3.6 | 2.8 | 3.2 | 3.7 | 3.8 | 3.6 | 4.0 | 3.9 | 0.0 | 3.8 | 3.6 | 3.2 | 4.0 | 4.0 | 3.8 | 4.0 |
| 4 | Pro | 3.4 | 3.9 | 3.1 | 3.9 | 0.0 | 0.0 | 3.3 | 0.0 | 0.0 | 3.7 | 3.6 | 3.7 | 0.0 | 3.2 | 4.5 | 3.3 | 4.1 | 4.2 | 3.6 | 4.3 | 3.9 |
| 4 | Gly | 2.8 | 3.0 | 0.0 | 0.0 | 4.0 | 3.2 | 3.5 | 4.0 | 3.9 | 3.4 | 4.0 | 3.3 | 3.8 | 4.5 | 3.5 | 4.2 | 4.3 | 4.0 | 4.5 | 4.2 | 4.4 |
| 4 | Thr | 3.4 | 3.9 | 2.9 | 3.5 | 3.5 | 2.9 | 2.9 | 3.7 | 3.4 | 3.5 | 3.9 | 3.9 | 3.6 | 3.3 | 4.2 | 3.2 | 3.9 | 4.4 | 4.2 | 4.2 | 4.3 |
| 4 | Ala | 3.2 | 3.8 | 2.9 | 3.5 | 3.3 | 3.0 | 3.9 | 3.6 | 3.3 | 3.5 | 4.2 | 3.8 | 3.2 | 4.1 | 4.3 | 3.9 | 4.5 | 4.4 | 4.3 | 4.4 | 4.3 |
| 4 | Val | 3.6 | 3.0 | 3.4 | 3.5 | 3.3 | 3.9 | 4.0 | 4.0 | 4.0 | 4.0 | 3.8 | 3.9 | 4.0 | 4.2 | 4.0 | 4.4 | 4.4 | 3.6 | 4.3 | 4.4 | 4.1 |
| 6 | Leu | 3.7 | 4.0 | 3.9 | 4.2 | 0.0 | 4.0 | 4.1 | 3.7 | 3.7 | 4.0 | 3.7 | 4.3 | 4.0 | 3.6 | 4.5 | 4.2 | 4.3 | 4.3 | 4.0 | 4.5 | 4.3 |
| 6 | Arg | 3.4 | 3.7 | 3.1 | 3.6 | 4.0 | 3.2 | 3.7 | 3.9 | 3.8 | 3.9 | 4.1 | 3.8 | 3.8 | 4.3 | 4.2 | 4.2 | 4.4 | 4.4 | 4.5 | 4.5 | 4.6 |
| 6 | Ser | 4.0 | 3.8 | 3.9 | 4.2 | 3.2 | 3.7 | 3.9 | 3.5 | 3.8 | 4.2 | 4.0 | 4.2 | 3.8 | 3.8 | 4.5 | 4.2 | 4.4 | 4.2 | 4.3 | 4.6 | 4.1 |
Each value is the accumulated affinity (dG) between synonymous codons corresponding to the indicated amino acids (log-kcal/mol);
CF: codon frequency/number of synonymous codons/amino acid. Highest (>4) and lowest (<3) values are indicated.