Fig 8. Disfavored structures of a GB loop with various three-stranded β-sheets identified by the simulation.

The structures are categorized according to their register shifts. (A) Conformation of the system V exhibiting inter-atomic collision between the helix and S2’. This atomic collision was one of the dominant factors for the decrease of structures satisfying the condition (b) not only in the system V, but also in the systems with $R_{2-2^{\prime }}^N\le 0$. (B)-(D) Disfavored conformations of the system VIII. (B) Conformation with inter-atomic collision between S1 and the GB loop and (C) that between the helix and S2’. (D) Unsatisfied polar groups and their frequencies of unsatisfaction. (E) Conformation in which the most frequently unsatisfied hydrogen bond donor did not meet the hydrogen bond satisfaction condition. (F)-(I) Disfavored conformations of the system IX. (F) Frequency of structures that satisfied the various conditions imposed on the structures corresponding to the survivors of the system VIII. (G) Polar group that violate the condition (a) or (c) and their frequencies. (H) Conformation that did not satisfy condition (a). (I) Conformation in which the most frequently unsatisfied hydrogen bond donor did not meet the condition (c). In (A), (B), (C), (E), and (I), protein atoms and virtual water molecules that collide with other atoms are depicted as transparent spheres colored in CPK and purple, respectively.