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Table 1 Accumulated Affinity between Codons

From: Correlation between nucleotide composition and folding energy of coding sequences with special attention to wobble bases

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
  1. Each value is the accumulated affinity (dG) between synonymous codons corresponding to the indicated amino acids (log-kcal/mol);
  2. CF: codon frequency/number of synonymous codons/amino acid. Highest (>4) and lowest (<3) values are indicated.