LGA
Sequence Independent Analysis (LGA)
Frame of reference: Cat.Q2246_545_491.5wLII_11346_169
Total number of 3D structures: 12
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 |
2dt9_A |
153 |
97 |
69 |
1.66 |
14.49 |
67.245 |
3.925 |
T P |
2dtj_A |
164 |
97 |
64 |
1.88 |
9.38 |
58.080 |
3.226 |
T P |
1y7p_B |
217 |
97 |
60 |
1.99 |
8.33 |
54.348 |
2.877 |
T P |
2fgc_A |
161 |
97 |
63 |
2.13 |
11.11 |
51.333 |
2.828 |
T P |
1sc6_A |
390 |
97 |
57 |
2.10 |
7.02 |
50.442 |
2.592 |
T P |
1psd_A |
404 |
97 |
59 |
2.17 |
8.47 |
48.621 |
2.602 |
T P |
1yba_A |
406 |
97 |
58 |
2.07 |
6.90 |
47.929 |
2.677 |
T P |
2iq8_A |
264 |
97 |
58 |
2.02 |
12.07 |
47.395 |
2.738 |
T P |
2p9c_A |
405 |
97 |
56 |
2.03 |
7.14 |
47.206 |
2.629 |
T P |
2p9g_A |
404 |
97 |
56 |
2.01 |
7.14 |
47.092 |
2.658 |
T P |
1ygy_A |
527 |
97 |
55 |
2.12 |
10.91 |
42.857 |
2.474 |
T P |
3ddn_A |
527 |
97 |
55 |
2.13 |
10.91 |
42.718 |
2.469 |
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]