Table 3.
Groove computation with 3 coefficients for a reduced amino acid set. This table is identical in intent to Table S2. Here, however, the bases themselves are also tabulated, together with the products of their coefficients and the corresponding element of the design matrix. Inspection of Figure 1 will confirm the entries in columns 3–7. The intercept for this model is 1, the coefficients are: −1(Y/R) = 2, 1(Y/R) = 1, and 2(Y/R)*73(Y/R) = −1, leading to the respective contributions in columns 9–11 to the total in column 12.
| Class I | Base 1 | Base 2 | Base 72 | Base 73 | Constant | −1 | 1Y/R | 2Y/R*73Y/R | Total | ||
|---|---|---|---|---|---|---|---|---|---|---|---|
| IA | Arg | G | C | C | G | 1 | 0 | −1 | 1 | 1 | |
| IA | Cys | G | G | C | U | 1 | 0 | −1 | 1 | 1 | |
| IA | Leu | G | U | C | G | 1 | 0 | −1 | 1 | 1 | |
| IA | Met | U | G | A | G | 1 | 0 | 1 | −1 | 1 | |
| IB | Glu | G | C | C | A | 1 | 0 | −1 | 1 | 1 | |
| IB | Gln | C | G | A | A | 1 | 0 | 1 | −1 | 1 | |
| IC | Tyr | G | G | C | A | 1 | 0 | −1 | −1 | −1 | |
| IC | Trp | A | G | U | G | 1 | 0 | −1 | −1 | −1 | |
| Class II | |||||||||||
| IIA | Ala | G | G | C | A | 1 | 0 | −1 | −1 | −1 | |
| IIA | Gly | G | G | C | G | 1 | 0 | −1 | −1 | −1 | |
| IIA | His | G | G | C | C | A | 1 | −2 | −1 | 1 | −1 |
| IIA | Ser | G | C | C | U | 1 | 0 | −1 | −1 | −1 | |
| IIB | Asp | G | G | C | G | 1 | 0 | −1 | −1 | −1 | |
| IIC | Phe | G | C | C | A | 1 | 0 | −1 | 1 | 1 |