LGA
Sequence Independent Analysis (LGA)
Frame of reference: Cat.Q2246_545_298.5wLII_11238_55
Total number of 3D structures: 9
LGA calculations using distance cutoff DIST: 4.0 A
Residues superimposed below 2.00 A: GREEN
Residues superimposed below 4.00 A: YELLOW
Residues superimposed below 6.00 A: ORANGE
Residues superimposed below 8.00 A: BROWN
Residues superimposed above 8.00 A or not aligned: RED
Terminal residues not aligned: GREY
Structure Deviation Summary
Calculations based on one final LGA superposition
(Bar representation of 3D plots, TEXT)
Structures ordered by LGA_S - score
Structure |
NS |
NT |
N(dist=4.0) |
RMSD(N) |
Seq_ID(N) |
LGA_S |
LGA_Q |
PLOTS |
3bul_A |
577 |
282 |
265 |
1.20 |
18.49 |
89.724 |
20.449 |
T P |
1msk_A |
327 |
282 |
265 |
1.46 |
18.49 |
87.601 |
16.951 |
T P |
1k7y_A |
577 |
282 |
265 |
1.45 |
18.49 |
87.281 |
17.132 |
T P |
2o2k_B |
333 |
282 |
247 |
1.65 |
14.17 |
80.380 |
14.121 |
T P |
1j6r_A |
197 |
282 |
154 |
2.28 |
14.29 |
38.750 |
6.478 |
T P |
2pyw_A |
417 |
282 |
58 |
2.63 |
12.07 |
13.545 |
2.122 |
T P |
1bmt_A |
246 |
282 |
50 |
2.44 |
8.00 |
12.990 |
1.967 |
T P |
2j1q_A |
339 |
282 |
40 |
2.07 |
2.50 |
10.604 |
1.843 |
T P |
2dm9_A |
118 |
282 |
38 |
2.78 |
7.89 |
9.164 |
1.319 |
T P |
NS : Total number of residues in Structure (rotated structure)
NT : Total number of residues in TARGET (frame of reference)
N : Total number of residues superimposed under 4.0 Angstrom distance cutoff
RMSD : RMS deviation calculated on all N residues superimposed under 4.0 Angstrom distance cutoff
Seq_Id : Sequence Identity. Percent of identical residues from the total of N aligned.
LGA_S : Structure similarity score calculated by internal LGA procedure (see LGA paper for details)
LGA_Q : Score (how tight is the superposition) calculated by the formula: Q = 0.1*N/(0.1+RMSD)
PLOTS : T - Flat text file (output from LGA program, rotated structure)
PLOTS : P - Plot of superimposed structures (3D plot colored as bars)
Citing LGA:
Zemla A., "LGA - a Method for Finding 3D Similarities in Protein Structures",
Nucleic Acids Research, 2003, Vol. 31, No. 13, pp. 3370-3374.
[MEDLINE]