LGA
Sequence Independent Analysis (LGA)
Frame of reference: Cat.Q2246_545_515.5wLII_11389_16
Total number of 3D structures: 9
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 |
2p6c_A |
137 |
138 |
137 |
0.16 |
63.50 |
99.275 |
51.722 |
T P |
1vmj_A |
139 |
138 |
137 |
0.69 |
51.09 |
98.598 |
17.450 |
T P |
1vph_C |
144 |
138 |
136 |
1.15 |
32.35 |
94.381 |
10.866 |
T P |
1vmf_A |
136 |
138 |
132 |
1.26 |
33.33 |
91.927 |
9.691 |
T P |
2p6h_A |
134 |
138 |
134 |
1.31 |
34.33 |
91.511 |
9.526 |
T P |
1ve0_A |
134 |
138 |
134 |
1.43 |
33.58 |
90.770 |
8.779 |
T P |
1xbf_A |
131 |
138 |
130 |
1.29 |
35.38 |
89.051 |
9.340 |
T P |
1vmh_A |
129 |
138 |
128 |
1.24 |
36.72 |
88.584 |
9.576 |
T P |
2cu5_A |
129 |
138 |
124 |
1.65 |
37.10 |
83.117 |
7.078 |
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]