LGA
Sequence Independent Analysis (LGA)
Frame of reference: Cat.Q2246_545_178.5wLII_11181_1
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 |
2r4l_B |
421 |
200 |
105 |
2.42 |
4.76 |
38.047 |
4.174 |
T P |
2r4o_A |
421 |
200 |
105 |
2.37 |
5.71 |
37.832 |
4.257 |
T P |
2r4p_A |
418 |
200 |
105 |
2.39 |
5.71 |
36.935 |
4.216 |
T P |
3dwo_X |
444 |
200 |
100 |
2.34 |
10.00 |
36.896 |
4.105 |
T P |
2r89_A |
363 |
200 |
96 |
2.24 |
5.21 |
36.065 |
4.099 |
T P |
3dwn_A |
421 |
200 |
97 |
2.31 |
12.37 |
35.913 |
4.029 |
T P |
2r4n_A |
421 |
200 |
102 |
2.45 |
7.84 |
35.844 |
4.001 |
T P |
1t16_A |
427 |
200 |
102 |
2.35 |
5.88 |
35.768 |
4.155 |
T P |
3bry_A |
389 |
200 |
96 |
2.31 |
13.54 |
35.691 |
3.991 |
T P |
2r8a_A |
360 |
200 |
96 |
2.41 |
5.21 |
35.085 |
3.822 |
T P |
2r88_A |
365 |
200 |
97 |
2.48 |
7.22 |
34.959 |
3.765 |
T P |
1pho_A |
330 |
200 |
101 |
2.30 |
5.94 |
34.653 |
4.215 |
T P |
3bs0_A |
414 |
200 |
94 |
2.19 |
12.77 |
34.550 |
4.101 |
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]