LGA
Sequence Independent Analysis (LGA)
Frame of reference: Cat.Q2246_545_439.5wLII_11277_268
Total number of 3D structures: 6
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 |
2dm9_A |
118 |
117 |
111 |
1.38 |
10.81 |
88.994 |
7.502 |
T P |
2dma_A |
118 |
117 |
111 |
1.38 |
9.91 |
88.810 |
7.488 |
T P |
1q9j_B |
399 |
117 |
47 |
2.47 |
4.26 |
30.877 |
1.832 |
T P |
1eqf_A |
267 |
117 |
45 |
2.34 |
11.11 |
27.588 |
1.844 |
T P |
2rf7_A |
441 |
117 |
43 |
2.50 |
4.65 |
24.208 |
1.651 |
T P |
2rdz_A |
441 |
117 |
39 |
2.77 |
10.26 |
23.581 |
1.361 |
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]