Figure 11.

Topological analysis of the alpha-helix structure from beta barrel 2GR8. The coarse-grained representation is employed with C_α atoms in the green color in a. The topological fingerprint of the alpha-helix structure is depicted in b. The details of the barcode enclosed in red boxes are demonstrated in c and d. It is seen from c that in the β₀ panel, the length of most bars is around 3.8Å except for those of three bars. Two of these β₀ bars end around 4.5Å, and the other lasts forever. These three bars represent the remaining isolated alpha helices when C_α atoms inside each alpha helix become connected at about 3.8Å. However, when the filtration parameter is increased to 4.5Å, which is exactly the smallest distance between alpha helices, three alpha helices are connected and the total number of independent entities becomes one. There are also three bars in the β₂ panel as shown in b. There is a total of 43 β₁ bars as shown in d.