Examples of the three types of flexible regions. 1) Pair (a1) and (a2) is an example of rotating regions. (a1) is chain A of protein 1l5e from Leu1 to Tyr100 and (a2) is protein 2ezm from Leu1 to Tyr 100. Both fragments share the same sequence, are build from two domains (colored gray and black) that also share the same structure, but the structures of the linkers (colored in light gray) are different. 2) Pair (b1) and (b2) is an example of regions with missing secondary structure. (b1) is chain A of protein 1ikx from Glu224 to Leu279 and (a2) is chain B of protein 1ikx f from Glu1224 to Leu1279. Both fragments share the same sequence. The Phe227 to Leu234 in (b1) forms a strand, while it forms a coil in (b2). 3) Pair (c1) and (c2) is an example of disarranging regions. (c1) is chain A of protein 1ffx from Ile171 to Cys200 and (c2) is chain A of protein 1jff from Ile171 to Cys200. The fragments share the same sequence, and have similar overall 3D-structure and secondary structure. At the same time, the URMSD between these two structures is larger than 0.8 since the middle region between 180Ala and 192His is disarranged. The spatial packing of the corresponding AAs is different for this region.
Chen et al. BMC Structural Biology 2007 7:25 doi:10.1186/1472-6807-7-25