LGA
Sequence Independent Analysis (LGA)
Frame of reference: Cat.Q2246_545_457.5wLII_11284_33
Total number of 3D structures: 7
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 |
1vq8_P |
143 |
100 |
57 |
2.45 |
22.81 |
42.340 |
2.235 |
T P |
1ffk_M |
143 |
100 |
59 |
2.64 |
13.56 |
39.172 |
2.155 |
T P |
3bew_A |
271 |
100 |
35 |
2.47 |
8.57 |
24.334 |
1.361 |
T P |
3bdm_C |
241 |
100 |
31 |
2.44 |
6.45 |
22.768 |
1.218 |
T P |
3bev_A |
274 |
100 |
33 |
2.65 |
12.12 |
22.290 |
1.199 |
T P |
2of7_A |
191 |
100 |
31 |
2.60 |
9.68 |
21.783 |
1.150 |
T P |
2vqp_A |
254 |
100 |
31 |
2.70 |
6.45 |
19.530 |
1.108 |
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]