
#######################################################
#                                                     #
#                        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   50 (  200),  selected   50 , name T0358TS383_4-D1
# Molecule2: number of CA atoms   65 ( 1035),  selected   65 , name T0358_D1.pdb
# PARAMETERS: T0358TS383_4-D1.T0358_D1.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    -       -      R      14           -
LGA    -       -      R      15           -
LGA    -       -      Q      16           -
LGA    -       -      A      17           -
LGA    -       -      Q      18           -
LGA    -       -      A      19           -
LGA    -       -      V      20           -
LGA    G      10      T      21          3.053
LGA    P      11      T      22          3.576
LGA    -       -      T      23           -
LGA    F      12      Y      24          3.608
LGA    T      13      S      25          5.261
LGA    R      14      -       -           -
LGA    R      15      -       -           -
LGA    Q      16      -       -           -
LGA    A      17      -       -           -
LGA    Q      18      -       -           -
LGA    A      19      N      26          1.455
LGA    V      20      I      27          1.912
LGA    T      21      T      28          2.883
LGA    T      22      L      29          2.660
LGA    T      23      E      30          1.463
LGA    Y      24      D      31          4.631
LGA    -       -      D      32           -
LGA    -       -      Q      33           -
LGA    -       -      G      34           -
LGA    -       -      S      35           -
LGA    -       -      H      36           -
LGA    -       -      F      37           -
LGA    -       -      R      38           -
LGA    S      25      L      39          2.660
LGA    N      26      V      40          1.851
LGA    I      27      V      41          0.529
LGA    T      28      R      42          0.797
LGA    L      29      D      43          2.556
LGA    -       -      T      44           -
LGA    E      30      E      45          2.942
LGA    D      31      G      46           #
LGA    D      32      -       -           -
LGA    Q      33      R      47           #
LGA    G      34      M      48           -
LGA    S      35      V      49           -
LGA    H      36      W      50           -
LGA    F      37      -       -           -
LGA    R      38      -       -           -
LGA    L      39      -       -           -
LGA    V      40      -       -           -
LGA    V      41      -       -           -
LGA    R      42      R      51           #
LGA    D      43      A      52           #
LGA    -       -      W      53           -
LGA    T      44      N      54          1.877
LGA    E      45      F      55          2.466
LGA    -       -      E      56           -
LGA    G      46      P      57          3.778
LGA    R      47      D      58          2.011
LGA    M      48      A      59          3.037
LGA    -       -      G      60           -
LGA    -       -      E      61           -
LGA    V      49      G      62          4.134
LGA    W      50      L      63          3.969
LGA    R      51      N      64          3.690
LGA    A      52      R      65          1.504
LGA    N      54      Y      66           #
LGA    -       -      I      67           -
LGA    -       -      R      68           -
LGA    F      55      T      69           #
LGA    E      56      S      70           -
LGA    P      57      G      71           -
LGA    D      58      I      72           -
LGA    A      59      R      73           -
LGA    G      60      T      74           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   50   65    5.0     25    2.97     8.00     23.297     0.815

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.012318 * X  +  -0.532896 * Y  +  -0.846091 * Z  +  20.664360
  Y_new =   0.994516 * X  +  -0.094412 * Y  +   0.044985 * Z  + -97.246078
  Z_new =  -0.103853 * X  +  -0.840897 * Y  +   0.531137 * Z  +  -0.425931 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.007443    2.134150  [ DEG:   -57.7222    122.2778 ]
  Theta =   0.104041    3.037552  [ DEG:     5.9611    174.0389 ]
  Phi   =   1.583182   -1.558411  [ DEG:    90.7096    -89.2904 ]
 
# 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_4-D1                               
REMARK     2: T0358_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0358TS383_4-D1.T0358_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   50   65   5.0   25   2.97    8.00  23.297
REMARK  ---------------------------------------------------------- 
MOLECULE T0358TS383_4-D1
PFRMAT TS
TARGET T0358
MODEL 4
PARENT 1bwuA
ATOM     25  N   GLY    10      -0.470  -2.018  -7.344  1.00  0.00
ATOM     26  CA  GLY    10       0.022  -3.389  -7.461  1.00  0.00
ATOM     27  C   GLY    10      -0.732  -4.338  -6.535  1.00  0.00
ATOM     28  O   GLY    10      -1.291  -3.906  -5.522  1.00  0.00
ATOM     29  N   PRO    11      -0.678  -5.634  -6.843  1.00  0.00
ATOM     30  CA  PRO    11      -1.373  -6.638  -6.038  1.00  0.00
ATOM     31  C   PRO    11      -0.917  -8.102  -6.180  1.00  0.00
ATOM     32  O   PRO    11      -0.159  -8.451  -7.094  1.00  0.00
ATOM     33  N   PHE    12      -1.335  -8.924  -5.216  1.00  0.00
ATOM     34  CA  PHE    12      -1.057 -10.357  -5.202  1.00  0.00
ATOM     35  C   PHE    12      -2.415 -10.983  -5.486  1.00  0.00
ATOM     36  O   PHE    12      -3.430 -10.495  -4.991  1.00  0.00
ATOM     37  N   THR    13      -2.434 -12.086  -6.228  1.00  0.00
ATOM     38  CA  THR    13      -3.690 -12.748  -6.581  1.00  0.00
ATOM     39  C   THR    13      -3.618 -14.279  -6.532  1.00  0.00
ATOM     40  O   THR    13      -2.561 -14.883  -6.727  1.00  0.00
ATOM     41  N   ARG    14      -4.764 -14.895  -6.269  1.00  0.00
ATOM     42  CA  ARG    14      -4.905 -16.344  -6.192  1.00  0.00
ATOM     43  C   ARG    14      -6.397 -16.614  -6.079  1.00  0.00
ATOM     44  O   ARG    14      -6.962 -16.551  -4.992  1.00  0.00
ATOM     45  N   ARG    15      -7.042 -16.881  -7.212  1.00  0.00
ATOM     46  CA  ARG    15      -8.488 -17.125  -7.236  1.00  0.00
ATOM     47  C   ARG    15      -9.148 -15.804  -6.821  1.00  0.00
ATOM     48  O   ARG    15      -8.482 -14.771  -6.815  1.00  0.00
ATOM     49  N   GLN    16     -10.474 -15.793  -6.565  1.00  0.00
ATOM     50  CA  GLN    16     -11.084 -14.520  -6.159  1.00  0.00
ATOM     51  C   GLN    16     -10.607 -14.075  -4.773  1.00  0.00
ATOM     52  O   GLN    16     -11.320 -14.221  -3.776  1.00  0.00
ATOM     53  N   ALA    17      -9.368 -13.598  -4.730  1.00  0.00
ATOM     54  CA  ALA    17      -8.712 -13.095  -3.529  1.00  0.00
ATOM     55  C   ALA    17      -7.822 -12.000  -4.095  1.00  0.00
ATOM     56  O   ALA    17      -7.282 -12.150  -5.189  1.00  0.00
ATOM     57  N   GLN    18      -7.657 -10.902  -3.368  1.00  0.00
ATOM     58  CA  GLN    18      -6.874  -9.798  -3.902  1.00  0.00
ATOM     59  C   GLN    18      -6.303  -8.895  -2.829  1.00  0.00
ATOM     60  O   GLN    18      -7.046  -8.243  -2.115  1.00  0.00
ATOM     61  N   ALA    19      -4.982  -8.858  -2.726  1.00  0.00
ATOM     62  CA  ALA    19      -4.298  -8.020  -1.749  1.00  0.00
ATOM     63  C   ALA    19      -3.778  -6.881  -2.598  1.00  0.00
ATOM     64  O   ALA    19      -2.932  -7.105  -3.469  1.00  0.00
ATOM     65  N   VAL    20      -4.268  -5.668  -2.361  1.00  0.00
ATOM     66  CA  VAL    20      -3.853  -4.528  -3.172  1.00  0.00
ATOM     67  C   VAL    20      -3.448  -3.290  -2.394  1.00  0.00
ATOM     68  O   VAL    20      -3.942  -3.044  -1.290  1.00  0.00
ATOM     69  N   THR    21      -2.505  -2.549  -2.973  1.00  0.00
ATOM     70  CA  THR    21      -2.009  -1.291  -2.419  1.00  0.00
ATOM     71  C   THR    21      -2.672  -0.246  -3.307  1.00  0.00
ATOM     72  O   THR    21      -2.203   0.029  -4.406  1.00  0.00
ATOM     73  N   THR    22      -3.788   0.301  -2.846  1.00  0.00
ATOM     74  CA  THR    22      -4.549   1.282  -3.620  1.00  0.00
ATOM     75  C   THR    22      -3.977   2.693  -3.603  1.00  0.00
ATOM     76  O   THR    22      -3.082   3.003  -2.816  1.00  0.00
ATOM     77  N   THR    23      -4.541   3.554  -4.442  1.00  0.00
ATOM     78  CA  THR    23      -4.114   4.950  -4.556  1.00  0.00
ATOM     79  C   THR    23      -4.622   5.767  -3.368  1.00  0.00
ATOM     80  O   THR    23      -4.368   6.969  -3.281  1.00  0.00
ATOM     81  N   TYR    24      -5.395   5.114  -2.502  1.00  0.00
ATOM     82  CA  TYR    24      -5.949   5.727  -1.299  1.00  0.00
ATOM     83  C   TYR    24      -4.965   5.526  -0.155  1.00  0.00
ATOM     84  O   TYR    24      -5.187   6.009   0.953  1.00  0.00
ATOM     85  N   SER    25      -3.927   4.734  -0.406  1.00  0.00
ATOM     86  CA  SER    25      -2.908   4.409   0.586  1.00  0.00
ATOM     87  C   SER    25      -3.451   3.415   1.610  1.00  0.00
ATOM     88  O   SER    25      -2.862   3.218   2.676  1.00  0.00
ATOM     89  N   ASN    26      -4.559   2.765   1.263  1.00  0.00
ATOM     90  CA  ASN    26      -5.194   1.784   2.138  1.00  0.00
ATOM     91  C   ASN    26      -4.931   0.365   1.607  1.00  0.00
ATOM     92  O   ASN    26      -5.301   0.049   0.471  1.00  0.00
ATOM     93  N   ILE    27      -4.241  -0.461   2.394  1.00  0.00
ATOM     94  CA  ILE    27      -3.955  -1.845   2.008  1.00  0.00
ATOM     95  C   ILE    27      -5.227  -2.639   2.274  1.00  0.00
ATOM     96  O   ILE    27      -5.689  -2.678   3.416  1.00  0.00
ATOM     97  N   THR    28      -5.785  -3.275   1.247  1.00  0.00
ATOM     98  CA  THR    28      -7.027  -4.030   1.412  1.00  0.00
ATOM     99  C   THR    28      -6.967  -5.451   0.834  1.00  0.00
ATOM    100  O   THR    28      -6.225  -5.706  -0.112  1.00  0.00
ATOM    101  N   LEU    29      -7.763  -6.355   1.409  1.00  0.00
ATOM    102  CA  LEU    29      -7.866  -7.748   0.974  1.00  0.00
ATOM    103  C   LEU    29      -9.312  -7.990   0.526  1.00  0.00
ATOM    104  O   LEU    29     -10.218  -7.977   1.358  1.00  0.00
ATOM    105  N   GLU    30      -9.512  -8.266  -0.765  1.00  0.00
ATOM    106  CA  GLU    30     -10.849  -8.464  -1.341  1.00  0.00
ATOM    107  C   GLU    30     -11.260  -9.864  -1.799  1.00  0.00
ATOM    108  O   GLU    30     -10.529 -10.511  -2.554  1.00  0.00
ATOM    109  N   ASP    31     -12.440 -10.311  -1.367  1.00  0.00
ATOM    110  CA  ASP    31     -12.998 -11.581  -1.830  1.00  0.00
ATOM    111  C   ASP    31     -13.927 -11.011  -2.888  1.00  0.00
ATOM    112  O   ASP    31     -14.898 -10.334  -2.559  1.00  0.00
ATOM    113  N   ASP    32     -13.609 -11.237  -4.155  1.00  0.00
ATOM    114  CA  ASP    32     -14.406 -10.681  -5.243  1.00  0.00
ATOM    115  C   ASP    32     -14.286  -9.158  -5.076  1.00  0.00
ATOM    116  O   ASP    32     -13.174  -8.638  -5.022  1.00  0.00
ATOM    117  N   GLN    33     -15.407  -8.453  -4.952  1.00  0.00
ATOM    118  CA  GLN    33     -15.383  -6.998  -4.777  1.00  0.00
ATOM    119  C   GLN    33     -15.488  -6.632  -3.298  1.00  0.00
ATOM    120  O   GLN    33     -15.093  -5.545  -2.875  1.00  0.00
ATOM    121  N   GLY    34      10.386  -6.469   4.656  1.00  0.00
ATOM    122  CA  GLY    34      11.795  -6.228   4.961  1.00  0.00
ATOM    123  C   GLY    34      12.572  -7.328   5.677  1.00  0.00
ATOM    124  O   GLY    34      11.992  -8.263   6.223  1.00  0.00
ATOM    125  N   SER    35      13.894  -7.167   5.696  1.00  0.00
ATOM    126  CA  SER    35      14.834  -8.109   6.307  1.00  0.00
ATOM    127  C   SER    35      14.587  -8.383   7.782  1.00  0.00
ATOM    128  O   SER    35      14.847  -9.486   8.257  1.00  0.00
ATOM    129  N   HIS    36      14.144  -7.373   8.521  1.00  0.00
ATOM    130  CA  HIS    36      13.864  -7.549   9.945  1.00  0.00
ATOM    131  C   HIS    36      12.535  -8.269  10.137  1.00  0.00
ATOM    132  O   HIS    36      12.102  -8.521  11.266  1.00  0.00
ATOM    133  N   PHE    37      11.899  -8.601   9.016  1.00  0.00
ATOM    134  CA  PHE    37      10.625  -9.293   9.045  1.00  0.00
ATOM    135  C   PHE    37       9.467  -8.361   9.320  1.00  0.00
ATOM    136  O   PHE    37       8.534  -8.733  10.025  1.00  0.00
ATOM    137  N   ARG    38       9.516  -7.158   8.754  1.00  0.00
ATOM    138  CA  ARG    38       8.458  -6.181   8.957  1.00  0.00
ATOM    139  C   ARG    38       7.804  -5.774   7.642  1.00  0.00
ATOM    140  O   ARG    38       8.491  -5.513   6.651  1.00  0.00
ATOM    141  N   LEU    39       6.474  -5.772   7.626  1.00  0.00
ATOM    142  CA  LEU    39       5.713  -5.388   6.443  1.00  0.00
ATOM    143  C   LEU    39       5.328  -3.936   6.663  1.00  0.00
ATOM    144  O   LEU    39       4.336  -3.656   7.338  1.00  0.00
ATOM    145  N   VAL    40       6.118  -3.015   6.125  1.00  0.00
ATOM    146  CA  VAL    40       5.841  -1.598   6.309  1.00  0.00
ATOM    147  C   VAL    40       5.218  -0.909   5.095  1.00  0.00
ATOM    148  O   VAL    40       5.600  -1.167   3.950  1.00  0.00
ATOM    149  N   VAL    41       4.212  -0.076   5.360  1.00  0.00
ATOM    150  CA  VAL    41       3.551   0.705   4.318  1.00  0.00
ATOM    151  C   VAL    41       4.160   2.093   4.462  1.00  0.00
ATOM    152  O   VAL    41       4.136   2.676   5.550  1.00  0.00
ATOM    153  N   ARG    42       4.742   2.600   3.384  1.00  0.00
ATOM    154  CA  ARG    42       5.391   3.897   3.419  1.00  0.00
ATOM    155  C   ARG    42       4.704   4.994   2.630  1.00  0.00
ATOM    156  O   ARG    42       4.096   4.757   1.579  1.00  0.00
ATOM    157  N   ASP    43       4.883   6.207   3.138  1.00  0.00
ATOM    158  CA  ASP    43       4.338   7.433   2.577  1.00  0.00
ATOM    159  C   ASP    43       5.007   7.753   1.242  1.00  0.00
ATOM    160  O   ASP    43       6.080   7.222   0.937  1.00  0.00
ATOM    161  N   THR    44       4.400   8.655   0.474  1.00  0.00
ATOM    162  CA  THR    44       4.938   9.060  -0.828  1.00  0.00
ATOM    163  C   THR    44       6.379   9.542  -0.700  1.00  0.00
ATOM    164  O   THR    44       7.168   9.416  -1.639  1.00  0.00
ATOM    165  N   GLU    45       6.705  10.117   0.456  1.00  0.00
ATOM    166  CA  GLU    45       8.057  10.593   0.715  1.00  0.00
ATOM    167  C   GLU    45       8.863   9.390   1.183  1.00  0.00
ATOM    168  O   GLU    45       9.604   8.786   0.409  1.00  0.00
ATOM    169  N   GLY    46       8.675   9.017   2.444  1.00  0.00
ATOM    170  CA  GLY    46       9.390   7.881   2.986  1.00  0.00
ATOM    171  C   GLY    46       9.164   7.667   4.467  1.00  0.00
ATOM    172  O   GLY    46      10.101   7.309   5.186  1.00  0.00
ATOM    173  N   ARG    47       7.943   7.911   4.944  1.00  0.00
ATOM    174  CA  ARG    47       7.644   7.710   6.356  1.00  0.00
ATOM    175  C   ARG    47       6.564   6.688   6.613  1.00  0.00
ATOM    176  O   ARG    47       5.707   6.431   5.772  1.00  0.00
ATOM    177  N   MET    48       6.639   6.092   7.791  1.00  0.00
ATOM    178  CA  MET    48       5.732   5.039   8.200  1.00  0.00
ATOM    179  C   MET    48       4.275   5.435   8.427  1.00  0.00
ATOM    180  O   MET    48       3.979   6.416   9.113  1.00  0.00
ATOM    181  N   VAL    49       3.374   4.652   7.839  1.00  0.00
ATOM    182  CA  VAL    49       1.934   4.859   7.972  1.00  0.00
ATOM    183  C   VAL    49       1.347   3.679   8.747  1.00  0.00
ATOM    184  O   VAL    49       0.521   3.859   9.646  1.00  0.00
ATOM    185  N   TRP    50       1.781   2.474   8.383  1.00  0.00
ATOM    186  CA  TRP    50       1.340   1.237   9.027  1.00  0.00
ATOM    187  C   TRP    50       2.479   0.223   8.982  1.00  0.00
ATOM    188  O   TRP    50       3.356   0.289   8.112  1.00  0.00
ATOM    189  N   ARG    51       2.466  -0.705   9.927  1.00  0.00
ATOM    190  CA  ARG    51       3.490  -1.726   9.997  1.00  0.00
ATOM    191  C   ARG    51       2.944  -2.919  10.759  1.00  0.00
ATOM    192  O   ARG    51       2.284  -2.754  11.788  1.00  0.00
ATOM    193  N   ALA    52       3.200  -4.112  10.236  1.00  0.00
ATOM    194  CA  ALA    52       2.750  -5.345  10.866  1.00  0.00
ATOM    195  C   ALA    52       3.468  -5.549  12.200  1.00  0.00
ATOM    196  O   ALA    52       2.943  -6.190  13.117  1.00  0.00
ATOM    197  N   ASN    54       4.663  -4.971  12.295  1.00  0.00
ATOM    198  CA  ASN    54       5.513  -5.051  13.482  1.00  0.00
ATOM    199  C   ASN    54       5.960  -6.466  13.820  1.00  0.00
ATOM    200  O   ASN    54       6.032  -6.858  14.989  1.00  0.00
ATOM    201  N   PHE    55       6.314  -7.206  12.776  1.00  0.00
ATOM    202  CA  PHE    55       6.785  -8.572  12.914  1.00  0.00
ATOM    203  C   PHE    55       8.318  -8.622  12.911  1.00  0.00
ATOM    204  O   PHE    55       8.925  -9.612  12.501  1.00  0.00
ATOM    205  N   GLU    56       8.937  -7.541  13.380  1.00  0.00
ATOM    206  CA  GLU    56      10.392  -7.453  13.447  1.00  0.00
ATOM    207  C   GLU    56      10.935  -8.508  14.400  1.00  0.00
ATOM    208  O   GLU    56      10.720  -8.434  15.612  1.00  0.00
ATOM    209  N   PRO    57      11.604  -9.510  13.843  1.00  0.00
ATOM    210  CA  PRO    57      12.178 -10.579  14.648  1.00  0.00
ATOM    211  C   PRO    57      13.630 -10.870  14.283  1.00  0.00
ATOM    212  O   PRO    57      14.057 -12.026  14.266  1.00  0.00
ATOM    213  N   ASP    58      14.395  -9.811  14.040  1.00  0.00
ATOM    214  CA  ASP    58      15.797  -9.969  13.694  1.00  0.00
ATOM    215  C   ASP    58      16.026 -10.140  12.206  1.00  0.00
ATOM    216  O   ASP    58      15.114 -10.486  11.462  1.00  0.00
ATOM    217  N   ALA    59      17.247  -9.864  11.764  1.00  0.00
ATOM    218  CA  ALA    59      17.593  -9.989  10.354  1.00  0.00
ATOM    219  C   ALA    59      17.567 -11.458   9.909  1.00  0.00
ATOM    220  O   ALA    59      18.092 -12.338  10.600  1.00  0.00
ATOM    221  N   GLY    60      16.944 -11.699   8.757  1.00  0.00
ATOM    222  CA  GLY    60      16.839 -13.037   8.204  1.00  0.00
ATOM    223  C   GLY    60      16.227 -12.983   6.817  1.00  0.00
ATOM    224  O   GLY    60      16.339 -11.969   6.134  1.00  0.00
TER
END
