
#######################################################
#                                                     #
#                        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   48 (  192),  selected   48 , name T0358TS383_5
# Molecule2: number of CA atoms   66 ( 1047),  selected   66 , name T0358.pdb
# PARAMETERS: T0358TS383_5.T0358.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      G      10           -
LGA    -       -      P      11           -
LGA    -       -      F      12           -
LGA    -       -      T      13           -
LGA    S       4      R      14          4.802
LGA    V       5      R      15          2.316
LGA    L       6      -       -           -
LGA    L       7      -       -           -
LGA    P       8      -       -           -
LGA    P       9      -       -           -
LGA    G      10      -       -           -
LGA    P      11      -       -           -
LGA    F      12      -       -           -
LGA    T      13      -       -           -
LGA    R      14      Q      16          2.526
LGA    R      15      A      17          4.369
LGA    Q      16      Q      18           -
LGA    A      17      A      19           -
LGA    Q      18      V      20          4.613
LGA    A      19      T      21           #
LGA    V      20      T      22           -
LGA    T      21      T      23          3.958
LGA    T      22      Y      24          3.283
LGA    -       -      S      25           -
LGA    T      23      N      26          2.246
LGA    Y      24      I      27          1.756
LGA    S      25      T      28          1.271
LGA    N      26      L      29          0.618
LGA    I      27      E      30          0.867
LGA    T      28      D      31          2.201
LGA    L      29      D      32          5.432
LGA    E      30      -       -           -
LGA    D      31      -       -           -
LGA    F      37      Q      33          5.316
LGA    -       -      G      34           -
LGA    -       -      S      35           -
LGA    R      38      H      36          4.013
LGA    L      39      F      37          0.376
LGA    V      40      R      38          0.692
LGA    V      41      L      39          1.088
LGA    R      42      V      40          1.230
LGA    D      43      V      41          1.756
LGA    T      44      R      42          1.735
LGA    E      45      D      43          3.665
LGA    -       -      T      44           -
LGA    -       -      E      45           -
LGA    -       -      G      46           -
LGA    -       -      R      47           -
LGA    G      46      M      48          2.267
LGA    R      47      V      49          3.819
LGA    M      48      W      50          4.205
LGA    V      49      R      51           #
LGA    W      50      A      52           #
LGA    R      51      W      53          1.770
LGA    A      52      N      54          2.503
LGA    W      53      F      55          3.354
LGA    N      54      E      56           -
LGA    F      55      P      57           -
LGA    P      57      D      58           -
LGA    -       -      A      59           -
LGA    -       -      G      60           -
LGA    -       -      E      61           -
LGA    -       -      G      62           -
LGA    -       -      L      63           -
LGA    -       -      N      64           -
LGA    -       -      R      65           -
LGA    -       -      Y      66           -
LGA    -       -      I      67           -
LGA    -       -      R      68           -
LGA    -       -      T      69           -
LGA    -       -      S      70           -
LGA    -       -      G      71           -
LGA    -       -      I      72           -
LGA    -       -      R      73           -
LGA    -       -      T      74           -
LGA    -       -      D      75           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   48   66    5.0     29    3.06     3.45     29.745     0.917

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.089996 * X  +  -0.943009 * Y  +   0.320366 * Z  +  15.393513
  Y_new =  -0.670668 * X  +   0.295187 * Y  +   0.680492 * Z  +  16.519375
  Z_new =  -0.736278 * X  +  -0.153618 * Y  +  -0.659011 * Z  +  13.982190 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.912579    0.229013  [ DEG:  -166.8785     13.1215 ]
  Theta =   0.827554    2.314039  [ DEG:    47.4153    132.5847 ]
  Phi   =  -1.704188    1.437404  [ DEG:   -97.6428     82.3572 ]
 
# 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: T0358TS383_5                                  
REMARK     2: T0358.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0358TS383_5.T0358.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   48   66   5.0   29   3.06    3.45  29.745
REMARK  ---------------------------------------------------------- 
MOLECULE T0358TS383_5
PFRMAT TS
TARGET T0358
MODEL 5
PARENT 1xd6A
ATOM      1  N   SER     4       5.006  -1.132  -5.472  1.00  0.00
ATOM      2  CA  SER     4       4.911  -0.355  -6.701  1.00  0.00
ATOM      3  C   SER     4       6.304  -0.334  -7.329  1.00  0.00
ATOM      4  O   SER     4       7.248   0.040  -6.668  1.00  0.00
ATOM      5  N   VAL     5       6.442  -0.767  -8.584  1.00  0.00
ATOM      6  CA  VAL     5       7.767  -0.922  -9.196  1.00  0.00
ATOM      7  C   VAL     5       7.786  -0.393 -10.622  1.00  0.00
ATOM      8  O   VAL     5       6.901  -0.710 -11.422  1.00  0.00
ATOM      9  N   LEU     6       8.800   0.412 -10.935  1.00  0.00
ATOM     10  CA  LEU     6       9.087   0.821 -12.311  1.00  0.00
ATOM     11  C   LEU     6      10.041  -0.214 -12.927  1.00  0.00
ATOM     12  O   LEU     6      11.096  -0.479 -12.365  1.00  0.00
ATOM     13  N   LEU     7       9.637  -0.801 -14.057  1.00  0.00
ATOM     14  CA  LEU     7      10.464  -1.738 -14.833  1.00  0.00
ATOM     15  C   LEU     7      10.897  -1.123 -16.153  1.00  0.00
ATOM     16  O   LEU     7      10.161  -0.336 -16.757  1.00  0.00
ATOM     17  N   PRO     8      12.093  -1.484 -16.590  1.00  0.00
ATOM     18  CA  PRO     8      12.544  -1.201 -17.946  1.00  0.00
ATOM     19  C   PRO     8      13.017  -2.544 -18.435  1.00  0.00
ATOM     20  O   PRO     8      14.013  -3.060 -17.941  1.00  0.00
ATOM     21  N   PRO     9      12.284  -3.136 -19.364  1.00  0.00
ATOM     22  CA  PRO     9      12.532  -4.528 -19.691  1.00  0.00
ATOM     23  C   PRO     9      12.271  -5.327 -18.425  1.00  0.00
ATOM     24  O   PRO     9      11.273  -5.095 -17.737  1.00  0.00
ATOM     25  N   GLY    10      13.172  -6.243 -18.095  1.00  0.00
ATOM     26  CA  GLY    10      12.972  -7.078 -16.911  1.00  0.00
ATOM     27  C   GLY    10      13.621  -6.499 -15.638  1.00  0.00
ATOM     28  O   GLY    10      13.431  -7.037 -14.534  1.00  0.00
ATOM     29  N   PRO    11      14.226  -3.828 -12.586  1.00  0.00
ATOM     30  CA  PRO    11      13.569  -2.854 -11.712  1.00  0.00
ATOM     31  C   PRO    11      14.396  -1.564 -11.644  1.00  0.00
ATOM     32  O   PRO    11      15.587  -1.618 -11.400  1.00  0.00
ATOM     33  N   PHE    12      13.750  -0.421 -11.868  1.00  0.00
ATOM     34  CA  PHE    12      14.395   0.888 -11.839  1.00  0.00
ATOM     35  C   PHE    12      14.199   1.568 -10.482  1.00  0.00
ATOM     36  O   PHE    12      15.048   2.358 -10.031  1.00  0.00
ATOM     37  N   THR    13      13.083   1.241  -9.832  1.00  0.00
ATOM     38  CA  THR    13      12.639   1.920  -8.620  1.00  0.00
ATOM     39  C   THR    13      11.543   1.083  -7.993  1.00  0.00
ATOM     40  O   THR    13      10.730   0.505  -8.702  1.00  0.00
ATOM     41  N   ARG    14      11.520   1.023  -6.667  1.00  0.00
ATOM     42  CA  ARG    14      10.474   0.305  -5.937  1.00  0.00
ATOM     43  C   ARG    14      10.038   1.075  -4.700  1.00  0.00
ATOM     44  O   ARG    14      10.856   1.749  -4.046  1.00  0.00
ATOM     45  N   ARG    15       8.762   0.934  -4.357  1.00  0.00
ATOM     46  CA  ARG    15       8.214   1.557  -3.157  1.00  0.00
ATOM     47  C   ARG    15       8.726   0.862  -1.883  1.00  0.00
ATOM     48  O   ARG    15       8.649   1.438  -0.789  1.00  0.00
ATOM     49  N   GLN    16       9.221  -0.368  -2.032  1.00  0.00
ATOM     50  CA  GLN    16       9.786  -1.155  -0.931  1.00  0.00
ATOM     51  C   GLN    16       8.770  -1.369   0.201  1.00  0.00
ATOM     52  O   GLN    16       9.094  -1.217   1.377  1.00  0.00
ATOM     53  N   ALA    17       7.544  -1.700  -0.188  1.00  0.00
ATOM     54  CA  ALA    17       6.456  -1.966   0.738  1.00  0.00
ATOM     55  C   ALA    17       6.018  -3.362   0.441  1.00  0.00
ATOM     56  O   ALA    17       4.926  -3.600  -0.087  1.00  0.00
ATOM     57  N   GLN    18       6.911  -4.293   0.760  1.00  0.00
ATOM     58  CA  GLN    18       6.652  -5.696   0.503  1.00  0.00
ATOM     59  C   GLN    18       5.804  -6.326   1.609  1.00  0.00
ATOM     60  O   GLN    18       6.080  -6.167   2.801  1.00  0.00
ATOM     61  N   ALA    19       4.744  -6.993   1.171  1.00  0.00
ATOM     62  CA  ALA    19       3.937  -7.880   1.988  1.00  0.00
ATOM     63  C   ALA    19       3.716  -9.078   1.078  1.00  0.00
ATOM     64  O   ALA    19       4.597  -9.397   0.270  1.00  0.00
ATOM     65  N   VAL    20       2.572  -9.742   1.170  1.00  0.00
ATOM     66  CA  VAL    20       2.371 -10.938   0.351  1.00  0.00
ATOM     67  C   VAL    20       1.280 -10.733  -0.683  1.00  0.00
ATOM     68  O   VAL    20       0.625  -9.693  -0.691  1.00  0.00
ATOM     69  N   THR    21       1.108 -11.728  -1.555  1.00  0.00
ATOM     70  CA  THR    21       0.108 -11.682  -2.617  1.00  0.00
ATOM     71  C   THR    21      -1.264 -11.340  -2.037  1.00  0.00
ATOM     72  O   THR    21      -1.724 -11.988  -1.098  1.00  0.00
ATOM     73  N   THR    22      -1.895 -10.303  -2.576  1.00  0.00
ATOM     74  CA  THR    22      -3.173  -9.839  -2.076  1.00  0.00
ATOM     75  C   THR    22      -3.860  -8.924  -3.063  1.00  0.00
ATOM     76  O   THR    22      -3.562  -8.959  -4.263  1.00  0.00
ATOM     77  N   THR    23      -4.763  -8.089  -2.558  1.00  0.00
ATOM     78  CA  THR    23      -5.583  -7.244  -3.418  1.00  0.00
ATOM     79  C   THR    23      -5.372  -5.746  -3.220  1.00  0.00
ATOM     80  O   THR    23      -6.312  -4.993  -2.927  1.00  0.00
ATOM     81  N   TYR    24      -4.131  -5.322  -3.416  1.00  0.00
ATOM     82  CA  TYR    24      -3.738  -3.923  -3.280  1.00  0.00
ATOM     83  C   TYR    24      -4.209  -3.095  -4.440  1.00  0.00
ATOM     84  O   TYR    24      -4.508  -3.610  -5.514  1.00  0.00
ATOM     85  N   SER    25      -4.271  -1.797  -4.213  1.00  0.00
ATOM     86  CA  SER    25      -4.534  -0.880  -5.295  1.00  0.00
ATOM     87  C   SER    25      -3.884   0.456  -5.028  1.00  0.00
ATOM     88  O   SER    25      -3.720   0.863  -3.874  1.00  0.00
ATOM     89  N   ASN    26      -3.471   1.104  -6.113  1.00  0.00
ATOM     90  CA  ASN    26      -2.875   2.416  -6.050  1.00  0.00
ATOM     91  C   ASN    26      -3.994   3.370  -6.397  1.00  0.00
ATOM     92  O   ASN    26      -4.711   3.141  -7.360  1.00  0.00
ATOM     93  N   ILE    27      -4.136   4.435  -5.614  1.00  0.00
ATOM     94  CA  ILE    27      -5.173   5.430  -5.852  1.00  0.00
ATOM     95  C   ILE    27      -4.598   6.839  -5.769  1.00  0.00
ATOM     96  O   ILE    27      -3.877   7.162  -4.836  1.00  0.00
ATOM     97  N   THR    28      -4.911   7.667  -6.765  1.00  0.00
ATOM     98  CA  THR    28      -4.690   9.101  -6.651  1.00  0.00
ATOM     99  C   THR    28      -5.932   9.670  -5.956  1.00  0.00
ATOM    100  O   THR    28      -7.008   9.744  -6.549  1.00  0.00
ATOM    101  N   LEU    29      -5.769  10.068  -4.703  1.00  0.00
ATOM    102  CA  LEU    29      -6.898  10.539  -3.902  1.00  0.00
ATOM    103  C   LEU    29      -7.312  11.978  -4.182  1.00  0.00
ATOM    104  O   LEU    29      -6.503  12.796  -4.643  1.00  0.00
ATOM    105  N   GLU    30      -8.569  12.279  -3.860  1.00  0.00
ATOM    106  CA  GLU    30      -9.143  13.624  -4.020  1.00  0.00
ATOM    107  C   GLU    30      -8.354  14.675  -3.226  1.00  0.00
ATOM    108  O   GLU    30      -8.395  15.860  -3.539  1.00  0.00
ATOM    109  N   ASP    31      -7.642  14.248  -2.192  1.00  0.00
ATOM    110  CA  ASP    31      -6.824  15.175  -1.416  1.00  0.00
ATOM    111  C   ASP    31      -5.379  15.296  -1.942  1.00  0.00
ATOM    112  O   ASP    31      -4.511  15.868  -1.268  1.00  0.00
ATOM    113  N   PHE    37      -5.143  14.769  -3.147  1.00  0.00
ATOM    114  CA  PHE    37      -3.843  14.828  -3.835  1.00  0.00
ATOM    115  C   PHE    37      -2.780  13.845  -3.333  1.00  0.00
ATOM    116  O   PHE    37      -1.667  13.817  -3.868  1.00  0.00
ATOM    117  N   ARG    38      -3.091  13.071  -2.298  1.00  0.00
ATOM    118  CA  ARG    38      -2.189  11.997  -1.875  1.00  0.00
ATOM    119  C   ARG    38      -2.308  10.835  -2.866  1.00  0.00
ATOM    120  O   ARG    38      -3.386  10.582  -3.420  1.00  0.00
ATOM    121  N   LEU    39      -1.196  10.146  -3.099  1.00  0.00
ATOM    122  CA  LEU    39      -1.222   8.915  -3.861  1.00  0.00
ATOM    123  C   LEU    39      -0.902   7.809  -2.864  1.00  0.00
ATOM    124  O   LEU    39       0.119   7.848  -2.208  1.00  0.00
ATOM    125  N   VAL    40      -1.777   6.821  -2.762  1.00  0.00
ATOM    126  CA  VAL    40      -1.701   5.881  -1.657  1.00  0.00
ATOM    127  C   VAL    40      -1.859   4.480  -2.214  1.00  0.00
ATOM    128  O   VAL    40      -2.614   4.272  -3.167  1.00  0.00
ATOM    129  N   VAL    41      -1.124   3.531  -1.637  1.00  0.00
ATOM    130  CA  VAL    41      -1.372   2.112  -1.880  1.00  0.00
ATOM    131  C   VAL    41      -2.134   1.557  -0.679  1.00  0.00
ATOM    132  O   VAL    41      -1.663   1.662   0.466  1.00  0.00
ATOM    133  N   ARG    42      -3.299   0.967  -0.952  1.00  0.00
ATOM    134  CA  ARG    42      -4.125   0.330   0.077  1.00  0.00
ATOM    135  C   ARG    42      -4.095  -1.196  -0.041  1.00  0.00
ATOM    136  O   ARG    42      -3.950  -1.726  -1.140  1.00  0.00
ATOM    137  N   ASP    43      -4.232  -1.890   1.090  1.00  0.00
ATOM    138  CA  ASP    43      -4.339  -3.351   1.105  1.00  0.00
ATOM    139  C   ASP    43      -5.822  -3.770   1.049  1.00  0.00
ATOM    140  O   ASP    43      -6.702  -2.911   0.904  1.00  0.00
ATOM    141  N   THR    44      -6.097  -5.074   1.123  1.00  0.00
ATOM    142  CA  THR    44      -7.477  -5.562   1.040  1.00  0.00
ATOM    143  C   THR    44      -8.411  -4.998   2.128  1.00  0.00
ATOM    144  O   THR    44      -9.629  -4.965   1.944  1.00  0.00
ATOM    145  N   GLU    45      -7.817  -4.541   3.231  1.00  0.00
ATOM    146  CA  GLU    45      -8.547  -4.007   4.381  1.00  0.00
ATOM    147  C   GLU    45      -8.687  -2.481   4.338  1.00  0.00
ATOM    148  O   GLU    45      -9.246  -1.886   5.261  1.00  0.00
ATOM    149  N   GLY    46      -8.176  -1.851   3.286  1.00  0.00
ATOM    150  CA  GLY    46      -8.250  -0.405   3.146  1.00  0.00
ATOM    151  C   GLY    46      -7.340   0.322   4.116  1.00  0.00
ATOM    152  O   GLY    46      -7.601   1.460   4.497  1.00  0.00
ATOM    153  N   ARG    47      -6.274  -0.351   4.519  1.00  0.00
ATOM    154  CA  ARG    47      -5.204   0.289   5.247  1.00  0.00
ATOM    155  C   ARG    47      -4.096   0.702   4.290  1.00  0.00
ATOM    156  O   ARG    47      -3.686  -0.079   3.436  1.00  0.00
ATOM    157  N   MET    48      -3.669   1.953   4.428  1.00  0.00
ATOM    158  CA  MET    48      -2.534   2.521   3.710  1.00  0.00
ATOM    159  C   MET    48      -1.206   1.851   4.093  1.00  0.00
ATOM    160  O   MET    48      -0.813   1.864   5.269  1.00  0.00
ATOM    161  N   VAL    49      -0.516   1.304   3.097  1.00  0.00
ATOM    162  CA  VAL    49       0.825   0.743   3.292  1.00  0.00
ATOM    163  C   VAL    49       1.941   1.643   2.734  1.00  0.00
ATOM    164  O   VAL    49       3.100   1.512   3.129  1.00  0.00
ATOM    165  N   TRP    50       1.583   2.567   1.838  1.00  0.00
ATOM    166  CA  TRP    50       2.523   3.515   1.262  1.00  0.00
ATOM    167  C   TRP    50       1.739   4.765   0.847  1.00  0.00
ATOM    168  O   TRP    50       0.606   4.657   0.378  1.00  0.00
ATOM    169  N   ARG    51       2.337   5.941   1.033  1.00  0.00
ATOM    170  CA  ARG    51       1.740   7.193   0.566  1.00  0.00
ATOM    171  C   ARG    51       2.841   8.084   0.012  1.00  0.00
ATOM    172  O   ARG    51       3.968   8.002   0.462  1.00  0.00
ATOM    173  N   ALA    52       2.516   8.920  -0.970  1.00  0.00
ATOM    174  CA  ALA    52       3.477   9.911  -1.462  1.00  0.00
ATOM    175  C   ALA    52       3.646  11.083  -0.493  1.00  0.00
ATOM    176  O   ALA    52       4.626  11.815  -0.584  1.00  0.00
ATOM    177  N   TRP    53       2.672  11.278   0.398  1.00  0.00
ATOM    178  CA  TRP    53       2.681  12.391   1.336  1.00  0.00
ATOM    179  C   TRP    53       2.445  13.737   0.683  1.00  0.00
ATOM    180  O   TRP    53       2.968  14.755   1.136  1.00  0.00
ATOM    181  N   ASN    54       1.658  13.754  -0.390  1.00  0.00
ATOM    182  CA  ASN    54       1.449  14.982  -1.141  1.00  0.00
ATOM    183  C   ASN    54       0.045  15.545  -0.948  1.00  0.00
ATOM    184  O   ASN    54      -0.426  16.338  -1.764  1.00  0.00
ATOM    185  N   PHE    55      -0.613  15.140   0.133  1.00  0.00
ATOM    186  CA  PHE    55      -1.925  15.669   0.482  1.00  0.00
ATOM    187  C   PHE    55      -1.917  17.174   0.775  1.00  0.00
ATOM    188  O   PHE    55      -0.987  17.695   1.391  1.00  0.00
ATOM    189  N   PRO    57      -2.960  17.855   0.307  1.00  0.00
ATOM    190  CA  PRO    57      -3.165  19.276   0.581  1.00  0.00
ATOM    191  C   PRO    57      -4.295  19.450   1.593  1.00  0.00
ATOM    192  O   PRO    57      -5.101  18.534   1.809  1.00  0.00
TER
END
