Project name: LL 37

Status: done

submitted: 2020-06-20 12:35:42, status changed: 2020-06-25 14:02:18
Settings
Chain sequence(s) A: LLGDFFRKSKEKIGKEFKRIVQRIKDFLRNLVPRTES
Distance of aggregation 10 Å
Dynamic mode Yes
Show buried residues

Minimal score value
-3.0742
Maximal score value
2.6791
Average score
-0.512
Total score value
-18.9446

The table below lists A3D score for protein residues. Residues with A3D score > 0.0000 are marked by yellow rows.

residue index residue name chain Aggrescan3D score mutation
residue index residue name chain Aggrescan3D score
mutation
1 L A 2.4694
2 L A 2.6791
3 G A 1.0213
4 D A 0.4152
5 F A 1.9263
6 F A 1.0402
7 R A -2.0525
8 K A -2.4001
9 S A -2.0218
10 K A -2.9711
11 E A -3.0401
12 K A -3.0742
13 I A -0.8640
14 G A -1.6240
15 K A -2.5824
16 E A -0.9636
17 F A 0.7482
18 K A -1.3573
19 R A -1.1772
20 I A 0.9043
21 V A 0.7737
22 Q A -1.2636
23 R A -1.1323
24 I A 0.7120
25 K A -1.2473
26 D A -0.8205
27 F A 1.5301
28 L A 1.5186
29 R A -0.7177
30 N A -0.1296
31 L A 2.0119
32 V A 1.6619
33 P A -0.2812
34 R A -2.3164
35 T A -2.1885
36 E A -2.7173
37 S A -1.4141

Above is the comparison between the input structure and the most aggregation prone model (predicted in the flexibility simulations, download both models in the PDB file format , download table with rmsd values ). The picture presents the most aggregation prone model (in blue) superimposed on the input structure (in red). The plot shows rmsd profile (distances between residues of the superimposed structures).

Dynamic mode uses CABS-flex simulations of protein structure fluctuations. The structure fluctuations may have impact on the size and extent of aggregation "hot-spots" on the protein surface. The dynamic mode uses the following pipeline: (1) based on the input structure, CABS-flex predicts a set of different models reflecting protein dynamics in solution; (2) for each of these models A3D score is calculated; (3) finally, the most aggregation prone model (the model with the highest A3D score, -0.512 in this case) is selected and presented in A3D results.


 

Laboratory of Theory of Biopolymers 2015