The Effects of the Context-Dependent Codon Usage Bias on the Structure of the nsp1α of Porcine Reproductive and Respiratory Syndrome Virus

Table 1

The relationship between the synonymous codon usage and the formation of the specific secondary structure unit.

Amino acid	Codon	^a𝑃 value	^b𝑃 value	^c𝑃 value
Phe	UUU	0.40	0.07	−0.21
Phe	UUC	−0.92	−0.40	0.26
Leu	UUA	−1.07	1.47	−1.22
Leu	UUG	−0.16	−0.53	0.15
Leu	CUU	0.68	^d—	−0.06
Leu	CUC	−5.53	−5.32	0.48
Leu	CUA	0.17	−1.37	0.13
Leu	CUG	0.00	−4.15	0.24
Ile	AUU	0.99	0.92	−5.46
Ile	AUC	1.50	−1.17	^d—
Ile	AUA	0.69	1.12	−2.46
Val	GUU	0.58	0.28	−0.45
Val	GUC	0.32	0.20	−0.21
Val	GUA	1.27	0.02	−2.17
Val	GUG	−0.52	1.21	−0.73
Ser	UCU	0.76	^d—	−0.12
Ser	UCC	−4.45	−3.14	0.47
Ser	UCA	^d—	1.76	^d—
Ser	UCG	^d—	^d—	^d—
Ser	AGU	−4.79	1.35	−0.61
Ser	AGC	1.24	−0.25	−1.53
Pro	CCU	−0.48	−2.90	0.33
Pro	CCC	−2.85	−0.28	0.33
Pro	CCA	−0.32	−4.40	0.31
Pro	CCG	−0.23	−2.69	0.28
Thr	ACU	−0.08	0.58	−0.21
Thr	ACC	−0.57	0.53	−0.05
Thr	ACA	0.58	1.28	−5.24
Thr	ACG	−4.40	^d—	0.48
Ala	GCU	0.55	−2.56	0.00
Ala	GCC	−0.07	0.10	−0.01
Ala	GCA	0.78	0.16	−0.61
Ala	GCG	0.76	1.15	−4.18
Tyr	UAU	0.95	−1.60	−0.39
Tyr	UAC	0.21	1.37	−2.22
His	CAU	−4.21	1.75	−4.18
His	CAC	^d—	1.75	−3.81
Gln	CAA	0.62	−0.82	−0.15
Gln	CAG	−2.74	0.63	0.07
Asn	AAU	−4.47	−0.58	0.38
Asn	AAC	^d—	0.18	0.25
Lys	AAA	−0.90	^d—	0.39
Lys	AAG	1.18	^d—	−0.69
Asp	GAU	^d—	−3.17	0.48
Asp	GAC	^d—	^d—	0.48
Glu	GAA	0.93	^d—	−0.28
Glu	GAG	−1.15	−5.28	0.41
Cys	UGU	^d—	−4.75	0.48
Cys	UGC	−5.41	0.04	0.28
Arg	CGU	−1.82	0.28	0.18
Arg	CGC	^d—	1.52	−1.03
Arg	CGA	0.83	−2.13	−0.22
Arg	CGG	−0.04	0.16	−0.04
Arg	AGA	1.37	−4.30	−1.32
Arg	AGG	^d—	0.76	0.03
Gly	GGU	0.52	^d—	0.04
Gly	GGC	−0.34	−4.61	0.32
Gly	GGA	−4.76	−4.55	0.48
Gly	GGG	^d—	−4.62	0.48
Met	AUG	1.01	−0.35	−0.72
Trp	UGG	0.45	0.66	−0.61

^a𝑟𝑒𝑝𝑟𝑒𝑠𝑒𝑛𝑡𝑠α-helix.
^b𝑟𝑒𝑝𝑟𝑒𝑠𝑒𝑛𝑡𝑠β-strand.
^c𝑟𝑒𝑝𝑟𝑒𝑠𝑒𝑛𝑡𝑠 The coil.
^d𝑟𝑒𝑝𝑟𝑒𝑠𝑒𝑛𝑡𝑠 The corresponding codon is not selected in the specific secondary structure unit.
Italic indicates that the corresponding codon has a weak bias to be selected in a specific secondary structure unit.
Bold indicates that the corresponding codon has a tendency to be selected in a specific secondary structure unit.