Table 1.
Topological constraints of the PK motif, defined by the size of H1–L1–L2–L3–H2. We use loop L2 to exhaustively sample all the possible two-helix configurations in the MBB of H1–L2–H2. Fx is the fraction of the Vfold-allowed helical configurations with the corresponding loops. FPK (F123) denotes the total topological constraints of a PK structure
| PDB | Size | F 2 | F 12 | F 23 | F PK |
|---|---|---|---|---|---|
| 1a60 | 3–4–0–3–5 | 5.2E–3 | 1.8E–4 | 2.0E–4 | 4.6E–5 |
| 1e95 | 6–1–0–9–6 | 3.2E–3 | 1.8E–6 | 2.9E–3 | 1.8E–6 |
| 1hvu | 5–2–0–3–6 | 4.3E–3 | 6.5E–6 | 3.8E–5 | 1.2E–7 |
| 1ymo | 6–8–0–8–9 | 3.2E–3 | 2.5E–3 | 2.2E–3 | 1.7E–3 |
| 2n6q | 4–3–0–4–8 | 4.9E–3 | 3.9E–5 | 2.8E–4 | 9.2E–6 |
| 2tpk | 5–1–0–7–7 | 4.3E–3 | 7.1E–8 | 1.5E–3 | 7.1E–8 |
| 4p5j | 3–3–0–3–6 | 5.2E–3 | 4.2E–5 | 2.0E–4 | 2.1E–5 |
| 2m8k | 5–6–0–5–12 | 4.3E–3 | 5.8E–4 | 2.4E–4 | 2.6E–5 |
| 2ap0 | 5–1–1–9–3 | 2.8E–2 | 1.0E–4 | 2.6E–2 | 1.0E–4 |
| 1kpd | 5–3–1–7–5 | 2.7E–2 | 3.8E–4 | 9.6E–3 | 3.1E–4 |
| 1rnk | 5–2–1–8–6 | 2.7E–2 | 6.3E–5 | 1.7E–2 | 6.3E–5 |
| 1yg4 | 5–2–1–9–3 | 2.8E–2 | 4.6E–4 | 2.6E–2 | 4.5E–4 |
| 2a43 | 4–2–1–9–3 | 3.1E–2 | 4.6E–4 | 3.0E–2 | 4.6E–4 |
| 2rp1 | 5–2–1–8–3 | 2.8E–2 | 4.6E–4 | 2.0E–2 | 3.8E–4 |
| 2xdd | 4–4–1–6–3 | 3.1E–2 | 3.6E–3 | 1.0E–2 | 1.6E–3 |
| 4ato | 3–3–1–5–4 | 3.2E–2 | 8.6E–4 | 6.9E–3 | 5.4E–4 |
| 437d | 5–2–1–7–3 | 2.8E–2 | 4.6E–4 | 1.2E–2 | 2.3E–4 |
| 4rmo | 5–3–2–9–5 | 5.6E–2 | 8.3E–4 | 4.2E–2 | 8.3E–4 |
| 1kaj | 5–3–2–8–4 | 5.7E–2 | 1.6E–3 | 3.1E–2 | 1.4E–3 |
| 2m58 | 3–3–3–7–4 | 9.7E–2 | 3.3E–3 | 6.1E–2 | 3.0E–3 |
| Average | 2.5E–2 | 7.9E–4 | 1.5E–2 | 5.6E–4 | |