
#######################################################
#                                                     #
#                        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   27 (  203),  selected   27 , name T0335TS174_1u-D1
# Molecule2: number of CA atoms   36 (  584),  selected   36 , name T0335_D1.pdb
# PARAMETERS: T0335TS174_1u-D1.T0335_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    A       5      -       -           -
LGA    K       6      A       5          4.536
LGA    I       7      K       6          5.096
LGA    A       8      I       7          4.433
LGA    R       9      A       8          2.246
LGA    I      10      R       9          4.671
LGA    N      11      I      10          4.237
LGA    E      12      N      11          3.419
LGA    L      13      E      12          1.216
LGA    A      14      L      13          2.093
LGA    A      15      A      14          1.811
LGA    K      16      A      15          2.677
LGA    A      17      K      16          2.726
LGA    K      18      A      17          1.968
LGA    A      19      K      18          2.468
LGA    -       -      A      19           -
LGA    -       -      G      20           -
LGA    G      20      V      21          2.482
LGA    V      21      I      22          1.874
LGA    I      22      T      23          2.029
LGA    T      23      E      24          0.366
LGA    -       -      E      25           -
LGA    E      24      E      26          2.804
LGA    E      25      K      27          2.285
LGA    E      26      A      28          2.212
LGA    K      27      E      29          2.827
LGA    A      28      Q      30          2.031
LGA    E      29      Q      31          1.514
LGA    Q      30      K      32          3.313
LGA    Q      31      L      33          4.341
LGA    -       -      R      34           -
LGA    -       -      Q      35           -
LGA    -       -      E      36           -
LGA    -       -      Y      37           -
LGA    -       -      L      38           -
LGA    -       -      K      39           -
LGA    -       -      G      40           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   27   36    5.0     26    2.99     7.69     51.410     0.841

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.489096 * X  +  -0.421196 * Y  +   0.763792 * Z  + -11.310642
  Y_new =  -0.829327 * X  +  -0.046690 * Y  +  -0.556809 * Z  +  12.955449
  Z_new =   0.270187 * X  +  -0.905767 * Y  +  -0.326473 * Z  + -13.274487 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.916740    1.224853  [ DEG:  -109.8211     70.1789 ]
  Theta =  -0.273587   -2.868006  [ DEG:   -15.6754   -164.3246 ]
  Phi   =  -2.103646    1.037947  [ DEG:  -120.5300     59.4700 ]
 
# 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: T0335TS174_1u-D1                              
REMARK     2: T0335_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0335TS174_1u-D1.T0335_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   27   36   5.0   26   2.99    7.69  51.410
REMARK  ---------------------------------------------------------- 
MOLECULE T0335TS174_1u-D1
PFRMAT TS
TARGET T0335
MODEL 1  UNREFINED
PARENT 351c 
ATOM     31  N   ALA     5      -6.858  -9.630  -7.303  1.00  1.00
ATOM     32  CA  ALA     5      -5.471  -9.995  -6.935  1.00  1.00
ATOM     33  C   ALA     5      -4.756 -10.650  -8.123  1.00  1.00
ATOM     34  O   ALA     5      -5.313 -11.532  -8.792  1.00  1.00
ATOM     35  CB  ALA     5      -5.474 -10.914  -5.705  1.00  1.00
ATOM     36  N   LYS     6      -3.584 -10.181  -8.385  1.00  1.00
ATOM     37  CA  LYS     6      -2.788 -10.737  -9.502  1.00  1.00
ATOM     38  C   LYS     6      -1.541 -11.450  -8.969  1.00  1.00
ATOM     39  O   LYS     6      -1.616 -12.594  -8.497  1.00  1.00
ATOM     40  CB  LYS     6      -2.419  -9.625 -10.494  1.00  1.00
ATOM     41  CG  LYS     6      -3.567  -9.162 -11.132  1.00  1.00
ATOM     42  CD  LYS     6      -3.233  -8.066 -12.142  1.00  1.00
ATOM     43  CE  LYS     6      -4.491  -7.551 -12.843  1.00  1.00
ATOM     44  NZ  LYS     6      -4.165  -6.491 -13.813  1.00  1.00
ATOM     45  N   ILE     7      -0.476 -10.760  -8.892  1.00  1.00
ATOM     46  CA  ILE     7       0.751 -11.298  -8.260  1.00  1.00
ATOM     47  C   ILE     7       0.857 -10.825  -6.806  1.00  1.00
ATOM     48  O   ILE     7       1.200 -11.607  -5.907  1.00  1.00
ATOM     49  CB  ILE     7       1.988 -10.893  -9.073  1.00  1.00
ATOM     50  CG1 ILE     7       2.158  -9.383  -9.095  1.00  1.00
ATOM     51  CG2 ILE     7       1.904 -11.392 -10.501  1.00  1.00
ATOM     52  CD1 ILE     7       3.147  -8.826  -8.074  1.00  1.00
ATOM     53  N   ALA     8       0.461  -9.546  -6.679  1.00  1.00
ATOM     54  CA  ALA     8       0.382  -8.944  -5.328  1.00  1.00
ATOM     55  C   ALA     8      -1.073  -8.626  -4.967  1.00  1.00
ATOM     56  O   ALA     8      -1.988  -8.823  -5.781  1.00  1.00
ATOM     57  CB  ALA     8       1.265  -7.690  -5.254  1.00  1.00
ATOM     58  N   ARG     9      -1.392  -8.228  -3.818  1.00  1.00
ATOM     59  CA  ARG     9      -2.783  -7.925  -3.412  1.00  1.00
ATOM     60  C   ARG     9      -3.383  -6.846  -4.320  1.00  1.00
ATOM     61  O   ARG     9      -2.654  -6.037  -4.914  1.00  1.00
ATOM     62  CB  ARG     9      -2.823  -7.502  -1.937  1.00  1.00
ATOM     63  CG  ARG     9      -2.082  -6.343  -1.759  1.00  1.00
ATOM     64  CD  ARG     9      -2.121  -5.890  -0.299  1.00  1.00
ATOM     65  NE  ARG     9      -1.441  -4.786  -0.036  1.00  1.00
ATOM     66  CZ  ARG     9      -1.345  -4.224   1.188  1.00  1.00
ATOM     67  NH1 ARG     9      -0.636  -3.121   1.332  1.00  1.00
ATOM     68  NH2 ARG     9      -2.109  -5.011   2.185  1.00  1.00
ATOM     69  N   ILE    10      -4.797  -6.924  -4.195  1.00  1.00
ATOM     70  CA  ILE    10      -5.625  -5.883  -4.845  1.00  1.00
ATOM     71  C   ILE    10      -5.617  -4.596  -4.014  1.00  1.00
ATOM     72  O   ILE    10      -5.618  -4.640  -2.774  1.00  1.00
ATOM     73  CB  ILE    10      -7.054  -6.402  -5.063  1.00  1.00
ATOM     74  CG1 ILE    10      -7.733  -6.706  -3.738  1.00  1.00
ATOM     75  CG2 ILE    10      -7.069  -7.654  -5.917  1.00  1.00
ATOM     76  CD1 ILE    10      -9.242  -6.955  -3.816  1.00  1.00
ATOM     77  N   ASN    11      -5.531  -3.490  -4.626  1.00  1.00
ATOM     78  CA  ASN    11      -5.420  -2.201  -3.905  1.00  1.00
ATOM     79  C   ASN    11      -6.619  -2.005  -2.971  1.00  1.00
ATOM     80  O   ASN    11      -6.491  -1.416  -1.888  1.00  1.00
ATOM     81  CB  ASN    11      -5.291  -1.044  -4.906  1.00  1.00
ATOM     82  CG  ASN    11      -3.944  -1.078  -5.606  1.00  1.00
ATOM     83  OD1 ASN    11      -2.930  -0.638  -5.050  1.00  1.00
ATOM     84  ND2 ASN    11      -3.940  -1.596  -6.814  1.00  1.00
ATOM     85  N   GLU    12      -7.769  -2.355  -3.380  1.00  1.00
ATOM     86  CA  GLU    12      -8.982  -2.190  -2.547  1.00  1.00
ATOM     87  C   GLU    12      -8.830  -2.949  -1.224  1.00  1.00
ATOM     88  O   GLU    12      -9.335  -2.510  -0.179  1.00  1.00
ATOM     89  CB  GLU    12     -10.222  -2.655  -3.322  1.00  1.00
ATOM     90  CG  GLU    12     -10.563  -1.784  -4.506  1.00  1.00
ATOM     91  CD  GLU    12     -11.802  -2.249  -5.242  1.00  1.00
ATOM     92  OE1 GLU    12     -12.331  -3.303  -5.022  1.00  1.00
ATOM     93  OE2 GLU    12     -12.207  -1.381  -6.127  1.00  1.00
ATOM     94  N   LEU    13      -8.139  -4.074  -1.292  1.00  1.00
ATOM     95  CA  LEU    13      -7.899  -4.896  -0.085  1.00  1.00
ATOM     96  C   LEU    13      -6.847  -4.236   0.814  1.00  1.00
ATOM     97  O   LEU    13      -6.936  -4.302   2.049  1.00  1.00
ATOM     98  CB  LEU    13      -7.481  -6.318  -0.487  1.00  1.00
ATOM     99  CG  LEU    13      -7.287  -7.248   0.714  1.00  1.00
ATOM    100  CD1 LEU    13      -8.546  -7.544   1.507  1.00  1.00
ATOM    101  CD2 LEU    13      -6.618  -8.532   0.181  1.00  1.00
ATOM    102  N   ALA    14      -5.905  -3.654   0.183  1.00  1.00
ATOM    103  CA  ALA    14      -4.829  -2.973   0.938  1.00  1.00
ATOM    104  C   ALA    14      -5.378  -1.733   1.653  1.00  1.00
ATOM    105  O   ALA    14      -5.065  -1.487   2.827  1.00  1.00
ATOM    106  CB  ALA    14      -3.669  -2.613  -0.001  1.00  1.00
ATOM    107  N   ALA    15      -6.189  -1.046   0.916  1.00  1.00
ATOM    108  CA  ALA    15      -6.824   0.166   1.484  1.00  1.00
ATOM    109  C   ALA    15      -7.778  -0.212   2.622  1.00  1.00
ATOM    110  O   ALA    15      -7.913   0.526   3.610  1.00  1.00
ATOM    111  CB  ALA    15      -7.549   0.950   0.380  1.00  1.00
ATOM    112  N   LYS    16      -8.385  -1.325   2.452  1.00  1.00
ATOM    113  CA  LYS    16      -9.344  -1.800   3.474  1.00  1.00
ATOM    114  C   LYS    16      -8.609  -2.171   4.767  1.00  1.00
ATOM    115  O   LYS    16      -9.071  -1.857   5.873  1.00  1.00
ATOM    116  CB  LYS    16     -10.156  -2.983   2.930  1.00  1.00
ATOM    117  CG  LYS    16     -10.989  -2.549   1.902  1.00  1.00
ATOM    118  CD  LYS    16     -11.827  -3.701   1.349  1.00  1.00
ATOM    119  CE  LYS    16     -12.742  -3.231   0.216  1.00  1.00
ATOM    120  NZ  LYS    16     -13.546  -4.344  -0.316  1.00  1.00
ATOM    121  N   ALA    17      -7.519  -2.849   4.608  1.00  1.00
ATOM    122  CA  ALA    17      -6.708  -3.254   5.779  1.00  1.00
ATOM    123  C   ALA    17      -6.134  -2.022   6.486  1.00  1.00
ATOM    124  O   ALA    17      -6.191  -1.913   7.721  1.00  1.00
ATOM    125  CB  ALA    17      -5.597  -4.221   5.345  1.00  1.00
ATOM    126  N   LYS    18      -5.568  -1.215   5.784  1.00  1.00
ATOM    127  CA  LYS    18      -4.875  -0.059   6.396  1.00  1.00
ATOM    128  C   LYS    18      -5.862   1.088   6.645  1.00  1.00
ATOM    129  O   LYS    18      -5.456   2.216   6.960  1.00  1.00
ATOM    130  CB  LYS    18      -3.706   0.389   5.506  1.00  1.00
ATOM    131  CG  LYS    18      -4.187   0.804   4.273  1.00  1.00
ATOM    132  CD  LYS    18      -3.043   1.273   3.372  1.00  1.00
ATOM    133  CE  LYS    18      -2.145   0.102   2.971  1.00  1.00
ATOM    134  NZ  LYS    18      -1.043   0.556   2.097  1.00  1.00
ATOM    135  N   ALA    19      -7.120   0.680   6.347  1.00  1.00
ATOM    136  CA  ALA    19      -8.254   1.577   6.668  1.00  1.00
ATOM    137  C   ALA    19      -7.751   2.995   6.958  1.00  1.00
ATOM    138  O   ALA    19      -7.378   3.737   6.036  1.00  1.00
ATOM    139  CB  ALA    19      -9.056   1.013   7.850  1.00  1.00
ATOM    140  N   GLY    20      -7.945   3.361   8.190  1.00  1.00
ATOM    141  CA  GLY    20      -7.607   4.743   8.600  1.00  1.00
ATOM    142  C   GLY    20      -6.650   4.726   9.798  1.00  1.00
ATOM    143  O   GLY    20      -6.893   5.396  10.814  1.00  1.00
ATOM    144  N   VAL    21      -5.631   3.817   9.569  1.00  1.00
ATOM    145  CA  VAL    21      -4.605   3.618  10.619  1.00  1.00
ATOM    146  C   VAL    21      -3.577   4.754  10.586  1.00  1.00
ATOM    147  O   VAL    21      -3.056   5.110   9.518  1.00  1.00
ATOM    148  CB  VAL    21      -3.934   2.247  10.450  1.00  1.00
ATOM    149  CG1 VAL    21      -4.932   1.110  10.561  1.00  1.00
ATOM    150  CG2 VAL    21      -2.838   2.114  11.484  1.00  1.00
ATOM    151  N   ILE    22      -3.343   5.298  11.729  1.00  1.00
ATOM    152  CA  ILE    22      -2.342   6.383  11.842  1.00  1.00
ATOM    153  C   ILE    22      -0.981   5.913  11.316  1.00  1.00
ATOM    154  O   ILE    22      -0.460   4.872  11.742  1.00  1.00
ATOM    155  CB  ILE    22      -2.245   6.866  13.296  1.00  1.00
ATOM    156  CG1 ILE    22      -1.758   5.754  14.211  1.00  1.00
ATOM    157  CG2 ILE    22      -3.581   7.367  13.808  1.00  1.00
ATOM    158  CD1 ILE    22      -1.351   6.194  15.621  1.00  1.00
ATOM    159  N   THR    23      -0.403   6.770  10.457  1.00  1.00
ATOM    160  CA  THR    23       0.959   6.516   9.935  1.00  1.00
ATOM    161  C   THR    23       0.926   5.430   8.854  1.00  1.00
ATOM    162  O   THR    23       1.974   5.014   8.339  1.00  1.00
ATOM    163  CB  THR    23       1.905   6.136  11.084  1.00  1.00
ATOM    164  OG1 THR    23       1.978   7.312  11.893  1.00  1.00
ATOM    165  CG2 THR    23       3.267   5.754  10.570  1.00  1.00
ATOM    166  N   GLU    24      -0.033   4.987   8.340  1.00  1.00
ATOM    167  CA  GLU    24      -0.039   3.959   7.274  1.00  1.00
ATOM    168  C   GLU    24       0.618   4.504   6.001  1.00  1.00
ATOM    169  O   GLU    24       1.290   3.763   5.267  1.00  1.00
ATOM    170  CB  GLU    24      -1.473   3.481   7.005  1.00  1.00
ATOM    171  CG  GLU    24      -1.547   2.383   5.981  1.00  1.00
ATOM    172  CD  GLU    24      -0.870   1.102   6.435  1.00  1.00
ATOM    173  OE1 GLU    24      -0.492   0.927   7.560  1.00  1.00
ATOM    174  OE2 GLU    24      -0.755   0.240   5.459  1.00  1.00
ATOM    175  N   GLU    25       0.377   5.643   5.647  1.00  1.00
ATOM    176  CA  GLU    25       0.905   6.197   4.379  1.00  1.00
ATOM    177  C   GLU    25       2.435   6.108   4.352  1.00  1.00
ATOM    178  O   GLU    25       3.030   5.707   3.341  1.00  1.00
ATOM    179  CB  GLU    25       0.424   7.642   4.191  1.00  1.00
ATOM    180  CG  GLU    25       0.897   8.594   5.260  1.00  1.00
ATOM    181  CD  GLU    25       0.421  10.012   5.037  1.00  1.00
ATOM    182  OE1 GLU    25      -0.733  10.315   4.993  1.00  1.00
ATOM    183  OE2 GLU    25       1.421  10.847   4.897  1.00  1.00
ATOM    184  N   GLU    26       3.050   6.547   5.383  1.00  1.00
ATOM    185  CA  GLU    26       4.529   6.511   5.460  1.00  1.00
ATOM    186  C   GLU    26       5.030   5.062   5.471  1.00  1.00
ATOM    187  O   GLU    26       6.093   4.754   4.912  1.00  1.00
ATOM    188  CB  GLU    26       5.013   7.281   6.697  1.00  1.00
ATOM    189  CG  GLU    26       4.763   8.768   6.625  1.00  1.00
ATOM    190  CD  GLU    26       5.268   9.509   7.845  1.00  1.00
ATOM    191  OE1 GLU    26       5.643   8.949   8.837  1.00  1.00
ATOM    192  OE2 GLU    26       5.238  10.803   7.684  1.00  1.00
ATOM    193  N   LYS    27       4.279   4.245   6.075  1.00  1.00
ATOM    194  CA  LYS    27       4.679   2.824   6.188  1.00  1.00
ATOM    195  C   LYS    27       4.544   2.120   4.833  1.00  1.00
ATOM    196  O   LYS    27       5.377   1.276   4.470  1.00  1.00
ATOM    197  CB  LYS    27       3.846   2.123   7.270  1.00  1.00
ATOM    198  CG  LYS    27       4.172   2.637   8.523  1.00  1.00
ATOM    199  CD  LYS    27       3.374   1.947   9.626  1.00  1.00
ATOM    200  CE  LYS    27       3.726   2.509  11.006  1.00  1.00
ATOM    201  NZ  LYS    27       2.952   1.844  12.068  1.00  1.00
ATOM    202  N   ALA    28       3.505   2.386   4.179  1.00  1.00
ATOM    203  CA  ALA    28       3.285   1.775   2.849  1.00  1.00
ATOM    204  C   ALA    28       4.294   2.322   1.834  1.00  1.00
ATOM    205  O   ALA    28       4.803   1.581   0.981  1.00  1.00
ATOM    206  CB  ALA    28       1.840   2.013   2.388  1.00  1.00
ATOM    207  N   GLU    29       4.572   3.596   1.993  1.00  1.00
ATOM    208  CA  GLU    29       5.538   4.262   1.088  1.00  1.00
ATOM    209  C   GLU    29       6.914   3.596   1.190  1.00  1.00
ATOM    210  O   GLU    29       7.615   3.429   0.181  1.00  1.00
ATOM    211  CB  GLU    29       5.615   5.761   1.408  1.00  1.00
ATOM    212  CG  GLU    29       6.106   6.071   2.799  1.00  1.00
ATOM    213  CD  GLU    29       6.186   7.555   3.077  1.00  1.00
ATOM    214  OE1 GLU    29       5.242   8.282   3.030  1.00  1.00
ATOM    215  OE2 GLU    29       7.409   7.932   3.367  1.00  1.00
ATOM    216  N   GLN    30       7.262   3.272   2.374  1.00  1.00
ATOM    217  CA  GLN    30       8.566   2.608   2.603  1.00  1.00
ATOM    218  C   GLN    30       8.571   1.208   1.979  1.00  1.00
ATOM    219  O   GLN    30       9.588   0.764   1.424  1.00  1.00
ATOM    220  CB  GLN    30       8.877   2.553   4.105  1.00  1.00
ATOM    221  CG  GLN    30       9.117   3.957   4.673  1.00  1.00
ATOM    222  CD  GLN    30       9.449   3.891   6.157  1.00  1.00
ATOM    223  OE1 GLN    30      10.413   3.276   6.585  1.00  1.00
ATOM    224  NE2 GLN    30       8.598   4.562   6.932  1.00  1.00
ATOM    225  N   GLN    31       7.491   0.524   2.086  1.00  1.00
ATOM    226  CA  GLN    31       7.401  -0.856   1.557  1.00  1.00
ATOM    227  C   GLN    31       7.378  -0.843   0.025  1.00  1.00
ATOM    228  O   GLN    31       7.909  -1.754  -0.627  1.00  1.00
ATOM    229  CB  GLN    31       6.164  -1.563   2.131  1.00  1.00
ATOM    230  CG  GLN    31       6.309  -1.796   3.639  1.00  1.00
ATOM    231  CD  GLN    31       5.089  -2.520   4.195  1.00  1.00
ATOM    232  OE1 GLN    31       3.968  -2.044   4.125  1.00  1.00
ATOM    233  NE2 GLN    31       5.359  -3.697   4.754  1.00  1.00
TER
END
