LGA
Sequence Independent Analysis (LGA)
Frame of reference: Cat.Q2246_545_27.5wLII_10776_2
Total number of 3D structures: 10
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 |
2j4d_B |
499 |
115 |
109 |
1.09 |
16.51 |
93.169 |
9.140 |
T P |
2ijg_X |
492 |
115 |
105 |
1.19 |
18.10 |
88.841 |
8.167 |
T P |
1np7_A |
483 |
115 |
94 |
1.20 |
11.70 |
78.783 |
7.215 |
T P |
1qnf_A |
475 |
115 |
92 |
1.68 |
11.96 |
74.207 |
5.159 |
T P |
1tez_A |
474 |
115 |
91 |
1.51 |
12.09 |
73.993 |
5.662 |
T P |
1dnp_A |
469 |
115 |
88 |
1.54 |
11.36 |
72.517 |
5.363 |
T P |
2e0i_B |
431 |
115 |
88 |
1.75 |
11.36 |
71.537 |
4.768 |
T P |
1u3d_A |
485 |
115 |
85 |
1.43 |
9.41 |
71.461 |
5.566 |
T P |
3cvu_A |
501 |
115 |
87 |
1.60 |
10.34 |
70.248 |
5.104 |
T P |
2j07_A |
419 |
115 |
87 |
1.67 |
10.34 |
69.836 |
4.903 |
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]