Table 1.
An example of data from a contact-type scoring matrix
| ALA | ARG | ASN | ASP | CYS | GLN | GLU | GLY | HIS | ILE | LEU | LYS | MET | PHE | PRO | SER | THR | TRP | TYR | VAL | |
| ALA | 0.27 | -0.12 | -0.19 | -0.23 | -0.06 | -0.21 | -0.39 | 0.11 | -0.01 | 0.32 | 0.31 | -0.42 | 0.00 | 0.26 | -0.05 | -0.05 | 0.05 | 0.12 | 0.19 | 0.35 |
| ARG | -0.33 | -0.38 | -0.24 | -0.30 | -0.43 | -0.36 | -0.15 | -0.22 | -0.03 | 0.00 | -0.72 | -0.31 | -0.01 | -0.18 | -0.27 | -0.22 | -0.10 | -0.03 | -0.01 | |
| ASN | -0.04 | -0.30 | -0.28 | -0.34 | -0.57 | -0.09 | -0.19 | -0.02 | -0.14 | -0.47 | -0.30 | -0.01 | -0.20 | -0.13 | -0.09 | -0.10 | 0.02 | -0.07 | ||
| ASP | -0.44 | -0.41 | -0.48 | -0.70 | -0.18 | -0.19 | -0.14 | -0.22 | -0.43 | -0.44 | -0.15 | -0.29 | -0.28 | -0.24 | -0.19 | -0.08 | -0.15 | |||
| CYS | 0.67 | -0.33 | -0.63 | -0.08 | -0.02 | 0.15 | 0.12 | -0.57 | -0.06 | 0.19 | -0.19 | -0.13 | -0.11 | 0.03 | 0.07 | 0.14 | ||||
| GLN | -0.36 | -0.67 | -0.26 | -0.27 | -0.10 | -0.09 | -0.64 | -0.34 | -0.08 | -0.26 | -0.28 | -0.23 | -0.13 | -0.08 | -0.11 | |||||
| GLU | -0.77 | -0.45 | -0.39 | -0.23 | -0.27 | -0.53 | -0.57 | -0.27 | -0.46 | -0.51 | -0.44 | -0.38 | -0.23 | -0.25 | ||||||
| GLY | 0.16 | 0.02 | 0.16 | 0.08 | -0.43 | -0.10 | 0.15 | -0.04 | -0.01 | 0.04 | 0.08 | 0.14 | 0.19 | |||||||
| HIS | 0.16 | 0.09 | 0.07 | -0.55 | -0.11 | 0.16 | -0.08 | -0.05 | -0.03 | 0.11 | 0.16 | 0.09 | ||||||||
| ILE | 0.71 | 0.55 | -0.13 | 0.24 | 0.55 | -0.03 | 0.09 | 0.20 | 0.28 | 0.43 | 0.58 | |||||||||
| LEU | 0.58 | -0.26 | 0.15 | 0.49 | -0.01 | 0.02 | 0.12 | 0.27 | 0.35 | 0.51 | ||||||||||
| LYS | -0.63 | -0.56 | -0.23 | -0.49 | -0.47 | -0.41 | -0.45 | -0.20 | -0.22 | |||||||||||
| MET | 0.24 | 0.25 | -0.23 | -0.20 | -0.11 | 0.09 | 0.14 | 0.16 | ||||||||||||
| PHE | 0.60 | 0.04 | 0.10 | 0.16 | 0.39 | 0.47 | 0.48 | |||||||||||||
| PRO | -0.04 | -0.15 | -0.11 | 0.06 | 0.09 | 0.02 | ||||||||||||||
| SER | -0.04 | -0.03 | 0.01 | 0.07 | 0.07 | |||||||||||||||
| THR | 0.06 | 0.05 | 0.13 | 0.21 | ||||||||||||||||
| TRP | 0.48 | 0.35 | 0.26 | |||||||||||||||||
| TYR | 0.42 | 0.37 | ||||||||||||||||||
| VAL | 0.59 |
An example of one of the contact-type scoring matrices used in this work. The scores are defined as described in the Methods Section. In this matrix residue-residue contacts were defined using a 12 Å distance threshold between Cβ atoms and using a sequence separation filter to remove short-range interactions.