
#######################################################
#                                                     #
#                        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   28 (  219),  selected   28 , name T0335TS186_4-D1
# Molecule2: number of CA atoms   36 (  584),  selected   36 , name T0335_D1.pdb
# PARAMETERS: T0335TS186_4-D1.T0335_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

# WARNING! The change of the parameter DIST cutoff may give you better result.

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      A       5           -
LGA    -       -      K       6           -
LGA    L      13      I       7          3.315
LGA    A      14      A       8          3.361
LGA    A      15      R       9          3.497
LGA    K      16      I      10          2.471
LGA    A      17      N      11          2.951
LGA    -       -      E      12           -
LGA    K      18      L      13          3.343
LGA    A      19      A      14          1.747
LGA    -       -      A      15           -
LGA    -       -      K      16           -
LGA    -       -      A      17           -
LGA    -       -      K      18           -
LGA    -       -      A      19           -
LGA    G      20      G      20          5.371
LGA    V      21      V      21           -
LGA    I      22      I      22           #
LGA    -       -      T      23           -
LGA    -       -      E      24           -
LGA    -       -      E      25           -
LGA    T      23      E      26          0.743
LGA    E      24      K      27          1.851
LGA    E      25      A      28          1.219
LGA    E      26      E      29          0.792
LGA    K      27      Q      30          2.705
LGA    A      28      Q      31          2.970
LGA    E      29      K      32          1.608
LGA    Q      30      L      33          1.895
LGA    -       -      R      34           -
LGA    Q      31      Q      35           #
LGA    K      32      E      36          4.504
LGA    L      33      Y      37          2.203
LGA    R      34      L      38          3.082
LGA    -       -      K      39           -
LGA    Q      35      G      40          4.534
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)   28   36    5.0     20    2.97    20.00     37.215     0.652

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.514001 * X  +   0.739434 * Y  +   0.434788 * Z  +  -1.195310
  Y_new =  -0.825894 * X  +   0.289671 * Y  +   0.483725 * Z  +   7.068777
  Z_new =   0.231737 * X  +  -0.607724 * Y  +   0.759585 * Z  +  -1.287685 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.674786    2.466807  [ DEG:   -38.6624    141.3376 ]
  Theta =  -0.233863   -2.907729  [ DEG:   -13.3994   -166.6006 ]
  Phi   =  -1.014100    2.127493  [ DEG:   -58.1036    121.8964 ]
 
# 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: T0335TS186_4-D1                               
REMARK     2: T0335_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0335TS186_4-D1.T0335_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   28   36   5.0   20   2.97   20.00  37.215
REMARK  ---------------------------------------------------------- 
MOLECULE T0335TS186_4-D1
PFRMAT TS
TARGET T0335
MODEL  4
PARENT 1gxg_A
ATOM      1  N   LEU    13      -0.863  -1.751  -9.172  1.00  0.00
ATOM      2  CA  LEU    13      -0.226  -2.973  -8.644  1.00  0.00
ATOM      3  C   LEU    13      -1.176  -3.734  -7.717  1.00  0.00
ATOM      4  O   LEU    13      -1.915  -3.124  -6.948  1.00  0.00
ATOM      5  CB  LEU    13       1.033  -2.621  -7.849  1.00  0.00
ATOM      6  CG  LEU    13       2.201  -2.043  -8.650  1.00  0.00
ATOM      7  CD1 LEU    13       3.329  -1.617  -7.724  1.00  0.00
ATOM      8  CD2 LEU    13       2.748  -3.077  -9.622  1.00  0.00
ATOM      9  N   ALA    14      -1.127  -5.071  -7.718  1.00  0.00
ATOM     10  CA  ALA    14      -1.997  -5.994  -6.976  1.00  0.00
ATOM     11  C   ALA    14      -1.628  -6.142  -5.489  1.00  0.00
ATOM     12  O   ALA    14      -1.713  -7.214  -4.886  1.00  0.00
ATOM     13  CB  ALA    14      -1.933  -7.387  -7.583  1.00  0.00
ATOM     14  N   ALA    15      -1.175  -5.044  -4.902  1.00  0.00
ATOM     15  CA  ALA    15      -0.729  -4.894  -3.549  1.00  0.00
ATOM     16  C   ALA    15      -1.884  -5.064  -2.541  1.00  0.00
ATOM     17  O   ALA    15      -3.025  -5.327  -2.929  1.00  0.00
ATOM     18  CB  ALA    15      -0.129  -3.513  -3.339  1.00  0.00
ATOM     19  N   LYS    16      -1.591  -4.904  -1.236  1.00  0.00
ATOM     20  CA  LYS    16      -2.537  -4.994  -0.109  1.00  0.00
ATOM     21  C   LYS    16      -3.878  -4.425  -0.515  1.00  0.00
ATOM     22  O   LYS    16      -3.978  -3.253  -0.853  1.00  0.00
ATOM     23  CB  LYS    16      -2.039  -4.272   1.146  1.00  0.00
ATOM     24  CG  LYS    16      -0.593  -4.500   1.605  1.00  0.00
ATOM     25  CD  LYS    16      -0.182  -3.298   2.470  1.00  0.00
ATOM     26  CE  LYS    16       0.972  -3.615   3.413  1.00  0.00
ATOM     27  NZ  LYS    16       0.508  -4.078   4.736  1.00  0.00
ATOM     28  N   ALA    17      -4.900  -5.275  -0.504  1.00  0.00
ATOM     29  CA  ALA    17      -6.127  -5.001  -1.231  1.00  0.00
ATOM     30  C   ALA    17      -6.961  -3.942  -0.516  1.00  0.00
ATOM     31  O   ALA    17      -8.066  -3.642  -0.965  1.00  0.00
ATOM     32  CB  ALA    17      -6.964  -6.266  -1.352  1.00  0.00
ATOM     33  N   LYS    18      -6.518  -3.395   0.625  1.00  0.00
ATOM     34  CA  LYS    18      -7.179  -2.251   1.208  1.00  0.00
ATOM     35  C   LYS    18      -6.232  -1.378   2.013  1.00  0.00
ATOM     36  O   LYS    18      -5.278  -1.874   2.617  1.00  0.00
ATOM     37  CB  LYS    18      -8.297  -2.702   2.151  1.00  0.00
ATOM     38  CG  LYS    18      -7.810  -3.472   3.367  1.00  0.00
ATOM     39  CD  LYS    18      -8.971  -3.904   4.248  1.00  0.00
ATOM     40  CE  LYS    18      -8.484  -4.665   5.470  1.00  0.00
ATOM     41  NZ  LYS    18      -9.606  -5.046   6.372  1.00  0.00
ATOM     42  N   ALA    19      -6.614  -0.108   2.161  1.00  0.00
ATOM     43  CA  ALA    19      -5.969   0.877   3.016  1.00  0.00
ATOM     44  C   ALA    19      -5.826   0.358   4.444  1.00  0.00
ATOM     45  O   ALA    19      -4.795   0.573   5.058  1.00  0.00
ATOM     46  CB  ALA    19      -6.788   2.159   3.059  1.00  0.00
ATOM     47  N   GLY    20      -6.814  -0.345   4.995  1.00  0.00
ATOM     48  CA  GLY    20      -6.712  -0.771   6.387  1.00  0.00
ATOM     49  C   GLY    20      -5.735  -1.941   6.564  1.00  0.00
ATOM     50  O   GLY    20      -5.435  -2.279   7.718  1.00  0.00
ATOM     51  N   VAL    21      -5.224  -2.559   5.486  1.00  0.00
ATOM     52  CA  VAL    21      -4.038  -3.391   5.642  1.00  0.00
ATOM     53  C   VAL    21      -2.749  -2.581   5.503  1.00  0.00
ATOM     54  O   VAL    21      -1.727  -2.947   6.090  1.00  0.00
ATOM     55  CB  VAL    21      -3.987  -4.508   4.582  1.00  0.00
ATOM     56  CG1 VAL    21      -2.670  -5.262   4.665  1.00  0.00
ATOM     57  CG2 VAL    21      -5.122  -5.498   4.797  1.00  0.00
ATOM     58  N   ILE    22      -2.778  -1.450   4.800  1.00  0.00
ATOM     59  CA  ILE    22      -1.695  -0.503   4.884  1.00  0.00
ATOM     60  C   ILE    22      -1.633   0.015   6.326  1.00  0.00
ATOM     61  O   ILE    22      -2.574  -0.083   7.118  1.00  0.00
ATOM     62  CB  ILE    22      -1.908   0.685   3.927  1.00  0.00
ATOM     63  CG1 ILE    22      -3.180   1.449   4.299  1.00  0.00
ATOM     64  CG2 ILE    22      -2.042   0.195   2.493  1.00  0.00
ATOM     65  CD1 ILE    22      -3.368   2.734   3.523  1.00  0.00
ATOM     66  N   THR    23      -0.493   0.584   6.654  1.00  0.00
ATOM     67  CA  THR    23      -0.131   1.468   7.718  1.00  0.00
ATOM     68  C   THR    23       0.165   2.774   7.006  1.00  0.00
ATOM     69  O   THR    23       0.336   2.822   5.781  1.00  0.00
ATOM     70  CB  THR    23       1.146   0.947   8.394  1.00  0.00
ATOM     71  OG1 THR    23       2.124   0.732   7.421  1.00  0.00
ATOM     72  CG2 THR    23       0.959  -0.390   9.089  1.00  0.00
ATOM     73  N   GLU    24       0.261   3.818   7.806  1.00  0.00
ATOM     74  CA  GLU    24       0.672   5.106   7.245  1.00  0.00
ATOM     75  C   GLU    24       2.067   5.012   6.599  1.00  0.00
ATOM     76  O   GLU    24       2.309   5.624   5.560  1.00  0.00
ATOM     77  CB  GLU    24       0.521   6.230   8.280  1.00  0.00
ATOM     78  CG  GLU    24       1.585   6.268   9.386  1.00  0.00
ATOM     79  CD  GLU    24       2.801   7.125   9.006  1.00  0.00
ATOM     80  OE1 GLU    24       3.901   6.568   8.784  1.00  0.00
ATOM     81  OE2 GLU    24       2.660   8.358   8.870  1.00  0.00
ATOM     82  N   GLU    25       2.967   4.199   7.154  1.00  0.00
ATOM     83  CA  GLU    25       4.367   4.194   6.753  1.00  0.00
ATOM     84  C   GLU    25       4.597   3.272   5.541  1.00  0.00
ATOM     85  O   GLU    25       5.413   3.587   4.679  1.00  0.00
ATOM     86  CB  GLU    25       5.251   3.698   7.898  1.00  0.00
ATOM     87  CG  GLU    25       5.255   4.607   9.117  1.00  0.00
ATOM     88  CD  GLU    25       6.099   4.057  10.251  1.00  0.00
ATOM     89  OE1 GLU    25       6.697   2.975  10.075  1.00  0.00
ATOM     90  OE2 GLU    25       6.163   4.709  11.314  1.00  0.00
ATOM     91  N   GLU    26       3.876   2.148   5.418  1.00  0.00
ATOM     92  CA  GLU    26       3.900   1.349   4.198  1.00  0.00
ATOM     93  C   GLU    26       3.360   2.176   3.036  1.00  0.00
ATOM     94  O   GLU    26       3.914   2.136   1.933  1.00  0.00
ATOM     95  CB  GLU    26       3.039   0.097   4.382  1.00  0.00
ATOM     96  CG  GLU    26       3.658  -0.870   5.400  1.00  0.00
ATOM     97  CD  GLU    26       2.668  -1.977   5.781  1.00  0.00
ATOM     98  OE1 GLU    26       2.961  -3.181   5.611  1.00  0.00
ATOM     99  OE2 GLU    26       1.546  -1.620   6.209  1.00  0.00
ATOM    100  N   LYS    27       2.291   2.945   3.286  1.00  0.00
ATOM    101  CA  LYS    27       1.758   3.814   2.258  1.00  0.00
ATOM    102  C   LYS    27       2.793   4.870   1.910  1.00  0.00
ATOM    103  O   LYS    27       3.031   5.077   0.736  1.00  0.00
ATOM    104  CB  LYS    27       0.484   4.504   2.748  1.00  0.00
ATOM    105  CG  LYS    27      -0.180   5.393   1.709  1.00  0.00
ATOM    106  CD  LYS    27      -0.753   4.572   0.566  1.00  0.00
ATOM    107  CE  LYS    27      -1.533   5.445  -0.404  1.00  0.00
ATOM    108  NZ  LYS    27      -2.109   4.652  -1.524  1.00  0.00
ATOM    109  N   ALA    28       3.516   5.445   2.877  1.00  0.00
ATOM    110  CA  ALA    28       4.671   6.292   2.610  1.00  0.00
ATOM    111  C   ALA    28       5.581   5.596   1.627  1.00  0.00
ATOM    112  O   ALA    28       5.808   6.221   0.617  1.00  0.00
ATOM    113  CB  ALA    28       5.428   6.591   3.907  1.00  0.00
ATOM    114  N   GLU    29       6.057   4.353   1.797  1.00  0.00
ATOM    115  CA  GLU    29       7.315   3.589   0.398  1.00  0.00
ATOM    116  C   GLU    29       6.449   2.410  -0.013  1.00  0.00
ATOM    117  O   GLU    29       5.667   1.895   0.787  1.00  0.00
ATOM    118  CB  GLU    29       8.655   3.212   1.032  1.00  0.00
ATOM    119  CG  GLU    29       9.437   4.395   1.581  1.00  0.00
ATOM    120  CD  GLU    29      10.781   3.990   2.154  1.00  0.00
ATOM    121  OE1 GLU    29      11.082   2.777   2.161  1.00  0.00
ATOM    122  OE2 GLU    29      11.531   4.885   2.596  1.00  0.00
ATOM    123  N   GLN    30       6.553   2.089  -0.954  1.00  0.00
ATOM    124  CA  GLN    30       5.967   1.108  -1.533  1.00  0.00
ATOM    125  C   GLN    30       6.741  -0.048  -2.146  1.00  0.00
ATOM    126  O   GLN    30       7.839   0.139  -2.672  1.00  0.00
ATOM    127  CB  GLN    30       5.137   1.603  -2.719  1.00  0.00
ATOM    128  CG  GLN    30       4.080   2.632  -2.349  1.00  0.00
ATOM    129  CD  GLN    30       2.980   2.051  -1.483  1.00  0.00
ATOM    130  OE1 GLN    30       2.504   0.943  -1.727  1.00  0.00
ATOM    131  NE2 GLN    30       2.574   2.800  -0.464  1.00  0.00
ATOM    132  N   GLN    31       6.187  -1.206  -2.082  1.00  0.00
ATOM    133  CA  GLN    31       6.700  -2.375  -2.817  1.00  0.00
ATOM    134  C   GLN    31       7.268  -2.328  -4.226  1.00  0.00
ATOM    135  O   GLN    31       8.008  -1.408  -4.575  1.00  0.00
ATOM    136  CB  GLN    31       5.601  -3.425  -2.988  1.00  0.00
ATOM    137  CG  GLN    31       5.163  -4.082  -1.688  1.00  0.00
ATOM    138  CD  GLN    31       4.034  -5.074  -1.889  1.00  0.00
ATOM    139  OE1 GLN    31       3.553  -5.265  -3.006  1.00  0.00
ATOM    140  NE2 GLN    31       3.607  -5.709  -0.804  1.00  0.00
ATOM    141  N   LYS    32       7.005  -3.076  -4.836  1.00  0.00
ATOM    142  CA  LYS    32       7.394  -3.190  -6.169  1.00  0.00
ATOM    143  C   LYS    32       6.374  -2.710  -7.188  1.00  0.00
ATOM    144  O   LYS    32       6.576  -2.848  -8.394  1.00  0.00
ATOM    145  CB  LYS    32       7.679  -4.651  -6.521  1.00  0.00
ATOM    146  CG  LYS    32       8.843  -5.258  -5.755  1.00  0.00
ATOM    147  CD  LYS    32       9.077  -6.704  -6.160  1.00  0.00
ATOM    148  CE  LYS    32      10.203  -7.329  -5.352  1.00  0.00
ATOM    149  NZ  LYS    32      10.474  -8.732  -5.769  1.00  0.00
ATOM    150  N   LEU    33       5.547  -2.284  -6.821  1.00  0.00
ATOM    151  CA  LEU    33       4.549  -1.708  -7.753  1.00  0.00
ATOM    152  C   LEU    33       4.960  -0.540  -8.635  1.00  0.00
ATOM    153  O   LEU    33       4.110   0.165  -9.180  1.00  0.00
ATOM    154  CB  LEU    33       3.338  -1.182  -6.983  1.00  0.00
ATOM    155  CG  LEU    33       2.510  -2.223  -6.227  1.00  0.00
ATOM    156  CD1 LEU    33       1.422  -1.552  -5.403  1.00  0.00
ATOM    157  CD2 LEU    33       1.845  -3.188  -7.197  1.00  0.00
ATOM    158  N   ARG    34       5.942  -0.385  -8.739  1.00  0.00
ATOM    159  CA  ARG    34       6.543   0.646  -9.468  1.00  0.00
ATOM    160  C   ARG    34       5.833   0.806 -10.804  1.00  0.00
ATOM    161  O   ARG    34       5.553   1.923 -11.236  1.00  0.00
ATOM    162  CB  ARG    34       8.018   0.332  -9.725  1.00  0.00
ATOM    163  CG  ARG    34       8.767   1.430 -10.462  1.00  0.00
ATOM    164  CD  ARG    34      10.251   1.117 -10.558  1.00  0.00
ATOM    165  NE  ARG    34      10.968   2.103 -11.364  1.00  0.00
ATOM    166  CZ  ARG    34      12.290   2.145 -11.493  1.00  0.00
ATOM    167  NH1 ARG    34      12.854   3.079 -12.247  1.00  0.00
ATOM    168  NH2 ARG    34      13.045   1.255 -10.864  1.00  0.00
ATOM    169  N   GLN    35       5.615  -0.038 -11.294  1.00  0.00
ATOM    170  CA  GLN    35       4.863  -0.229 -12.577  1.00  0.00
ATOM    171  C   GLN    35       3.582   0.578 -12.709  1.00  0.00
ATOM    172  O   GLN    35       3.431   1.371 -13.638  1.00  0.00
ATOM    173  CB  GLN    35       4.454  -1.693 -12.745  1.00  0.00
ATOM    174  CG  GLN    35       3.694  -1.982 -14.030  1.00  0.00
ATOM    175  CD  GLN    35       3.357  -3.451 -14.190  1.00  0.00
ATOM    176  OE1 GLN    35       3.543  -4.245 -13.267  1.00  0.00
ATOM    177  NE2 GLN    35       2.858  -3.818 -15.365  1.00  0.00
ATOM    178  N   GLU    36       2.652   0.374 -11.770  1.00  0.00
ATOM    179  CA  GLU    36       1.400   1.113 -11.738  1.00  0.00
ATOM    180  C   GLU    36       0.928   1.555 -10.363  1.00  0.00
ATOM    181  O   GLU    36      -0.127   1.127  -9.893  1.00  0.00
ATOM    182  CB  GLU    36       0.263   0.266 -12.311  1.00  0.00
ATOM    183  CG  GLU    36       0.428  -0.079 -13.783  1.00  0.00
ATOM    184  CD  GLU    36      -0.756  -0.848 -14.337  1.00  0.00
ATOM    185  OE1 GLU    36      -1.082  -1.918 -13.783  1.00  0.00
ATOM    186  OE2 GLU    36      -1.358  -0.379 -15.326  1.00  0.00
ATOM    187  N   TYR    37       1.516   2.200  -9.876  1.00  0.00
ATOM    188  CA  TYR    37       1.204   2.762  -8.668  1.00  0.00
ATOM    189  C   TYR    37       0.066   3.763  -8.552  1.00  0.00
ATOM    190  O   TYR    37      -0.703   3.731  -7.591  1.00  0.00
ATOM    191  CB  TYR    37       2.401   3.535  -8.112  1.00  0.00
ATOM    192  CG  TYR    37       2.140   4.190  -6.775  1.00  0.00
ATOM    193  CD1 TYR    37       2.143   3.443  -5.604  1.00  0.00
ATOM    194  CD2 TYR    37       1.890   5.554  -6.687  1.00  0.00
ATOM    195  CE1 TYR    37       1.905   4.033  -4.377  1.00  0.00
ATOM    196  CE2 TYR    37       1.650   6.160  -5.469  1.00  0.00
ATOM    197  CZ  TYR    37       1.660   5.387  -4.309  1.00  0.00
ATOM    198  OH  TYR    37       1.423   5.977  -3.089  1.00  0.00
ATOM    199  N   LEU    38      -0.014   4.434  -9.289  1.00  0.00
ATOM    200  CA  LEU    38      -1.135   5.432  -9.342  1.00  0.00
ATOM    201  C   LEU    38      -2.541   4.857  -9.395  1.00  0.00
ATOM    202  O   LEU    38      -3.469   5.411  -8.807  1.00  0.00
ATOM    203  CB  LEU    38      -1.008   6.315 -10.585  1.00  0.00
ATOM    204  CG  LEU    38       0.160   7.304 -10.598  1.00  0.00
ATOM    205  CD1 LEU    38       0.274   7.982 -11.954  1.00  0.00
ATOM    206  CD2 LEU    38      -0.036   8.381  -9.542  1.00  0.00
ATOM    207  N   LYS    39      -2.696   3.747 -10.101  1.00  0.00
ATOM    208  CA  LYS    39      -3.852   2.857  -9.972  1.00  0.00
ATOM    209  C   LYS    39      -3.997   2.456  -8.515  1.00  0.00
ATOM    210  O   LYS    39      -5.049   2.680  -7.924  1.00  0.00
ATOM    211  CB  LYS    39      -3.662   1.603 -10.827  1.00  0.00
ATOM    212  CG  LYS    39      -4.837   0.639 -10.786  1.00  0.00
ATOM    213  CD  LYS    39      -4.607  -0.550 -11.704  1.00  0.00
ATOM    214  CE  LYS    39      -5.759  -1.539 -11.626  1.00  0.00
ATOM    215  NZ  LYS    39      -5.559  -2.699 -12.537  1.00  0.00
ATOM    216  N   GLY    40      -2.942   1.906  -7.919  1.00  0.00
ATOM    217  CA  GLY    40      -2.989   1.412  -6.555  1.00  0.00
ATOM    218  C   GLY    40      -3.395   2.510  -5.554  1.00  0.00
ATOM    219  O   GLY    40      -4.210   2.272  -4.666  1.00  0.00
TER
END
