Figure 7
From: A local average distance descriptor for flexible protein structure comparison
Illustrating the variation between LAD ED and LAD GD for a self-connection case.The 3D domain-swapped Ribonuclease A consists of a protein body (green/blue surface), a hinge loop (red surface) and a swapped domain (yellow surface). (a) The open-form Ribonuclease A (PDB code: 1js0, chain A) (b) The domain-swapped closed homolog of (a) (PDB code: 3di8, chain A). (c) and (d) are LADED and LADGD profiles of both closed- and open-form structures respectively. The red solid curve of (a) and (b) denotes a GD path, which is the shortest path along the surface (white surface region) connecting two residues H105 and V108 (red spheres). The residues from H105 to A109 of both proteins are shown as magenta sticks and highlighted within a magenta box in (c) and (d). The black dashed line of (a) and (b) indicates the ED path between the residues H105 and V108. Note that the magenta box has shown that the LADGD profile is more sensitive at the topological changed locations than the LADED profile.