
#######################################################
#                                                     #
#                        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   54 (  216),  selected   54 , name T0349TS383_1-D1
# Molecule2: number of CA atoms   57 (  873),  selected   57 , name T0349_D1.pdb
# PARAMETERS: T0349TS383_1-D1.T0349_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      M       1           -
LGA    R       2      R       2          1.163
LGA    E       3      E       3          1.059
LGA    L       4      L       4          0.724
LGA    L       5      L       5          0.361
LGA    R       6      R       6          1.337
LGA    T       7      T       7          2.614
LGA    N       8      N       8          4.365
LGA    D       9      D       9          1.061
LGA    A      10      A      10          1.537
LGA    V      11      V      11          1.032
LGA    L      12      L      12          0.375
LGA    L      13      L      13          1.221
LGA    S      14      S      14          1.250
LGA    A      15      A      15          0.739
LGA    V      16      V      16          0.471
LGA    G      17      G      17          0.997
LGA    A      18      A      18          0.992
LGA    L      19      L      19          0.758
LGA    L      20      L      20          0.792
LGA    D      21      D      21          0.981
LGA    G      22      G      22          0.469
LGA    A      23      A      23          1.079
LGA    D      24      D      24          1.854
LGA    I      25      I      25          0.526
LGA    G      26      G      26          1.496
LGA    H      27      H      27          1.197
LGA    L      28      L      28          1.214
LGA    V      29      V      29          1.188
LGA    R      46      P      45          3.894
LGA    -       -      R      46           -
LGA    R      47      R      47          0.808
LGA    V      48      V      48          0.783
LGA    L      49      L      49          0.745
LGA    V      50      V      50          0.638
LGA    H      51      H      51          1.105
LGA    E      52      E      52          1.876
LGA    D      53      D      53          2.289
LGA    D      54      D      54          1.518
LGA    L      55      L      55          0.905
LGA    A      56      A      56          0.261
LGA    G      57      G      57          0.441
LGA    A      58      A      58          0.296
LGA    R      59      R      59          0.510
LGA    R      60      R      60          0.720
LGA    L      61      L      61          0.584
LGA    L      62      L      62          0.298
LGA    T      63      T      63          0.622
LGA    D      64      D      64          1.446
LGA    A      65      A      65          2.069
LGA    G      66      G      66          3.718
LGA    -       -      L      67           -
LGA    L      67      A      68          3.481
LGA    A      68      H      69           -
LGA    H      69      E      70           -
LGA    E      70      L      71           -
LGA    L      71      R      72           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   54   57    5.0     50    1.55    96.00     82.033     3.033

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.698307 * X  +  -0.623725 * Y  +   0.351190 * Z  +   6.307714
  Y_new =   0.667945 * X  +   0.744182 * Y  +  -0.006451 * Z  + -66.603218
  Z_new =  -0.257326 * X  +   0.239080 * Y  +   0.936282 * Z  + -40.315666 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.250008   -2.891584  [ DEG:    14.3244   -165.6756 ]
  Theta =   0.260253    2.881339  [ DEG:    14.9114    165.0886 ]
  Phi   =   0.763179   -2.378413  [ DEG:    43.7270   -136.2730 ]
 
# 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: T0349TS383_1-D1                               
REMARK     2: T0349_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0349TS383_1-D1.T0349_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   54   57   5.0   50   1.55   96.00  82.033
REMARK  ---------------------------------------------------------- 
MOLECULE T0349TS383_1-D1
PFRMAT TS
TARGET T0349
MODEL 1
PARENT 1yj7A
ATOM      1  N   ARG     2       2.804   8.730  -5.843  1.00  0.00
ATOM      2  CA  ARG     2       3.993   7.974  -5.494  1.00  0.00
ATOM      3  C   ARG     2       3.630   6.830  -4.560  1.00  0.00
ATOM      4  O   ARG     2       2.966   7.043  -3.556  1.00  0.00
ATOM      5  N   GLU     3       4.064   5.627  -4.918  1.00  0.00
ATOM      6  CA  GLU     3       3.802   4.447  -4.099  1.00  0.00
ATOM      7  C   GLU     3       4.561   4.608  -2.804  1.00  0.00
ATOM      8  O   GLU     3       5.685   5.081  -2.810  1.00  0.00
ATOM      9  N   LEU     4       3.937   4.242  -1.708  1.00  0.00
ATOM     10  CA  LEU     4       4.651   4.128  -0.419  1.00  0.00
ATOM     11  C   LEU     4       5.100   2.685  -0.205  1.00  0.00
ATOM     12  O   LEU     4       6.293   2.385  -0.209  1.00  0.00
ATOM     13  N   LEU     5       4.135   1.785  -0.070  1.00  0.00
ATOM     14  CA  LEU     5       4.386   0.387   0.231  1.00  0.00
ATOM     15  C   LEU     5       3.441  -0.534  -0.550  1.00  0.00
ATOM     16  O   LEU     5       2.272  -0.218  -0.731  1.00  0.00
ATOM     17  N   ARG     6       3.973  -1.664  -0.993  1.00  0.00
ATOM     18  CA  ARG     6       3.189  -2.793  -1.502  1.00  0.00
ATOM     19  C   ARG     6       3.317  -4.005  -0.575  1.00  0.00
ATOM     20  O   ARG     6       4.104  -4.004   0.391  1.00  0.00
ATOM     21  N   THR     7       2.549  -5.052  -0.878  1.00  0.00
ATOM     22  CA  THR     7       2.642  -6.309  -0.155  1.00  0.00
ATOM     23  C   THR     7       2.032  -6.288   1.230  1.00  0.00
ATOM     24  O   THR     7       2.340  -7.146   2.065  1.00  0.00
ATOM     25  N   ASN     8       1.177  -5.304   1.516  1.00  0.00
ATOM     26  CA  ASN     8       0.614  -5.164   2.859  1.00  0.00
ATOM     27  C   ASN     8      -0.613  -6.065   3.048  1.00  0.00
ATOM     28  O   ASN     8      -1.373  -6.301   2.106  1.00  0.00
ATOM     29  N   ASP     9      -0.819  -6.546   4.275  1.00  0.00
ATOM     30  CA  ASP     9      -2.095  -7.165   4.635  1.00  0.00
ATOM     31  C   ASP     9      -3.186  -6.113   4.630  1.00  0.00
ATOM     32  O   ASP     9      -2.922  -4.912   4.722  1.00  0.00
ATOM     33  N   ALA    10      -4.429  -6.567   4.533  1.00  0.00
ATOM     34  CA  ALA    10      -5.546  -5.645   4.575  1.00  0.00
ATOM     35  C   ALA    10      -5.570  -4.896   5.911  1.00  0.00
ATOM     36  O   ALA    10      -5.749  -3.681   5.935  1.00  0.00
ATOM     37  N   VAL    11      -5.338  -5.600   7.019  1.00  0.00
ATOM     38  CA  VAL    11      -5.388  -4.990   8.351  1.00  0.00
ATOM     39  C   VAL    11      -4.337  -3.885   8.517  1.00  0.00
ATOM     40  O   VAL    11      -4.647  -2.794   8.996  1.00  0.00
ATOM     41  N   LEU    12      -3.099  -4.169   8.121  1.00  0.00
ATOM     42  CA  LEU    12      -2.032  -3.188   8.284  1.00  0.00
ATOM     43  C   LEU    12      -2.188  -2.009   7.315  1.00  0.00
ATOM     44  O   LEU    12      -1.964  -0.869   7.716  1.00  0.00
ATOM     45  N   LEU    13      -2.566  -2.265   6.064  1.00  0.00
ATOM     46  CA  LEU    13      -2.821  -1.169   5.135  1.00  0.00
ATOM     47  C   LEU    13      -3.906  -0.284   5.721  1.00  0.00
ATOM     48  O   LEU    13      -3.813   0.928   5.631  1.00  0.00
ATOM     49  N   SER    14      -4.950  -0.877   6.310  1.00  0.00
ATOM     50  CA  SER    14      -5.993  -0.073   6.935  1.00  0.00
ATOM     51  C   SER    14      -5.493   0.786   8.086  1.00  0.00
ATOM     52  O   SER    14      -5.888   1.937   8.216  1.00  0.00
ATOM     53  N   ALA    15      -4.625   0.224   8.916  1.00  0.00
ATOM     54  CA  ALA    15      -4.058   0.971  10.027  1.00  0.00
ATOM     55  C   ALA    15      -3.226   2.153   9.508  1.00  0.00
ATOM     56  O   ALA    15      -3.348   3.274   9.996  1.00  0.00
ATOM     57  N   VAL    16      -2.427   1.900   8.490  1.00  0.00
ATOM     58  CA  VAL    16      -1.572   2.935   7.897  1.00  0.00
ATOM     59  C   VAL    16      -2.389   4.023   7.189  1.00  0.00
ATOM     60  O   VAL    16      -2.086   5.220   7.312  1.00  0.00
ATOM     61  N   GLY    17      -3.423   3.608   6.445  1.00  0.00
ATOM     62  CA  GLY    17      -4.300   4.525   5.733  1.00  0.00
ATOM     63  C   GLY    17      -5.061   5.411   6.710  1.00  0.00
ATOM     64  O   GLY    17      -5.111   6.629   6.554  1.00  0.00
ATOM     65  N   ALA    18      -5.607   4.819   7.768  1.00  0.00
ATOM     66  CA  ALA    18      -6.319   5.609   8.762  1.00  0.00
ATOM     67  C   ALA    18      -5.384   6.562   9.504  1.00  0.00
ATOM     68  O   ALA    18      -5.749   7.699   9.766  1.00  0.00
ATOM     69  N   LEU    19      -4.169   6.117   9.815  1.00  0.00
ATOM     70  CA  LEU    19      -3.185   6.972  10.459  1.00  0.00
ATOM     71  C   LEU    19      -2.850   8.210   9.609  1.00  0.00
ATOM     72  O   LEU    19      -2.806   9.336  10.103  1.00  0.00
ATOM     73  N   LEU    20      -2.622   7.990   8.323  1.00  0.00
ATOM     74  CA  LEU    20      -2.297   9.091   7.409  1.00  0.00
ATOM     75  C   LEU    20      -3.474  10.032   7.277  1.00  0.00
ATOM     76  O   LEU    20      -3.318  11.248   7.428  1.00  0.00
ATOM     77  N   ASP    21      -4.667   9.499   7.020  1.00  0.00
ATOM     78  CA  ASP    21      -5.821  10.369   6.851  1.00  0.00
ATOM     79  C   ASP    21      -6.063  11.199   8.109  1.00  0.00
ATOM     80  O   ASP    21      -6.386  12.382   8.030  1.00  0.00
ATOM     81  N   GLY    22      -5.882  10.594   9.277  1.00  0.00
ATOM     82  CA  GLY    22      -6.181  11.305  10.521  1.00  0.00
ATOM     83  C   GLY    22      -5.109  12.339  10.872  1.00  0.00
ATOM     84  O   GLY    22      -5.340  13.222  11.705  1.00  0.00
ATOM     85  N   ALA    23      -3.962  12.246  10.201  1.00  0.00
ATOM     86  CA  ALA    23      -2.874  13.198  10.297  1.00  0.00
ATOM     87  C   ALA    23      -2.784  14.089   9.035  1.00  0.00
ATOM     88  O   ALA    23      -1.719  14.609   8.676  1.00  0.00
ATOM     89  N   ASP    24      -3.919  14.234   8.366  1.00  0.00
ATOM     90  CA  ASP    24      -4.097  15.190   7.280  1.00  0.00
ATOM     91  C   ASP    24      -3.153  14.968   6.106  1.00  0.00
ATOM     92  O   ASP    24      -2.626  15.904   5.492  1.00  0.00
ATOM     93  N   ILE    25      -3.001  13.696   5.759  1.00  0.00
ATOM     94  CA  ILE    25      -2.368  13.288   4.520  1.00  0.00
ATOM     95  C   ILE    25      -3.314  12.391   3.733  1.00  0.00
ATOM     96  O   ILE    25      -3.738  11.334   4.215  1.00  0.00
ATOM     97  N   GLY    26      -3.639  12.812   2.513  1.00  0.00
ATOM     98  CA  GLY    26      -4.444  12.011   1.602  1.00  0.00
ATOM     99  C   GLY    26      -3.723  10.728   1.234  1.00  0.00
ATOM    100  O   GLY    26      -2.502  10.706   1.166  1.00  0.00
ATOM    101  N   HIS    27      -4.476   9.663   1.005  1.00  0.00
ATOM    102  CA  HIS    27      -3.875   8.405   0.592  1.00  0.00
ATOM    103  C   HIS    27      -4.841   7.624  -0.298  1.00  0.00
ATOM    104  O   HIS    27      -6.074   7.721  -0.159  1.00  0.00
ATOM    105  N   LEU    28      -4.269   6.893  -1.254  1.00  0.00
ATOM    106  CA  LEU    28      -5.022   6.019  -2.118  1.00  0.00
ATOM    107  C   LEU    28      -4.537   4.587  -1.931  1.00  0.00
ATOM    108  O   LEU    28      -3.390   4.347  -1.576  1.00  0.00
ATOM    109  N   VAL    29      -5.432   3.637  -2.164  1.00  0.00
ATOM    110  CA  VAL    29      -5.167   2.239  -1.915  1.00  0.00
ATOM    111  C   VAL    29      -5.617   1.402  -3.098  1.00  0.00
ATOM    112  O   VAL    29      -6.640   1.705  -3.716  1.00  0.00
ATOM    141  N   ARG    46      -2.076  -5.359  -0.540  1.00  0.00
ATOM    142  CA  ARG    46      -2.495  -3.971  -0.628  1.00  0.00
ATOM    143  C   ARG    46      -1.316  -3.044  -0.866  1.00  0.00
ATOM    144  O   ARG    46      -0.239  -3.248  -0.315  1.00  0.00
ATOM    145  N   ARG    47      -1.551  -2.038  -1.701  1.00  0.00
ATOM    146  CA  ARG    47      -0.586  -0.989  -2.001  1.00  0.00
ATOM    147  C   ARG    47      -1.163   0.354  -1.576  1.00  0.00
ATOM    148  O   ARG    47      -2.314   0.661  -1.883  1.00  0.00
ATOM    149  N   VAL    48      -0.369   1.150  -0.861  1.00  0.00
ATOM    150  CA  VAL    48      -0.747   2.502  -0.478  1.00  0.00
ATOM    151  C   VAL    48       0.143   3.478  -1.220  1.00  0.00
ATOM    152  O   VAL    48       1.348   3.255  -1.337  1.00  0.00
ATOM    153  N   LEU    49      -0.469   4.539  -1.737  1.00  0.00
ATOM    154  CA  LEU    49       0.208   5.632  -2.439  1.00  0.00
ATOM    155  C   LEU    49      -0.244   6.980  -1.901  1.00  0.00
ATOM    156  O   LEU    49      -1.300   7.082  -1.282  1.00  0.00
ATOM    157  N   VAL    50       0.542   8.015  -2.163  1.00  0.00
ATOM    158  CA  VAL    50       0.182   9.384  -1.829  1.00  0.00
ATOM    159  C   VAL    50       0.474  10.291  -3.022  1.00  0.00
ATOM    160  O   VAL    50       1.186   9.912  -3.947  1.00  0.00
ATOM    161  N   HIS    51      -0.066  11.498  -2.985  1.00  0.00
ATOM    162  CA  HIS    51       0.337  12.522  -3.943  1.00  0.00
ATOM    163  C   HIS    51       1.818  12.755  -3.730  1.00  0.00
ATOM    164  O   HIS    51       2.300  12.742  -2.584  1.00  0.00
ATOM    165  N   GLU    52       2.577  12.930  -4.813  1.00  0.00
ATOM    166  CA  GLU    52       4.034  13.009  -4.680  1.00  0.00
ATOM    167  C   GLU    52       4.519  14.084  -3.722  1.00  0.00
ATOM    168  O   GLU    52       5.515  13.882  -3.030  1.00  0.00
ATOM    169  N   ASP    53       3.816  15.216  -3.661  1.00  0.00
ATOM    170  CA  ASP    53       4.214  16.335  -2.837  1.00  0.00
ATOM    171  C   ASP    53       4.113  15.999  -1.360  1.00  0.00
ATOM    172  O   ASP    53       4.761  16.640  -0.539  1.00  0.00
ATOM    173  N   ASP    54       3.315  14.986  -1.043  1.00  0.00
ATOM    174  CA  ASP    54       3.067  14.580   0.335  1.00  0.00
ATOM    175  C   ASP    54       3.992  13.456   0.814  1.00  0.00
ATOM    176  O   ASP    54       3.854  12.970   1.955  1.00  0.00
ATOM    177  N   LEU    55       4.931  13.030  -0.033  1.00  0.00
ATOM    178  CA  LEU    55       5.713  11.848   0.275  1.00  0.00
ATOM    179  C   LEU    55       6.512  11.988   1.587  1.00  0.00
ATOM    180  O   LEU    55       6.482  11.090   2.433  1.00  0.00
ATOM    181  N   ALA    56       7.196  13.100   1.766  1.00  0.00
ATOM    182  CA  ALA    56       8.027  13.264   2.975  1.00  0.00
ATOM    183  C   ALA    56       7.163  13.290   4.245  1.00  0.00
ATOM    184  O   ALA    56       7.462  12.596   5.209  1.00  0.00
ATOM    185  N   GLY    57       6.077  14.052   4.235  1.00  0.00
ATOM    186  CA  GLY    57       5.139  14.106   5.355  1.00  0.00
ATOM    187  C   GLY    57       4.604  12.724   5.687  1.00  0.00
ATOM    188  O   GLY    57       4.532  12.334   6.857  1.00  0.00
ATOM    189  N   ALA    58       4.234  11.967   4.649  1.00  0.00
ATOM    190  CA  ALA    58       3.704  10.617   4.829  1.00  0.00
ATOM    191  C   ALA    58       4.696   9.644   5.449  1.00  0.00
ATOM    192  O   ALA    58       4.362   8.934   6.403  1.00  0.00
ATOM    193  N   ARG    59       5.915   9.601   4.920  1.00  0.00
ATOM    194  CA  ARG    59       6.935   8.715   5.457  1.00  0.00
ATOM    195  C   ARG    59       7.280   9.125   6.897  1.00  0.00
ATOM    196  O   ARG    59       7.508   8.253   7.729  1.00  0.00
ATOM    197  N   ARG    60       7.277  10.413   7.176  1.00  0.00
ATOM    198  CA  ARG    60       7.529  10.917   8.534  1.00  0.00
ATOM    199  C   ARG    60       6.512  10.369   9.530  1.00  0.00
ATOM    200  O   ARG    60       6.887   9.796  10.564  1.00  0.00
ATOM    201  N   LEU    61       5.224  10.494   9.193  1.00  0.00
ATOM    202  CA  LEU    61       4.144   9.994  10.011  1.00  0.00
ATOM    203  C   LEU    61       4.244   8.475  10.199  1.00  0.00
ATOM    204  O   LEU    61       4.072   7.967  11.310  1.00  0.00
ATOM    205  N   LEU    62       4.500   7.750   9.113  1.00  0.00
ATOM    206  CA  LEU    62       4.598   6.305   9.196  1.00  0.00
ATOM    207  C   LEU    62       5.792   5.896  10.074  1.00  0.00
ATOM    208  O   LEU    62       5.626   5.031  10.957  1.00  0.00
ATOM    209  N   THR    63       6.951   6.505   9.831  1.00  0.00
ATOM    210  CA  THR    63       8.176   6.232  10.602  1.00  0.00
ATOM    211  C   THR    63       7.927   6.482  12.092  1.00  0.00
ATOM    212  O   THR    63       8.330   5.665  12.949  1.00  0.00
ATOM    213  N   ASP    64       7.262   7.594  12.392  1.00  0.00
ATOM    214  CA  ASP    64       6.967   7.989  13.779  1.00  0.00
ATOM    215  C   ASP    64       6.009   7.062  14.485  1.00  0.00
ATOM    216  O   ASP    64       5.882   7.132  15.713  1.00  0.00
ATOM    217  N   ALA    65       5.297   6.216  13.735  1.00  0.00
ATOM    218  CA  ALA    65       4.384   5.246  14.302  1.00  0.00
ATOM    219  C   ALA    65       4.825   3.803  14.105  1.00  0.00
ATOM    220  O   ALA    65       4.072   2.875  14.383  1.00  0.00
ATOM    221  N   GLY    66       6.055   3.616  13.629  1.00  0.00
ATOM    222  CA  GLY    66       6.636   2.298  13.463  1.00  0.00
ATOM    223  C   GLY    66       6.087   1.451  12.327  1.00  0.00
ATOM    224  O   GLY    66       6.116   0.235  12.408  1.00  0.00
ATOM    225  N   LEU    67       5.551   2.094  11.287  1.00  0.00
ATOM    226  CA  LEU    67       5.005   1.380  10.130  1.00  0.00
ATOM    227  C   LEU    67       5.976   1.467   8.964  1.00  0.00
ATOM    228  O   LEU    67       6.626   2.503   8.780  1.00  0.00
ATOM    229  N   ALA    68       8.955 -16.516  15.022  1.00  0.00
ATOM    230  CA  ALA    68       7.825 -17.422  15.033  1.00  0.00
ATOM    231  C   ALA    68       8.361 -18.716  15.624  1.00  0.00
ATOM    232  O   ALA    68       9.329 -19.275  15.109  1.00  0.00
ATOM    233  N   HIS    69       7.759 -19.174  16.716  1.00  0.00
ATOM    234  CA  HIS    69       8.186 -20.406  17.368  1.00  0.00
ATOM    235  C   HIS    69       8.244 -21.605  16.410  1.00  0.00
ATOM    236  O   HIS    69       9.101 -22.466  16.545  1.00  0.00
ATOM    237  N   GLU    70       7.332 -21.645  15.446  1.00  0.00
ATOM    238  CA  GLU    70       7.261 -22.743  14.468  1.00  0.00
ATOM    239  C   GLU    70       8.381 -22.721  13.431  1.00  0.00
ATOM    240  O   GLU    70       8.608 -23.713  12.741  1.00  0.00
ATOM    241  N   LEU    71       9.063 -21.587  13.312  1.00  0.00
ATOM    242  CA  LEU    71      10.277 -21.476  12.512  1.00  0.00
ATOM    243  C   LEU    71      11.539 -21.767  13.338  1.00  0.00
ATOM    244  O   LEU    71      12.451 -22.437  12.855  1.00  0.00
TER
END
