
#######################################################
#                                                     #
#                        LGA                          #
#                  ---------------                    #
#                                                     #
#               Local-Global Alignment                #
#        A Method for Finding 3-D Similarities        #
#               in Protein Structures                 #
#                                                     #
#                  --------------- 06/2006            #
#                                                     #
#      Adam Zemla (adamz@llnl.gov)                    #
#      Lawrence Livermore National Laboratory, CA     #
#                                                     #
#######################################################

# Molecule1: number of CA atoms   82 (   82),  selected   82 , name T0340TS168_4-D1
# Molecule2: number of CA atoms   82 (  626),  selected   82 , name T0340_D1.pdb
# PARAMETERS: T0340TS168_4-D1.T0340_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    R       4      R       4          0.919
LGA    P       5      P       5          2.826
LGA    R       6      R       6          2.275
LGA    L       7      L       7          1.517
LGA    C       8      C       8          1.562
LGA    H       9      H       9          1.434
LGA    L      10      L      10          1.296
LGA    R      11      R      11          1.678
LGA    K      12      K      12          1.191
LGA    G      13      G      13          2.579
LGA    P      14      P      14          1.852
LGA    Q      15      Q      15          1.568
LGA    G      16      G      16          0.606
LGA    Y      17      Y      17          1.374
LGA    G      18      G      18          1.533
LGA    F      19      F      19          1.928
LGA    N      20      N      20          1.855
LGA    L      21      L      21          1.786
LGA    H      22      H      22          1.356
LGA    S      23      S      23          1.822
LGA    D      24      D      24          3.420
LGA    K      25      K      25          1.265
LGA    S      26      S      26          3.094
LGA    R      27      R      27          4.222
LGA    P      28      P      28          2.238
LGA    G      29      G      29          1.520
LGA    Q      30      Q      30          1.958
LGA    Y      31      Y      31          1.586
LGA    I      32      I      32          1.260
LGA    R      33      R      33          1.119
LGA    S      34      S      34          0.711
LGA    V      35      V      35          0.764
LGA    D      36      D      36          1.077
LGA    P      37      P      37          2.642
LGA    G      38      G      38          1.448
LGA    S      39      S      39          1.421
LGA    P      40      P      40          1.336
LGA    A      41      A      41          1.175
LGA    A      42      A      42          1.733
LGA    R      43      R      43          2.085
LGA    S      44      S      44          3.024
LGA    G      45      G      45          1.286
LGA    L      46      L      46          0.893
LGA    R      47      R      47          0.680
LGA    A      48      A      48          1.590
LGA    Q      49      Q      49          3.378
LGA    D      50      D      50          1.881
LGA    R      51      R      51          1.834
LGA    L      52      L      52          1.022
LGA    I      53      I      53          0.672
LGA    E      54      E      54          2.318
LGA    V      55      V      55          0.908
LGA    N      56      N      56          0.625
LGA    G      57      G      57          1.106
LGA    Q      58      Q      58          1.236
LGA    N      59      N      59          3.359
LGA    V      60      V      60          1.120
LGA    E      61      E      61          1.543
LGA    G      62      G      62          2.335
LGA    L      63      L      63          2.006
LGA    R      64      R      64          2.937
LGA    H      65      H      65          1.110
LGA    A      66      A      66          0.353
LGA    E      67      E      67          1.010
LGA    V      68      V      68          1.528
LGA    V      69      V      69          1.155
LGA    A      70      A      70          0.504
LGA    S      71      S      71          1.231
LGA    I      72      I      72          1.902
LGA    K      73      K      73          1.576
LGA    A      74      A      74          0.894
LGA    R      75      R      75          1.721
LGA    E      76      E      76          2.105
LGA    D      77      D      77          3.054
LGA    E      78      E      78          3.240
LGA    A      79      A      79          0.875
LGA    R      80      R      80          1.086
LGA    L      81      L      81          0.757
LGA    L      82      L      82          0.788
LGA    V      83      V      83          1.653
LGA    V      84      V      84          1.663
LGA    G      85      G      85          1.875

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   82   82    5.0     82    1.82   100.00     88.409     4.273

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.097369 * X  +   0.990907 * Y  +   0.092861 * Z  +  10.102544
  Y_new =  -0.969800 * X  +   0.115430 * Y  +  -0.214859 * Z  +  25.960966
  Z_new =  -0.223625 * X  +  -0.069136 * Y  +   0.972220 * Z  +   9.173252 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.070991    3.070601  [ DEG:    -4.0675    175.9325 ]
  Theta =   0.225532    2.916061  [ DEG:    12.9220    167.0780 ]
  Phi   =  -1.470730    1.670863  [ DEG:   -84.2666     95.7334 ]
 
# END of job
REMARK  ---------------------------------------------------------- 
REMARK   Citing LGA: 
REMARK   Zemla A., LGA - a Method for Finding 3D Similarities in  
REMARK   Protein Structures, Nucleic Acids Research, 2003, V. 31, 
REMARK   No. 13, pp. 3370-3374. 
REMARK  ---------------------------------------------------------- 
REMARK   Superimposed MOLECULES (1=>2)   Output: 1 molecule      
REMARK     1: T0340TS168_4-D1                               
REMARK     2: T0340_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0340TS168_4-D1.T0340_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   82   82   5.0   82   1.82  100.00  88.409
REMARK  ---------------------------------------------------------- 
MOLECULE T0340TS168_4-D1
PFRMAT TS
TARGET T0340
MODEL 4
PARENT N/A
ATOM      4  CA  ARG     4      14.898  40.419   9.200  1.00 25.00           C
ATOM      5  CA  PRO     5      11.877  38.277   9.940  1.00 25.00           C
ATOM      6  CA  ARG     6       8.676  36.844  11.548  1.00 25.00           C
ATOM      7  CA  LEU     7       9.041  33.415  13.230  1.00 25.00           C
ATOM      8  CA  CYS     8       5.643  32.033  13.998  1.00 25.00           C
ATOM      9  CA  HIS     9       5.251  31.365  17.766  1.00 25.00           C
ATOM     10  CA  LEU    10       4.146  27.729  17.655  1.00 25.00           C
ATOM     11  CA  ARG    11       2.789  24.490  19.121  1.00 25.00           C
ATOM     12  CA  LYS    12       1.627  20.947  18.758  1.00 25.00           C
ATOM     13  CA  GLY    13      -1.766  22.085  19.992  1.00 25.00           C
ATOM     14  CA  PRO    14      -2.809  18.534  19.000  1.00 25.00           C
ATOM     15  CA  GLN    15      -1.972  16.448  15.910  1.00 25.00           C
ATOM     16  CA  GLY    16       1.042  18.290  14.349  1.00 25.00           C
ATOM     17  CA  TYR    17       2.974  21.318  13.073  1.00 25.00           C
ATOM     18  CA  GLY    18       1.447  20.480   9.689  1.00 25.00           C
ATOM     19  CA  PHE    19       4.712  21.510   8.080  1.00 25.00           C
ATOM     20  CA  ASN    20       6.926  19.726   5.531  1.00 25.00           C
ATOM     21  CA  LEU    21      10.627  20.140   4.830  1.00 25.00           C
ATOM     22  CA  HIS    22      10.092  19.941   1.052  1.00 25.00           C
ATOM     23  CA  SER    23      13.675  20.338  -0.306  1.00 25.00           C
ATOM     24  CA  ASP    24      16.594  17.968  -1.079  1.00 25.00           C
ATOM     25  CA  LYS    25      17.701  19.096  -4.551  1.00 25.00           C
ATOM     26  CA  SER    26      21.073  20.921  -4.806  1.00 25.00           C
ATOM     27  CA  ARG    27      21.240  21.325  -1.027  1.00 25.00           C
ATOM     28  CA  PRO    28      21.875  23.976   1.637  1.00 25.00           C
ATOM     29  CA  GLY    29      18.790  24.847   3.630  1.00 25.00           C
ATOM     30  CA  GLN    30      15.148  24.170   2.964  1.00 25.00           C
ATOM     31  CA  TYR    31      11.752  24.841   1.422  1.00 25.00           C
ATOM     32  CA  ILE    32       9.154  25.227   4.127  1.00 25.00           C
ATOM     33  CA  ARG    33       6.671  23.730   1.604  1.00 25.00           C
ATOM     34  CA  SER    34       2.851  24.109   1.577  1.00 25.00           C
ATOM     35  CA  VAL    35       1.363  24.348   5.069  1.00 25.00           C
ATOM     36  CA  ASP    36      -1.995  22.547   5.483  1.00 25.00           C
ATOM     37  CA  PRO    37      -5.177  23.597   7.297  1.00 25.00           C
ATOM     38  CA  GLY    38      -6.037  25.651  10.347  1.00 25.00           C
ATOM     39  CA  SER    39      -2.982  24.678  12.486  1.00 25.00           C
ATOM     40  CA  PRO    40       0.064  26.588  13.708  1.00 25.00           C
ATOM     41  CA  ALA    41       2.030  27.260  10.492  1.00 25.00           C
ATOM     42  CA  ALA    42      -1.242  27.564   8.525  1.00 25.00           C
ATOM     43  CA  ARG    43      -2.609  30.015  11.130  1.00 25.00           C
ATOM     44  CA  SER    44      -0.150  32.658  12.345  1.00 25.00           C
ATOM     45  CA  GLY    45       2.130  32.844   9.242  1.00 25.00           C
ATOM     46  CA  LEU    46       5.226  30.705   8.649  1.00 25.00           C
ATOM     47  CA  ARG    47       4.393  30.521   4.959  1.00 25.00           C
ATOM     48  CA  ALA    48       3.669  28.979   1.573  1.00 25.00           C
ATOM     49  CA  GLN    49       6.124  30.869  -0.614  1.00 25.00           C
ATOM     50  CA  ASP    50       8.925  29.726   1.656  1.00 25.00           C
ATOM     51  CA  ARG    51      11.867  29.597   4.079  1.00 25.00           C
ATOM     52  CA  LEU    52      13.664  27.607   6.739  1.00 25.00           C
ATOM     53  CA  ILE    53      16.636  28.431   9.046  1.00 25.00           C
ATOM     54  CA  GLU    54      15.767  26.146  11.942  1.00 25.00           C
ATOM     55  CA  VAL    55      14.966  24.808  15.453  1.00 25.00           C
ATOM     56  CA  ASN    56      13.716  26.662  18.582  1.00 25.00           C
ATOM     57  CA  GLY    57      17.293  27.822  18.855  1.00 25.00           C
ATOM     58  CA  GLN    58      19.529  27.155  15.814  1.00 25.00           C
ATOM     59  CA  ASN    59      19.795  23.828  14.059  1.00 25.00           C
ATOM     60  CA  VAL    60      19.580  23.302  10.316  1.00 25.00           C
ATOM     61  CA  GLU    61      22.524  23.931   7.964  1.00 25.00           C
ATOM     62  CA  GLY    62      23.550  20.446   6.732  1.00 25.00           C
ATOM     63  CA  LEU    63      20.554  18.253   7.672  1.00 25.00           C
ATOM     64  CA  ARG    64      18.661  17.025   4.605  1.00 25.00           C
ATOM     65  CA  HIS    65      15.286  16.481   6.308  1.00 25.00           C
ATOM     66  CA  ALA    66      15.685  13.807   9.020  1.00 25.00           C
ATOM     67  CA  GLU    67      17.242  16.394  11.376  1.00 25.00           C
ATOM     68  CA  VAL    68      14.338  18.796  10.700  1.00 25.00           C
ATOM     69  CA  VAL    69      11.824  16.002  11.432  1.00 25.00           C
ATOM     70  CA  ALA    70      13.637  15.196  14.708  1.00 25.00           C
ATOM     71  CA  SER    71      13.556  18.896  15.692  1.00 25.00           C
ATOM     72  CA  ILE    72       9.806  19.043  14.928  1.00 25.00           C
ATOM     73  CA  LYS    73       9.224  15.918  17.064  1.00 25.00           C
ATOM     74  CA  ALA    74      11.212  17.483  19.940  1.00 25.00           C
ATOM     75  CA  ARG    75       8.956  20.472  20.878  1.00 25.00           C
ATOM     76  CA  GLU    76       5.724  20.522  22.913  1.00 25.00           C
ATOM     77  CA  ASP    77       5.713  24.328  23.276  1.00 25.00           C
ATOM     78  CA  GLU    78       8.272  25.898  20.940  1.00 25.00           C
ATOM     79  CA  ALA    79       9.049  24.598  17.450  1.00 25.00           C
ATOM     80  CA  ARG    80       9.123  28.243  16.474  1.00 25.00           C
ATOM     81  CA  LEU    81      10.708  27.745  13.100  1.00 25.00           C
ATOM     82  CA  LEU    82      13.310  30.523  12.510  1.00 25.00           C
ATOM     83  CA  VAL    83      12.606  32.694   9.521  1.00 25.00           C
ATOM     84  CA  VAL    84      14.269  34.043   6.381  1.00 25.00           C
ATOM     85  CA  GLY    85      11.615  34.843   3.756  1.00 25.00           C
TER
END
