
#######################################################
#                                                     #
#                        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 T0349TS307_5u-D1
# Molecule2: number of CA atoms   57 (  873),  selected   57 , name T0349_D1.pdb
# PARAMETERS: T0349TS307_5u-D1.T0349_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      M       1          4.620
LGA    R       2      R       2          2.434
LGA    E       3      E       3          1.913
LGA    L       4      L       4          1.379
LGA    L       5      L       5          1.662
LGA    R       6      R       6          4.695
LGA    T       7      T       7          3.940
LGA    N       8      N       8           #
LGA    D       9      D       9          2.556
LGA    A      10      A      10          3.834
LGA    V      11      V      11          1.154
LGA    L      12      L      12          1.178
LGA    L      13      L      13          0.742
LGA    S      14      S      14          0.450
LGA    A      15      A      15          0.680
LGA    V      16      V      16          0.542
LGA    G      17      G      17          0.234
LGA    A      18      A      18          0.399
LGA    L      19      L      19          0.658
LGA    L      20      L      20          0.338
LGA    D      21      D      21          0.898
LGA    G      22      G      22          1.585
LGA    A      23      A      23          1.451
LGA    D      24      D      24          0.796
LGA    I      25      I      25          0.441
LGA    G      26      G      26          1.548
LGA    H      27      H      27          1.951
LGA    L      28      L      28          4.254
LGA    V      29      V      29           #
LGA    -       -      P      45           -
LGA    -       -      R      46           -
LGA    R      47      R      47          2.527
LGA    V      48      V      48          2.927
LGA    L      49      L      49          2.972
LGA    V      50      V      50          1.438
LGA    D      53      H      51          2.437
LGA    -       -      E      52           -
LGA    -       -      D      53           -
LGA    D      54      D      54          1.601
LGA    L      55      L      55          1.302
LGA    A      56      A      56          0.775
LGA    G      57      G      57          0.523
LGA    A      58      A      58          0.633
LGA    R      59      R      59          0.463
LGA    R      60      R      60          0.760
LGA    L      61      L      61          0.682
LGA    L      62      L      62          0.737
LGA    T      63      T      63          0.929
LGA    D      64      D      64          1.739
LGA    A      65      A      65          3.422
LGA    -       -      G      66           -
LGA    G      66      L      67          1.287
LGA    L      67      A      68          2.810
LGA    A      68      H      69          1.849
LGA    -       -      E      70           -
LGA    H      69      L      71          1.077
LGA    E      70      R      72          1.818
LGA    L      71      -       -           -
LGA    R      72      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   53   57    5.0     49    2.03    87.76     72.726     2.300

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.897982 * X  +  -0.409360 * Y  +   0.161409 * Z  +   7.467681
  Y_new =  -0.391020 * X  +  -0.910579 * Y  +  -0.133977 * Z  +  36.547749
  Z_new =   0.201820 * X  +   0.057195 * Y  +  -0.977751 * Z  +   8.352027 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   3.083163   -0.058429  [ DEG:   176.6522     -3.3478 ]
  Theta =  -0.203216   -2.938377  [ DEG:   -11.6434   -168.3566 ]
  Phi   =  -0.410683    2.730910  [ DEG:   -23.5304    156.4696 ]
 
# 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: T0349TS307_5u-D1                              
REMARK     2: T0349_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0349TS307_5u-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   49   2.03   87.76  72.726
REMARK  ---------------------------------------------------------- 
MOLECULE T0349TS307_5u-D1
PFRMAT   TS
TARGET   T0349
MODEL    5  UNREFINED
PARENT   2f06_A
ATOM     1   N   MET     1       7.343  11.109 -10.062  1.00                    
ATOM     1   CA  MET     1       6.622  11.103  -8.823  1.00                    
ATOM     1   C   MET     1       7.136  10.047  -7.844  1.00                    
ATOM     1   O   MET     1       7.713   9.044  -8.210  1.00                    
ATOM     1   N   ARG     2       6.897  10.305  -6.569  1.00                    
ATOM     1   CA  ARG     2       7.232   9.381  -5.515  1.00                    
ATOM     1   C   ARG     2       6.004   8.511  -5.248  1.00                    
ATOM     1   O   ARG     2       4.895   9.009  -4.975  1.00                    
ATOM     1   N   GLU     3       6.201   7.204  -5.395  1.00                    
ATOM     1   CA  GLU     3       5.217   6.252  -4.978  1.00                    
ATOM     1   C   GLU     3       5.649   5.596  -3.670  1.00                    
ATOM     1   O   GLU     3       6.791   5.173  -3.512  1.00                    
ATOM     1   N   LEU     4       4.752   5.498  -2.717  1.00                    
ATOM     1   CA  LEU     4       5.063   4.713  -1.523  1.00                    
ATOM     1   C   LEU     4       4.770   3.234  -1.770  1.00                    
ATOM     1   O   LEU     4       3.720   2.850  -2.307  1.00                    
ATOM     1   N   LEU     5       4.433   0.073   0.717  1.00                    
ATOM     1   CA  LEU     5       4.294  -0.224   2.093  1.00                    
ATOM     1   C   LEU     5       4.031  -1.732   2.343  1.00                    
ATOM     1   O   LEU     5       3.034  -2.307   1.814  1.00                    
ATOM     1   N   ARG     6       4.907  -2.335   3.161  1.00                    
ATOM     1   CA  ARG     6       4.857  -3.772   3.485  1.00                    
ATOM     1   C   ARG     6       3.768  -3.999   4.541  1.00                    
ATOM     1   O   ARG     6       3.828  -3.438   5.616  1.00                    
ATOM     1   N   THR     7       2.715  -4.731   4.168  1.00                    
ATOM     1   CA  THR     7       1.555  -4.949   5.049  1.00                    
ATOM     1   C   THR     7       1.763  -6.382   5.502  1.00                    
ATOM     1   O   THR     7       1.609  -7.344   4.699  1.00                    
ATOM     1   N   ASN     8       0.891  -9.714   8.248  1.00                    
ATOM     1   CA  ASN     8      -0.419 -10.186   8.825  1.00                    
ATOM     1   C   ASN     8      -1.475 -10.372   7.651  1.00                    
ATOM     1   O   ASN     8      -1.177 -11.133   6.730  1.00                    
ATOM     1   N   ASP     9      -2.648  -9.708   7.651  1.00                    
ATOM     1   CA  ASP     9      -3.618  -9.647   6.467  1.00                    
ATOM     1   C   ASP     9      -4.957  -8.919   6.786  1.00                    
ATOM     1   O   ASP     9      -5.836  -8.865   5.914  1.00                    
ATOM     1   N   ALA    10      -5.080  -8.321   7.990  1.00                    
ATOM     1   CA  ALA    10      -6.309  -8.525   8.818  1.00                    
ATOM     1   C   ALA    10      -7.029  -7.471   9.741  1.00                    
ATOM     1   O   ALA    10      -7.924  -7.907  10.479  1.00                    
ATOM     1   N   VAL    11      -6.614  -6.210   9.903  1.00                    
ATOM     1   CA  VAL    11      -5.267  -5.867  10.229  1.00                    
ATOM     1   C   VAL    11      -4.687  -4.517   9.889  1.00                    
ATOM     1   O   VAL    11      -5.222  -3.439  10.199  1.00                    
ATOM     1   N   LEU    12      -3.539  -4.655   9.268  1.00                    
ATOM     1   CA  LEU    12      -2.548  -3.639   9.112  1.00                    
ATOM     1   C   LEU    12      -2.905  -2.663   8.049  1.00                    
ATOM     1   O   LEU    12      -2.468  -1.529   8.127  1.00                    
ATOM     1   N   LEU    13      -3.691  -3.088   7.056  1.00                    
ATOM     1   CA  LEU    13      -4.075  -2.140   6.002  1.00                    
ATOM     1   C   LEU    13      -4.965  -0.994   6.593  1.00                    
ATOM     1   O   LEU    13      -4.836   0.192   6.209  1.00                    
ATOM     1   N   SER    14      -5.840  -1.364   7.518  1.00                    
ATOM     1   CA  SER    14      -6.686  -0.367   8.150  1.00                    
ATOM     1   C   SER    14      -5.863   0.635   8.975  1.00                    
ATOM     1   O   SER    14      -5.994   1.860   8.786  1.00                    
ATOM     1   N   ALA    15      -4.984   0.118   9.818  1.00                    
ATOM     1   CA  ALA    15      -4.021   0.971  10.513  1.00                    
ATOM     1   C   ALA    15      -3.219   1.875   9.597  1.00                    
ATOM     1   O   ALA    15      -3.007   2.996   9.974  1.00                    
ATOM     1   N   VAL    16      -2.768   1.415   8.413  1.00                    
ATOM     1   CA  VAL    16      -1.992   2.275   7.502  1.00                    
ATOM     1   C   VAL    16      -2.863   3.403   7.009  1.00                    
ATOM     1   O   VAL    16      -2.439   4.576   6.863  1.00                    
ATOM     1   N   GLY    17      -4.085   3.076   6.672  1.00                    
ATOM     1   CA  GLY    17      -4.961   4.151   6.161  1.00                    
ATOM     1   C   GLY    17      -5.346   5.109   7.285  1.00                    
ATOM     1   O   GLY    17      -5.585   6.301   7.022  1.00                    
ATOM     1   N   ALA    18      -5.403   4.581   8.492  1.00                    
ATOM     1   CA  ALA    18      -5.560   5.417   9.712  1.00                    
ATOM     1   C   ALA    18      -4.383   6.374  10.032  1.00                    
ATOM     1   O   ALA    18      -4.611   7.536  10.331  1.00                    
ATOM     1   N   LEU    19      -3.152   5.888  10.063  1.00                    
ATOM     1   CA  LEU    19      -1.942   6.760  10.001  1.00                    
ATOM     1   C   LEU    19      -2.016   7.903   8.987  1.00                    
ATOM     1   O   LEU    19      -1.790   9.059   9.340  1.00                    
ATOM     1   N   LEU    20      -2.334   7.595   7.744  1.00                    
ATOM     1   CA  LEU    20      -2.438   8.616   6.723  1.00                    
ATOM     1   C   LEU    20      -3.595   9.586   6.927  1.00                    
ATOM     1   O   LEU    20      -3.391  10.782   6.729  1.00                    
ATOM     1   N   ASP    21      -4.783   9.091   7.325  1.00                    
ATOM     1   CA  ASP    21      -5.927   9.940   7.661  1.00                    
ATOM     1   C   ASP    21      -5.604  10.947   8.759  1.00                    
ATOM     1   O   ASP    21      -6.081  12.103   8.733  1.00                    
ATOM     1   N   GLY    22      -4.872  10.487   9.774  1.00                    
ATOM     1   CA  GLY    22      -4.583  11.329  10.941  1.00                    
ATOM     1   C   GLY    22      -3.702  12.543  10.537  1.00                    
ATOM     1   O   GLY    22      -3.754  13.615  11.185  1.00                    
ATOM     1   N   ALA    23      -2.907  12.371   9.469  1.00                    
ATOM     1   CA  ALA    23      -2.057  13.435   9.004  1.00                    
ATOM     1   C   ALA    23      -2.743  14.361   7.970  1.00                    
ATOM     1   O   ALA    23      -2.097  15.330   7.466  1.00                    
ATOM     1   N   ASP    24      -4.024  14.082   7.673  1.00                    
ATOM     1   CA  ASP    24      -4.808  14.726   6.599  1.00                    
ATOM     1   C   ASP    24      -4.067  14.543   5.276  1.00                    
ATOM     1   O   ASP    24      -3.930  15.484   4.488  1.00                    
ATOM     1   N   ILE    25      -3.569  13.313   5.060  1.00                    
ATOM     1   CA  ILE    25      -2.921  12.938   3.833  1.00                    
ATOM     1   C   ILE    25      -3.954  12.219   3.023  1.00                    
ATOM     1   O   ILE    25      -4.544  11.225   3.465  1.00                    
ATOM     1   N   GLY    26      -4.218  12.772   1.839  1.00                    
ATOM     1   CA  GLY    26      -5.131  12.157   0.865  1.00                    
ATOM     1   C   GLY    26      -4.427  11.104  -0.003  1.00                    
ATOM     1   O   GLY    26      -3.301  11.305  -0.535  1.00                    
ATOM     1   N   HIS    27      -5.146  10.019  -0.232  1.00                    
ATOM     1   CA  HIS    27      -4.735   8.991  -1.171  1.00                    
ATOM     1   C   HIS    27      -5.285   9.330  -2.561  1.00                    
ATOM     1   O   HIS    27      -6.459   9.540  -2.713  1.00                    
ATOM     1   N   LEU    28      -4.438   9.368  -3.577  1.00                    
ATOM     1   CA  LEU    28      -4.845   9.646  -4.971  1.00                    
ATOM     1   C   LEU    28      -5.116   8.412  -5.779  1.00                    
ATOM     1   O   LEU    28      -5.972   8.394  -6.646  1.00                    
ATOM     1   N   VAL    29      -4.306   7.411  -5.507  1.00                    
ATOM     1   CA  VAL    29      -4.227   6.189  -6.309  1.00                    
ATOM     1   C   VAL    29      -3.508   5.162  -5.470  1.00                    
ATOM     1   O   VAL    29      -2.449   5.442  -4.860  1.00                    
ATOM     1   N   ARG    47       1.002  -0.227  -2.824  1.00                    
ATOM     1   CA  ARG    47       1.568   0.806  -3.653  1.00                    
ATOM     1   C   ARG    47       0.625   1.996  -3.688  1.00                    
ATOM     1   O   ARG    47      -0.578   1.830  -3.912  1.00                    
ATOM     1   N   VAL    48       1.162   3.186  -3.493  1.00                    
ATOM     1   CA  VAL    48       0.336   4.284  -3.083  1.00                    
ATOM     1   C   VAL    48       0.848   5.590  -3.657  1.00                    
ATOM     1   O   VAL    48       2.020   5.913  -3.522  1.00                    
ATOM     1   N   LEU    49      -0.057   6.319  -4.294  1.00                    
ATOM     1   CA  LEU    49       0.140   7.750  -4.601  1.00                    
ATOM     1   C   LEU    49      -0.612   8.600  -3.568  1.00                    
ATOM     1   O   LEU    49      -1.829   8.486  -3.451  1.00                    
ATOM     1   N   VAL    50       0.114   9.413  -2.786  1.00                    
ATOM     1   CA  VAL    50      -0.517  10.235  -1.756  1.00                    
ATOM     1   C   VAL    50      -0.296  11.763  -2.010  1.00                    
ATOM     1   O   VAL    50       0.514  12.128  -2.882  1.00                    
ATOM     1   N   ASP    53      -0.978  12.614  -1.230  1.00                    
ATOM     1   CA  ASP    53      -0.907  14.093  -1.418  1.00                    
ATOM     1   C   ASP    53       0.411  14.756  -0.961  1.00                    
ATOM     1   O   ASP    53       0.791  15.826  -1.469  1.00                    
ATOM     1   N   ASP    54       1.094  14.113  -0.011  1.00                    
ATOM     1   CA  ASP    54       2.374  14.575   0.511  1.00                    
ATOM     1   C   ASP    54       3.263  13.348   0.823  1.00                    
ATOM     1   O   ASP    54       3.239  12.831   1.951  1.00                    
ATOM     1   N   LEU    55       4.013  12.844  -0.186  1.00                    
ATOM     1   CA  LEU    55       4.764  11.591   0.068  1.00                    
ATOM     1   C   LEU    55       5.831  11.639   1.187  1.00                    
ATOM     1   O   LEU    55       5.976  10.661   1.911  1.00                    
ATOM     1   N   ALA    56       6.496  12.772   1.374  1.00                    
ATOM     1   CA  ALA    56       7.542  12.903   2.399  1.00                    
ATOM     1   C   ALA    56       6.958  12.889   3.826  1.00                    
ATOM     1   O   ALA    56       7.501  12.221   4.714  1.00                    
ATOM     1   N   GLY    57       5.862  13.617   4.014  1.00                    
ATOM     1   CA  GLY    57       5.156  13.633   5.307  1.00                    
ATOM     1   C   GLY    57       4.594  12.227   5.589  1.00                    
ATOM     1   O   GLY    57       4.697  11.736   6.718  1.00                    
ATOM     1   N   ALA    58       4.000  11.602   4.565  1.00                    
ATOM     1   CA  ALA    58       3.471  10.246   4.669  1.00                    
ATOM     1   C   ALA    58       4.522   9.224   5.017  1.00                    
ATOM     1   O   ALA    58       4.319   8.425   5.969  1.00                    
ATOM     1   N   ARG    59       5.629   9.252   4.287  1.00                    
ATOM     1   CA  ARG    59       6.767   8.395   4.620  1.00                    
ATOM     1   C   ARG    59       7.251   8.513   6.078  1.00                    
ATOM     1   O   ARG    59       7.502   7.515   6.754  1.00                    
ATOM     1   N   ARG    60       7.415   9.725   6.574  1.00                    
ATOM     1   CA  ARG    60       7.949   9.851   7.938  1.00                    
ATOM     1   C   ARG    60       6.929   9.392   9.012  1.00                    
ATOM     1   O   ARG    60       7.326   8.790  10.021  1.00                    
ATOM     1   N   LEU    61       5.639   9.674   8.788  1.00                    
ATOM     1   CA  LEU    61       4.554   9.191   9.645  1.00                    
ATOM     1   C   LEU    61       4.510   7.633   9.729  1.00                    
ATOM     1   O   LEU    61       4.448   7.013  10.831  1.00                    
ATOM     1   N   LEU    62       4.585   7.005   8.570  1.00                    
ATOM     1   CA  LEU    62       4.662   5.569   8.491  1.00                    
ATOM     1   C   LEU    62       5.882   4.971   9.192  1.00                    
ATOM     1   O   LEU    62       5.699   4.040   9.965  1.00                    
ATOM     1   N   THR    63       7.100   5.476   8.938  1.00                    
ATOM     1   CA  THR    63       8.319   5.039   9.686  1.00                    
ATOM     1   C   THR    63       8.184   5.211  11.203  1.00                    
ATOM     1   O   THR    63       8.650   4.370  11.986  1.00                    
ATOM     1   N   ASP    64       7.594   6.340  11.607  1.00                    
ATOM     1   CA  ASP    64       7.316   6.664  13.004  1.00                    
ATOM     1   C   ASP    64       6.381   5.634  13.642  1.00                    
ATOM     1   O   ASP    64       6.492   5.368  14.845  1.00                    
ATOM     1   N   ALA    65       5.411   5.146  12.866  1.00                    
ATOM     1   CA  ALA    65       4.490   4.102  13.298  1.00                    
ATOM     1   C   ALA    65       4.979   2.678  13.011  1.00                    
ATOM     1   O   ALA    65       4.194   1.726  13.106  1.00                    
ATOM     1   N   GLY    66       6.262   2.560  12.632  1.00                    
ATOM     1   CA  GLY    66       7.002   1.291  12.538  1.00                    
ATOM     1   C   GLY    66       6.592   0.469  11.329  1.00                    
ATOM     1   O   GLY    66       6.785  -0.764  11.332  1.00                    
ATOM     1   N   LEU    67       6.089   1.140  10.277  1.00                    
ATOM     1   CA  LEU    67       5.870   0.482   8.993  1.00                    
ATOM     1   C   LEU    67       7.153   0.425   8.197  1.00                    
ATOM     1   O   LEU    67       8.000   1.303   8.340  1.00                    
ATOM     1   N   ALA    68       7.307  -0.636   7.388  1.00                    
ATOM     1   CA  ALA    68       8.353  -0.701   6.405  1.00                    
ATOM     1   C   ALA    68       7.827  -0.055   5.096  1.00                    
ATOM     1   O   ALA    68       6.891  -0.543   4.503  1.00                    
ATOM     1   N   HIS    69       8.430   1.053   4.662  1.00                    
ATOM     1   CA  HIS    69       8.015   1.820   3.473  1.00                    
ATOM     1   C   HIS    69       9.213   2.153   2.642  1.00                    
ATOM     1   O   HIS    69      10.253   2.555   3.153  1.00                    
ATOM     1   N   GLU    70       9.043   2.105   1.342  1.00                    
ATOM     1   CA  GLU    70      10.110   2.452   0.407  1.00                    
ATOM     1   C   GLU    70       9.472   3.412  -0.556  1.00                    
ATOM     1   O   GLU    70       8.258   3.359  -0.723  1.00                    
ATOM     1   N   LEU    71      10.260   4.289  -1.180  1.00                    
ATOM     1   CA  LEU    71       9.752   5.188  -2.234  1.00                    
ATOM     1   C   LEU    71      10.298   4.696  -3.565  1.00                    
ATOM     1   O   LEU    71      11.422   4.216  -3.620  1.00                    
ATOM     1   N   ARG    72       9.447   4.695  -4.590  1.00                    
ATOM     1   CA  ARG    72       9.818   4.315  -5.973  1.00                    
ATOM     1   C   ARG    72       9.435   5.471  -6.879  1.00                    
ATOM     1   O   ARG    72       8.444   6.138  -6.601  1.00                    
TER
END
