Table 1.
Protein superfamilies with minor groove contacts.
| SRF-like |
| IHF-like DNA-binding proteins |
| Histone-fold |
| DNA breaking-rejoining enzymes |
| Zn2/Cys6 DNA-binding domain |
| Homeodomain-like |
| p53-like transcription factors |
| lambda repressor-like DNA-binding domains |
| Winged helix DNA-binding domain |
| Leucine zipper domain |
| C-terminal effector domain of the bipartite response regulators |
| Restriction endonuclease-like |
| Glucocorticoid receptor-like (DNA-binding domain) |
| DNA repair protein MutS, domain I |
| Origin of replication-binding domain, RBD-like |
| DNA/RNA polymerases |
| Eukaryotic DNA topoisomerase I, N-terminal DNA-binding fragment |
| Ribonuclease H-like |
| TATA-box binding protein-like |
Listed are SCOP superfamilies47 that have an arginine-minor groove contact within a distance of <6.0 Å from the base. Superfamilies that use arginine to contact a narrow minor groove (<5.0 Å) have grey shading; those that use arginine to contact a non-narrow minor groove (≥5.0 Å) are unshaded. Only superfamilies with a minimum of ten protein chains in PDB structures bound to DNA at least one helical turn long are included. The percentages of chains with minor groove contacts vary considerably among SCOP superfamilies and are provided in Supplementary Table 1.