Project name: TTH04839

Status: done

submitted: 2019-02-15 17:07:13, status changed: 2019-02-15 19:26:54
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Chain sequence(s) D: PEVRAERYIPAPPERVYRLAKDLEGLKPYLKEVESLEVVAREGARTRSRWVAVAMGKKVRWLEEEEWDDENLRNRFFSPEGDFDRYEGTWVFLPEGEGTRVVLTLTYELTIPIFGGLLRKLVQKLMQENVESLLKGLEERVLAASS
Distance of aggregation 10 Å
Dynamic mode Yes
Show buried residues
Minimal score value
-3.7353
Maximal score value
3.2643
Average score
-0.7735
Total score value
-112.9249

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
2 P D -1.6326
3 E D -2.5156
4 V D 0.0000
5 R D -2.9246
6 A D -2.3109
7 E D -2.6905
8 R D -1.7384
9 Y D -0.4933
10 I D 0.0000
11 P D -0.7724
12 A D 0.0000
13 P D -1.8299
14 P D -1.9364
15 E D -2.6451
16 R D -1.8764
17 V D 0.0000
18 Y D 0.0000
19 R D -2.0472
20 L D 0.0000
21 A D 0.0000
22 K D -1.5808
23 D D -2.0972
24 L D 0.0000
25 E D -2.8470
26 G D -2.1153
27 L D 0.0000
28 K D -2.6943
29 P D -1.5360
30 Y D -0.3341
31 L D 0.0000
32 K D -2.4022
33 E D -1.0554
34 V D 0.0000
35 E D -0.9969
36 S D -0.9258
37 L D 0.0000
38 E D -1.4163
39 V D -0.2674
40 V D 0.7354
41 A D -0.4558
42 R D -2.1477
43 E D -2.8681
44 G D -1.7543
45 A D -1.5176
46 R D -1.8919
47 T D 0.0000
48 R D -0.8970
49 S D 0.0000
50 R D -0.7637
51 W D 0.0000
52 V D 0.0000
53 A D 0.0000
54 V D 0.3813
55 A D 0.0896
56 M D 0.6120
57 G D -0.7326
58 K D -1.7833
59 K D -1.8336
60 V D -1.2757
61 R D -1.4562
62 W D 0.0000
63 L D -1.0601
64 E D 0.0000
65 E D -0.5645
66 E D 0.0000
67 E D -1.2649
68 W D -1.3663
69 D D -2.2866
70 D D -3.7353
71 E D -3.4677
72 N D -2.7442
73 L D 0.0000
74 R D -2.0127
75 N D 0.0000
76 R D -0.7748
77 F D 0.0000
78 F D -0.4279
79 S D 0.0000
80 P D -1.6458
81 E D -2.6295
82 G D 0.0000
83 D D -2.8689
84 F D -1.8308
85 D D -2.2538
86 R D -2.1615
87 Y D 0.0000
88 E D -0.9442
89 G D 0.0000
90 T D -0.5084
91 W D 0.0000
92 V D -0.4082
93 F D 0.0000
94 L D 0.0505
95 P D -1.1908
96 E D -1.6936
97 G D -1.7415
98 E D -2.5656
99 G D 0.0000
100 T D 0.0000
101 R D -1.6091
102 V D 0.0000
103 V D -0.9334
104 L D 0.0000
105 T D 0.0000
106 L D 0.0000
107 T D -1.4573
108 Y D 0.0000
109 E D -1.4424
110 L D -0.6847
111 T D 0.0760
112 I D 1.2173
113 P D 1.3853
114 I D 3.0199
115 F D 3.2643
116 G D 1.9488
117 G D 1.0817
118 L D 2.0962
119 L D 1.4139
120 R D -0.2850
121 K D -1.2290
122 L D 0.3272
123 V D 0.0000
124 Q D -1.7619
125 K D -1.8138
126 L D 0.0000
127 M D 0.0000
128 Q D -2.2365
129 E D -1.8971
130 N D 0.0000
131 V D 0.0000
132 E D -2.6539
133 S D 0.0000
134 L D 0.0000
135 L D 0.0000
136 K D -2.3352
137 G D 0.0000
138 L D 0.0000
139 E D -1.2476
140 E D -1.7127
141 R D -1.0551
142 V D 0.0000
143 L D 0.6989
144 A D 0.1143
145 A D -0.0013
146 S D 0.0836
147 S D 0.0420

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View in JSmol

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, -0.7735 in this case) is selected and presented in A3D results.


 
Laboratory of Theory of Biopolymers 2015