LGA
Sequence Independent Analysis (LGA)
Frame of reference: Cat.Q2246_545_305.5wLII_11238_83
Total number of 3D structures: 13
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 |
3epv_A |
109 |
104 |
103 |
0.89 |
11.65 |
97.524 |
10.425 |
T P |
2dq0_A |
447 |
104 |
74 |
1.93 |
9.46 |
64.569 |
3.646 |
T P |
1y1u_A |
544 |
104 |
70 |
2.10 |
5.71 |
57.452 |
3.182 |
T P |
1wle_B |
469 |
104 |
69 |
2.16 |
5.80 |
55.323 |
3.058 |
T P |
1zvu_A |
685 |
104 |
64 |
1.94 |
9.38 |
53.673 |
3.144 |
T P |
1qvr_A |
803 |
104 |
63 |
1.98 |
9.52 |
52.707 |
3.028 |
T P |
1f5n_A |
570 |
104 |
67 |
2.32 |
7.46 |
47.458 |
2.770 |
T P |
1miu_A |
671 |
104 |
61 |
2.17 |
13.11 |
44.116 |
2.682 |
T P |
3cmn_A |
298 |
104 |
56 |
2.14 |
5.36 |
43.893 |
2.502 |
T P |
3ces_A |
531 |
104 |
44 |
2.10 |
4.55 |
36.848 |
2.004 |
T P |
1knv_B |
291 |
104 |
44 |
2.26 |
2.27 |
36.055 |
1.861 |
T P |
3cp2_A |
491 |
104 |
46 |
2.45 |
8.70 |
29.480 |
1.804 |
T P |
1hm6_A |
343 |
104 |
34 |
3.02 |
8.82 |
23.450 |
1.089 |
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]