
#######################################################
#                                                     #
#                        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   53 (  212),  selected   53 , name T0349TS550_2-D1
# Molecule2: number of CA atoms   57 (  873),  selected   57 , name T0349_D1.pdb
# PARAMETERS: T0349TS550_2-D1.T0349_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    L       4      M       1           -
LGA    L       5      R       2          4.959
LGA    R       6      E       3          2.772
LGA    T       7      L       4          3.751
LGA    N       8      L       5          3.985
LGA    D       9      R       6          4.022
LGA    A      10      T       7          1.762
LGA    V      11      N       8           -
LGA    L      12      D       9           -
LGA    L      13      A      10           -
LGA    S      14      -       -           -
LGA    A      15      -       -           -
LGA    V      16      -       -           -
LGA    G      17      -       -           -
LGA    A      18      -       -           -
LGA    L      19      -       -           -
LGA    L      20      -       -           -
LGA    D      21      -       -           -
LGA    G      22      -       -           -
LGA    A      23      -       -           -
LGA    D      24      -       -           -
LGA    I      25      -       -           -
LGA    G      26      -       -           -
LGA    H      27      -       -           -
LGA    L      28      -       -           -
LGA    V      29      -       -           -
LGA    P      45      -       -           -
LGA    R      46      -       -           -
LGA    R      47      -       -           -
LGA    V      48      -       -           -
LGA    L      49      -       -           -
LGA    V      50      V      11          5.460
LGA    H      51      L      12          1.076
LGA    E      52      L      13          0.913
LGA    D      53      S      14          1.138
LGA    D      54      A      15          0.305
LGA    L      55      V      16          1.277
LGA    A      56      G      17          1.445
LGA    G      57      A      18          1.132
LGA    A      58      L      19          1.366
LGA    R      59      L      20          2.194
LGA    R      60      D      21          1.201
LGA    L      61      G      22          2.563
LGA    L      62      A      23          3.863
LGA    -       -      D      24           -
LGA    T      63      I      25          1.466
LGA    D      64      G      26          1.337
LGA    -       -      H      27           -
LGA    -       -      L      28           -
LGA    -       -      V      29           -
LGA    -       -      P      45           -
LGA    -       -      R      46           -
LGA    -       -      R      47           -
LGA    -       -      V      48           -
LGA    -       -      L      49           -
LGA    A      65      V      50          5.019
LGA    G      66      H      51          3.496
LGA    L      67      E      52          2.975
LGA    A      68      D      53          2.695
LGA    H      69      D      54          1.857
LGA    -       -      L      55           -
LGA    -       -      A      56           -
LGA    E      70      G      57          3.394
LGA    L      71      A      58          3.013
LGA    -       -      R      59           -
LGA    -       -      R      60           -
LGA    -       -      L      61           -
LGA    -       -      L      62           -
LGA    -       -      T      63           -
LGA    -       -      D      64           -
LGA    -       -      A      65           -
LGA    -       -      G      66           -
LGA    -       -      L      67           -
LGA    -       -      A      68           -
LGA    -       -      H      69           -
LGA    -       -      E      70           -
LGA    -       -      L      71           -
LGA    -       -      R      72           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   53   57    5.0     28    2.87     3.57     34.186     0.942

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.014719 * X  +   0.990560 * Y  +  -0.136284 * Z  +  11.936735
  Y_new =  -0.998017 * X  +   0.006212 * Y  +  -0.062637 * Z  +   2.985068
  Z_new =  -0.061199 * X  +   0.136936 * Y  +   0.988688 * Z  +   5.889125 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.137627   -3.003966  [ DEG:     7.8854   -172.1146 ]
  Theta =   0.061237    3.080355  [ DEG:     3.5086    176.4914 ]
  Phi   =  -1.556049    1.585544  [ DEG:   -89.1550     90.8450 ]
 
# 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: T0349TS550_2-D1                               
REMARK     2: T0349_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0349TS550_2-D1.T0349_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   53   57   5.0   28   2.87    3.57  34.186
REMARK  ---------------------------------------------------------- 
MOLECULE T0349TS550_2-D1
PFRMAT TS
TARGET T0349
MODEL 2
PARENT 1tz1_A
ATOM      1  N   LEU     4       9.349   8.512   2.889  1.00  0.00
ATOM      2  CA  LEU     4       9.175   8.437   1.444  1.00  0.00
ATOM      3  C   LEU     4       7.867   9.095   1.022  1.00  0.00
ATOM      4  O   LEU     4       7.239   9.789   1.809  1.00  0.00
ATOM      5  N   LEU     5       7.475   8.855  -0.220  1.00  0.00
ATOM      6  CA  LEU     5       6.232   9.410  -0.751  1.00  0.00
ATOM      7  C   LEU     5       5.295   8.289  -1.153  1.00  0.00
ATOM      8  O   LEU     5       5.561   7.549  -2.094  1.00  0.00
ATOM      9  N   ARG     6       5.363   6.519  -0.799  1.00  0.00
ATOM     10  CA  ARG     6       4.826   5.337  -1.471  1.00  0.00
ATOM     11  C   ARG     6       3.631   4.736  -0.742  1.00  0.00
ATOM     12  O   ARG     6       3.336   5.097   0.396  1.00  0.00
ATOM     13  N   THR     7       2.968   3.797  -1.410  1.00  0.00
ATOM     14  CA  THR     7       1.712   3.234  -0.931  1.00  0.00
ATOM     15  C   THR     7       1.901   2.111   0.087  1.00  0.00
ATOM     16  O   THR     7       2.965   1.501   0.175  1.00  0.00
ATOM     17  N   ASN     8       0.831   1.845   0.830  1.00  0.00
ATOM     18  CA  ASN     8       0.795   0.821   1.867  1.00  0.00
ATOM     19  C   ASN     8      -0.297  -0.205   1.519  1.00  0.00
ATOM     20  O   ASN     8      -1.205   0.121   0.752  1.00  0.00
ATOM     21  N   ASP     9      -0.538  -2.034   2.223  1.00  0.00
ATOM     22  CA  ASP     9       0.549  -2.395   3.139  1.00  0.00
ATOM     23  C   ASP     9       1.593  -3.237   2.420  1.00  0.00
ATOM     24  O   ASP     9       2.777  -3.200   2.758  1.00  0.00
ATOM     25  N   ALA    10       1.152  -3.973   1.403  1.00  0.00
ATOM     26  CA  ALA    10       2.054  -4.793   0.615  1.00  0.00
ATOM     27  C   ALA    10       2.979  -3.898  -0.202  1.00  0.00
ATOM     28  O   ALA    10       4.196  -3.987  -0.090  1.00  0.00
ATOM     29  N   VAL    11       2.378  -3.015  -1.007  1.00  0.00
ATOM     30  CA  VAL    11       3.143  -2.092  -1.835  1.00  0.00
ATOM     31  C   VAL    11       4.056  -1.240  -0.957  1.00  0.00
ATOM     32  O   VAL    11       5.161  -0.878  -1.368  1.00  0.00
ATOM     33  N   LEU    12       3.594  -0.951   0.252  1.00  0.00
ATOM     34  CA  LEU    12       4.377  -0.155   1.199  1.00  0.00
ATOM     35  C   LEU    12       5.643  -0.901   1.569  1.00  0.00
ATOM     36  O   LEU    12       6.755  -0.367   1.463  1.00  0.00
ATOM     37  N   LEU    13       5.478  -2.143   2.014  1.00  0.00
ATOM     38  CA  LEU    13       6.601  -2.982   2.399  1.00  0.00
ATOM     39  C   LEU    13       7.607  -3.128   1.264  1.00  0.00
ATOM     40  O   LEU    13       8.787  -3.335   1.504  1.00  0.00
ATOM     41  N   SER    14       7.132  -2.999   0.023  1.00  0.00
ATOM     42  CA  SER    14       8.008  -3.105  -1.127  1.00  0.00
ATOM     43  C   SER    14       8.978  -1.925  -1.182  1.00  0.00
ATOM     44  O   SER    14      10.175  -2.107  -1.362  1.00  0.00
ATOM     45  N   ALA    15       8.440  -0.722  -0.998  1.00  0.00
ATOM     46  CA  ALA    15       9.260   0.482  -1.000  1.00  0.00
ATOM     47  C   ALA    15      10.357   0.374   0.054  1.00  0.00
ATOM     48  O   ALA    15      11.539   0.520  -0.249  1.00  0.00
ATOM     49  N   VAL    16       9.947   0.082   1.284  1.00  0.00
ATOM     50  CA  VAL    16      10.886  -0.072   2.385  1.00  0.00
ATOM     51  C   VAL    16      11.884  -1.181   2.078  1.00  0.00
ATOM     52  O   VAL    16      13.089  -0.979   2.186  1.00  0.00
ATOM     53  N   GLY    17      11.369  -2.337   1.691  1.00  0.00
ATOM     54  CA  GLY    17      12.198  -3.487   1.368  1.00  0.00
ATOM     55  C   GLY    17      13.206  -3.155   0.274  1.00  0.00
ATOM     56  O   GLY    17      14.270  -3.756   0.200  1.00  0.00
ATOM     57  N   ALA    18      12.861  -2.177  -0.561  1.00  0.00
ATOM     58  CA  ALA    18      13.745  -1.767  -1.647  1.00  0.00
ATOM     59  C   ALA    18      14.838  -0.831  -1.124  1.00  0.00
ATOM     60  O   ALA    18      15.900  -0.708  -1.728  1.00  0.00
ATOM     61  N   LEU    19      14.557  -0.182   0.001  1.00  0.00
ATOM     62  CA  LEU    19      15.508   0.737   0.605  1.00  0.00
ATOM     63  C   LEU    19      16.238   0.094   1.778  1.00  0.00
ATOM     64  O   LEU    19      17.097   0.710   2.400  1.00  0.00
ATOM     65  N   LEU    20      15.882  -1.152   2.075  1.00  0.00
ATOM     66  CA  LEU    20      16.500  -1.882   3.186  1.00  0.00
ATOM     67  C   LEU    20      17.253  -3.113   2.686  1.00  0.00
ATOM     68  O   LEU    20      18.243  -3.536   3.291  1.00  0.00
ATOM     69  N   ASP    21      18.710  -3.606   2.075  1.00  0.00
ATOM     70  CA  ASP    21      19.294  -4.923   2.044  1.00  0.00
ATOM     71  C   ASP    21      19.241  -5.551   3.429  1.00  0.00
ATOM     72  O   ASP    21      19.473  -4.889   4.414  1.00  0.00
ATOM     73  N   GLY    22      18.935  -6.835   3.462  1.00  0.00
ATOM     74  CA  GLY    22      19.111  -7.647   4.642  1.00  0.00
ATOM     75  C   GLY    22      20.622  -8.024   4.761  1.00  0.00
ATOM     76  O   GLY    22      21.437  -7.641   3.884  1.00  0.00
ATOM     77  N   ALA    23      20.984  -8.623   5.887  1.00  0.00
ATOM     78  CA  ALA    23      22.376  -8.895   6.240  1.00  0.00
ATOM     79  C   ALA    23      23.097  -9.793   5.260  1.00  0.00
ATOM     80  O   ALA    23      24.261  -9.578   4.966  1.00  0.00
ATOM     81  N   ASP    24      22.421 -10.795   4.722  1.00  0.00
ATOM     82  CA  ASP    24      22.997 -11.592   3.635  1.00  0.00
ATOM     83  C   ASP    24      23.616 -10.780   2.482  1.00  0.00
ATOM     84  O   ASP    24      24.683 -11.140   1.978  1.00  0.00
ATOM     85  N   ILE    25      22.980  -9.680   2.094  1.00  0.00
ATOM     86  CA  ILE    25      23.460  -8.839   1.017  1.00  0.00
ATOM     87  C   ILE    25      24.189  -7.574   1.492  1.00  0.00
ATOM     88  O   ILE    25      24.225  -6.563   0.793  1.00  0.00
ATOM     89  N   GLY    26      24.705  -7.639   2.721  1.00  0.00
ATOM     90  CA  GLY    26      25.518  -6.614   3.294  1.00  0.00
ATOM     91  C   GLY    26      24.804  -5.505   4.024  1.00  0.00
ATOM     92  O   GLY    26      25.451  -4.518   4.290  1.00  0.00
ATOM     93  N   HIS    27      23.495  -5.631   4.324  1.00  0.00
ATOM     94  CA  HIS    27      22.751  -4.575   5.014  1.00  0.00
ATOM     95  C   HIS    27      22.527  -5.007   6.462  1.00  0.00
ATOM     96  O   HIS    27      23.449  -5.501   7.105  1.00  0.00
ATOM     97  N   LEU    28      21.288  -4.894   6.953  1.00  0.00
ATOM     98  CA  LEU    28      20.937  -5.418   8.274  1.00  0.00
ATOM     99  C   LEU    28      19.645  -6.216   8.311  1.00  0.00
ATOM    100  O   LEU    28      18.698  -5.995   7.520  1.00  0.00
ATOM    101  N   VAL    29      19.601  -7.148   9.263  1.00  0.00
ATOM    102  CA  VAL    29      18.428  -7.958   9.428  1.00  0.00
ATOM    103  C   VAL    29      17.398  -7.161  10.161  1.00  0.00
ATOM    104  O   VAL    29      17.631  -6.015  10.599  1.00  0.00
ATOM    165  N   PRO    45       4.808  10.716  18.389  1.00  0.00
ATOM    166  CA  PRO    45       5.471   9.502  18.854  1.00  0.00
ATOM    167  C   PRO    45       5.493   8.455  17.740  1.00  0.00
ATOM    168  O   PRO    45       4.614   8.431  16.880  1.00  0.00
ATOM    169  N   ARG    46       6.393   7.801  17.365  1.00  0.00
ATOM    170  CA  ARG    46       6.232   6.607  16.539  1.00  0.00
ATOM    171  C   ARG    46       5.317   5.599  17.219  1.00  0.00
ATOM    172  O   ARG    46       5.319   5.474  18.445  1.00  0.00
ATOM    173  N   ARG    47       4.522   4.885  16.427  1.00  0.00
ATOM    174  CA  ARG    47       3.608   3.888  16.946  1.00  0.00
ATOM    175  C   ARG    47       3.758   2.562  16.215  1.00  0.00
ATOM    176  O   ARG    47       4.582   2.440  15.299  1.00  0.00
ATOM    177  N   VAL    48       2.973   1.584  16.611  1.00  0.00
ATOM    178  CA  VAL    48       3.035   0.260  16.000  1.00  0.00
ATOM    179  C   VAL    48       1.927   0.077  14.966  1.00  0.00
ATOM    180  O   VAL    48       0.751   0.039  15.297  1.00  0.00
ATOM    181  N   LEU    49       2.677  -0.509  13.900  1.00  0.00
ATOM    182  CA  LEU    49       2.147  -0.393  12.547  1.00  0.00
ATOM    183  C   LEU    49       1.010  -1.397  12.421  1.00  0.00
ATOM    184  O   LEU    49       0.831  -2.241  13.298  1.00  0.00
ATOM    185  N   VAL    50       0.236  -1.304  11.345  1.00  0.00
ATOM    186  CA  VAL    50      -0.884  -2.217  11.154  1.00  0.00
ATOM    187  C   VAL    50      -0.966  -2.763   9.737  1.00  0.00
ATOM    188  O   VAL    50      -0.469  -2.150   8.786  1.00  0.00
ATOM    189  N   HIS    51      -1.585  -3.933   9.605  1.00  0.00
ATOM    190  CA  HIS    51      -1.752  -4.562   8.301  1.00  0.00
ATOM    191  C   HIS    51      -2.911  -3.863   7.616  1.00  0.00
ATOM    192  O   HIS    51      -4.011  -3.795   8.167  1.00  0.00
ATOM    193  N   GLU    52      -2.706  -3.345   6.575  1.00  0.00
ATOM    194  CA  GLU    52      -3.537  -2.541   5.682  1.00  0.00
ATOM    195  C   GLU    52      -4.491  -1.672   6.485  1.00  0.00
ATOM    196  O   GLU    52      -4.899  -0.599   6.032  1.00  0.00
ATOM    197  N   ASP    53      -4.855  -2.132   7.680  1.00  0.00
ATOM    198  CA  ASP    53      -5.757  -1.387   8.544  1.00  0.00
ATOM    199  C   ASP    53      -5.147  -0.061   8.965  1.00  0.00
ATOM    200  O   ASP    53      -5.602   1.000   8.555  1.00  0.00
ATOM    201  N   ASP    54      -4.098  -0.135   9.782  1.00  0.00
ATOM    202  CA  ASP    54      -3.414   1.068  10.256  1.00  0.00
ATOM    203  C   ASP    54      -2.774   1.810   9.097  1.00  0.00
ATOM    204  O   ASP    54      -2.348   2.949   9.248  1.00  0.00
ATOM    205  N   LEU    55      -2.731   1.170   7.940  1.00  0.00
ATOM    206  CA  LEU    55      -2.147   1.792   6.755  1.00  0.00
ATOM    207  C   LEU    55      -3.179   2.691   6.073  1.00  0.00
ATOM    208  O   LEU    55      -2.855   3.794   5.651  1.00  0.00
ATOM    209  N   ALA    56      -4.409   2.216   6.005  1.00  0.00
ATOM    210  CA  ALA    56      -5.490   2.969   5.398  1.00  0.00
ATOM    211  C   ALA    56      -5.908   4.108   6.322  1.00  0.00
ATOM    212  O   ALA    56      -6.388   5.150   5.877  1.00  0.00
ATOM    213  N   GLY    57      -5.703   3.901   7.622  1.00  0.00
ATOM    214  CA  GLY    57      -6.039   4.907   8.621  1.00  0.00
ATOM    215  C   GLY    57      -4.960   5.973   8.655  1.00  0.00
ATOM    216  O   GLY    57      -5.247   7.167   8.559  1.00  0.00
ATOM    217  N   ALA    58      -3.703   5.533   8.780  1.00  0.00
ATOM    218  CA  ALA    58      -2.582   6.459   8.811  1.00  0.00
ATOM    219  C   ALA    58      -2.553   7.299   7.543  1.00  0.00
ATOM    220  O   ALA    58      -2.108   8.447   7.556  1.00  0.00
ATOM    221  N   ARG    59      -3.034   6.718   6.449  1.00  0.00
ATOM    222  CA  ARG    59      -3.083   7.407   5.161  1.00  0.00
ATOM    223  C   ARG    59      -4.067   8.562   5.220  1.00  0.00
ATOM    224  O   ARG    59      -3.739   9.692   4.841  1.00  0.00
ATOM    225  N   ARG    60      -5.273   8.284   5.703  1.00  0.00
ATOM    226  CA  ARG    60      -6.305   9.313   5.819  1.00  0.00
ATOM    227  C   ARG    60      -5.844  10.426   6.742  1.00  0.00
ATOM    228  O   ARG    60      -6.311  11.568   6.638  1.00  0.00
ATOM    229  N   LEU    61      -4.927  10.093   7.646  1.00  0.00
ATOM    230  CA  LEU    61      -4.388  11.065   8.591  1.00  0.00
ATOM    231  C   LEU    61      -3.397  11.995   7.886  1.00  0.00
ATOM    232  O   LEU    61      -3.299  13.179   8.218  1.00  0.00
ATOM    233  N   LEU    62      -2.674  11.454   6.910  1.00  0.00
ATOM    234  CA  LEU    62      -1.697  12.226   6.163  1.00  0.00
ATOM    235  C   LEU    62      -2.395  13.243   5.251  1.00  0.00
ATOM    236  O   LEU    62      -2.014  14.414   5.216  1.00  0.00
ATOM    237  N   THR    63      -1.828  13.169   4.202  1.00  0.00
ATOM    238  CA  THR    63      -2.091  14.039   3.065  1.00  0.00
ATOM    239  C   THR    63      -1.982  13.329   1.724  1.00  0.00
ATOM    240  O   THR    63      -1.045  13.546   0.954  1.00  0.00
ATOM    241  N   ASP    64      -2.956  12.453   1.426  1.00  0.00
ATOM    242  CA  ASP    64      -2.924  11.735   0.152  1.00  0.00
ATOM    243  C   ASP    64      -3.002  12.683  -1.041  1.00  0.00
ATOM    244  O   ASP    64      -3.626  13.745  -0.970  1.00  0.00
ATOM    245  N   ALA    65      -2.333  12.281  -2.119  1.00  0.00
ATOM    246  CA  ALA    65      -2.258  13.027  -3.369  1.00  0.00
ATOM    247  C   ALA    65      -1.530  14.362  -3.249  1.00  0.00
ATOM    248  O   ALA    65      -1.278  15.030  -4.250  1.00  0.00
ATOM    249  N   GLY    66      -1.186  14.749  -2.025  1.00  0.00
ATOM    250  CA  GLY    66      -0.495  16.011  -1.804  1.00  0.00
ATOM    251  C   GLY    66       0.964  15.921  -2.229  1.00  0.00
ATOM    252  O   GLY    66       1.592  14.868  -2.140  1.00  0.00
ATOM    253  N   LEU    67       1.499  17.045  -2.689  1.00  0.00
ATOM    254  CA  LEU    67       2.878  17.082  -3.145  1.00  0.00
ATOM    255  C   LEU    67       3.915  16.886  -2.056  1.00  0.00
ATOM    256  O   LEU    67       5.042  16.495  -2.339  1.00  0.00
ATOM    257  N   ALA    68       3.543  17.154  -0.810  1.00  0.00
ATOM    258  CA  ALA    68       4.479  17.012   0.300  1.00  0.00
ATOM    259  C   ALA    68       4.272  15.733   1.112  1.00  0.00
ATOM    260  O   ALA    68       4.878  15.560   2.172  1.00  0.00
ATOM    261  N   HIS    69       3.425  14.834   0.625  1.00  0.00
ATOM    262  CA  HIS    69       3.154  13.595   1.349  1.00  0.00
ATOM    263  C   HIS    69       4.414  12.764   1.550  1.00  0.00
ATOM    264  O   HIS    69       5.286  12.712   0.676  1.00  0.00
ATOM    265  N   GLU    70       4.115  12.095   2.829  1.00  0.00
ATOM    266  CA  GLU    70       5.294  11.356   3.248  1.00  0.00
ATOM    267  C   GLU    70       5.029  10.591   4.539  1.00  0.00
ATOM    268  O   GLU    70       4.291  11.048   5.407  1.00  0.00
ATOM    269  N   LEU    71       5.637   9.411   4.649  1.00  0.00
ATOM    270  CA  LEU    71       5.471   8.565   5.817  1.00  0.00
ATOM    271  C   LEU    71       6.832   8.227   6.428  1.00  0.00
ATOM    272  O   LEU    71       7.750   7.823   5.720  1.00  0.00
TER
END
