
#######################################################
#                                                     #
#                        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   48 (  192),  selected   48 , name T0349AL381_2-D1
# Molecule2: number of CA atoms   57 (  873),  selected   57 , name T0349_D1.pdb
# PARAMETERS: T0349AL381_2-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           -
LGA    -       -      E       3           -
LGA    -       -      L       4           -
LGA    -       -      L       5           -
LGA    R       6      R       6          0.766
LGA    T       7      T       7          2.475
LGA    N       8      N       8          3.606
LGA    D       9      D       9          0.420
LGA    A      10      A      10          2.172
LGA    V      11      V      11          2.880
LGA    L      12      L      12          1.301
LGA    L      13      L      13          1.520
LGA    S      14      S      14          2.713
LGA    A      15      A      15          1.309
LGA    V      16      V      16          1.240
LGA    G      17      G      17          2.278
LGA    A      18      A      18          1.494
LGA    L      19      L      19          2.326
LGA    -       -      L      20           -
LGA    L      20      D      21          1.199
LGA    D      21      G      22          3.103
LGA    G      22      A      23          3.104
LGA    A      23      D      24          1.975
LGA    D      24      I      25          2.631
LGA    I      25      -       -           -
LGA    G      26      G      26          0.911
LGA    H      27      H      27          2.347
LGA    L      28      L      28          4.180
LGA    V      29      V      29           #
LGA    -       -      P      45           -
LGA    -       -      R      46           -
LGA    P      45      R      47          1.804
LGA    R      46      V      48          3.889
LGA    R      47      L      49          2.180
LGA    V      48      V      50          1.635
LGA    L      49      H      51          2.619
LGA    V      50      E      52          1.258
LGA    H      51      D      53          1.548
LGA    E      52      D      54          4.194
LGA    D      53      L      55           -
LGA    D      54      A      56           #
LGA    L      55      G      57          1.342
LGA    A      56      -       -           -
LGA    G      57      -       -           -
LGA    A      58      A      58          2.242
LGA    R      59      R      59          2.047
LGA    R      60      R      60          2.719
LGA    L      61      L      61          2.482
LGA    L      62      L      62          1.739
LGA    T      63      T      63          1.825
LGA    D      64      D      64          3.968
LGA    -       -      A      65           -
LGA    -       -      G      66           -
LGA    A      65      L      67          1.222
LGA    G      66      A      68          1.495
LGA    L      67      H      69          5.044
LGA    A      68      E      70          2.543
LGA    -       -      L      71           -
LGA    -       -      R      72           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   48   57    5.0     42    2.45    59.52     50.335     1.647

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.443751 * X  +  -0.402377 * Y  +  -0.800736 * Z  +  -0.133867
  Y_new =   0.078374 * X  +   0.907531 * Y  +  -0.412609 * Z  +   5.059112
  Z_new =   0.892717 * X  +   0.120339 * Y  +   0.434253 * Z  +   3.378127 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.270333   -2.871259  [ DEG:    15.4889   -164.5110 ]
  Theta =  -1.103338   -2.038254  [ DEG:   -63.2166   -116.7834 ]
  Phi   =   0.174814   -2.966779  [ DEG:    10.0161   -169.9839 ]
 
# 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: T0349AL381_2-D1                               
REMARK     2: T0349_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0349AL381_2-D1.T0349_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   48   57   5.0   42   2.45   59.52  50.335
REMARK  ---------------------------------------------------------- 
MOLECULE T0349AL381_2-D1
REMARK Aligment from pdb entry: 1pba
ATOM      1  N   ARG     6       2.364  -0.531   0.197  1.00  0.00              
ATOM      2  CA  ARG     6       2.236  -1.976  -0.144  1.00  0.00              
ATOM      3  C   ARG     6       1.644  -2.721   1.066  1.00  0.00              
ATOM      4  O   ARG     6       2.380  -3.234   1.884  1.00  0.00              
ATOM      5  N   THR     7       0.354  -2.781   1.157  1.00  0.00              
ATOM      6  CA  THR     7      -0.252  -3.461   2.332  1.00  0.00              
ATOM      7  C   THR     7      -0.099  -4.971   2.185  1.00  0.00              
ATOM      8  O   THR     7      -0.254  -5.496   1.095  1.00  0.00              
ATOM      9  N   ASN     8       0.190  -5.630   3.279  1.00  0.00              
ATOM     10  CA  ASN     8       0.351  -7.113   3.227  1.00  0.00              
ATOM     11  C   ASN     8      -0.955  -7.759   3.640  1.00  0.00              
ATOM     12  O   ASN     8      -1.454  -8.622   2.952  1.00  0.00              
ATOM     13  N   ASP     9      -1.454  -7.364   4.769  1.00  0.00              
ATOM     14  CA  ASP     9      -2.748  -7.936   5.228  1.00  0.00              
ATOM     15  C   ASP     9      -3.505  -6.884   6.031  1.00  0.00              
ATOM     16  O   ASP     9      -3.281  -5.695   5.881  1.00  0.00              
ATOM     17  N   ALA    10      -4.370  -7.346   6.871  1.00  0.00              
ATOM     18  CA  ALA    10      -5.174  -6.421   7.678  1.00  0.00              
ATOM     19  C   ALA    10      -4.291  -5.630   8.655  1.00  0.00              
ATOM     20  O   ALA    10      -4.581  -4.482   8.939  1.00  0.00              
ATOM     21  N   VAL    11      -3.253  -6.247   9.174  1.00  0.00              
ATOM     22  CA  VAL    11      -2.349  -5.502  10.125  1.00  0.00              
ATOM     23  C   VAL    11      -1.965  -4.142   9.542  1.00  0.00              
ATOM     24  O   VAL    11      -2.279  -3.110  10.098  1.00  0.00              
ATOM     25  N   LEU    12      -1.243  -4.195   8.452  1.00  0.00              
ATOM     26  CA  LEU    12      -0.778  -2.951   7.756  1.00  0.00              
ATOM     27  C   LEU    12      -1.941  -1.959   7.588  1.00  0.00              
ATOM     28  O   LEU    12      -1.832  -0.794   7.953  1.00  0.00              
ATOM     29  N   LEU    13      -3.044  -2.455   7.076  1.00  0.00              
ATOM     30  CA  LEU    13      -4.236  -1.576   6.885  1.00  0.00              
ATOM     31  C   LEU    13      -4.564  -0.858   8.180  1.00  0.00              
ATOM     32  O   LEU    13      -4.549   0.356   8.255  1.00  0.00              
ATOM     33  N   SER    14      -4.847  -1.665   9.163  1.00  0.00              
ATOM     34  CA  SER    14      -5.228  -1.159  10.508  1.00  0.00              
ATOM     35  C   SER    14      -4.405   0.043  10.976  1.00  0.00              
ATOM     36  O   SER    14      -4.870   0.780  11.816  1.00  0.00              
ATOM     37  N   ALA    15      -3.227   0.226  10.433  1.00  0.00              
ATOM     38  CA  ALA    15      -2.403   1.391  10.873  1.00  0.00              
ATOM     39  C   ALA    15      -2.656   2.572   9.919  1.00  0.00              
ATOM     40  O   ALA    15      -3.172   3.602  10.321  1.00  0.00              
ATOM     41  N   VAL    16      -2.331   2.379   8.663  1.00  0.00              
ATOM     42  CA  VAL    16      -2.531   3.429   7.649  1.00  0.00              
ATOM     43  C   VAL    16      -3.961   3.989   7.703  1.00  0.00              
ATOM     44  O   VAL    16      -4.185   5.175   7.532  1.00  0.00              
ATOM     45  N   GLY    17      -4.886   3.091   7.903  1.00  0.00              
ATOM     46  CA  GLY    17      -6.328   3.453   7.990  1.00  0.00              
ATOM     47  C   GLY    17      -6.529   4.619   8.964  1.00  0.00              
ATOM     48  O   GLY    17      -7.274   5.530   8.678  1.00  0.00              
ATOM     49  N   ALA    18      -5.863   4.549  10.092  1.00  0.00              
ATOM     50  CA  ALA    18      -5.993   5.629  11.121  1.00  0.00              
ATOM     51  C   ALA    18      -5.764   7.015  10.497  1.00  0.00              
ATOM     52  O   ALA    18      -6.644   7.860  10.526  1.00  0.00              
ATOM     53  N   LEU    19      -4.569   7.202   9.984  1.00  0.00              
ATOM     54  CA  LEU    19      -4.190   8.491   9.323  1.00  0.00              
ATOM     55  C   LEU    19      -5.400   9.099   8.619  1.00  0.00              
ATOM     56  O   LEU    19      -5.689  10.253   8.826  1.00  0.00              
ATOM     57  N   LEU    20      -6.109   8.298   7.856  1.00  0.00              
ATOM     58  CA  LEU    20      -7.314   8.826   7.129  1.00  0.00              
ATOM     59  C   LEU    20      -8.038   9.896   7.972  1.00  0.00              
ATOM     60  O   LEU    20      -8.253  11.008   7.524  1.00  0.00              
ATOM     61  N   ASP    21      -8.385   9.515   9.181  1.00  0.00              
ATOM     62  CA  ASP    21      -9.090  10.442  10.131  1.00  0.00              
ATOM     63  C   ASP    21      -8.526  11.862  10.023  1.00  0.00              
ATOM     64  O   ASP    21      -9.248  12.838   9.979  1.00  0.00              
ATOM     65  N   GLY    22      -7.229  11.923  10.036  1.00  0.00              
ATOM     66  CA  GLY    22      -6.505  13.221   9.934  1.00  0.00              
ATOM     67  C   GLY    22      -5.490  13.117   8.782  1.00  0.00              
ATOM     68  O   GLY    22      -4.317  13.413   8.913  1.00  0.00              
ATOM     69  N   ALA    23      -5.978  12.651   7.668  1.00  0.00              
ATOM     70  CA  ALA    23      -5.103  12.487   6.468  1.00  0.00              
ATOM     71  C   ALA    23      -4.323  13.740   6.075  1.00  0.00              
ATOM     72  O   ALA    23      -4.856  14.663   5.473  1.00  0.00              
ATOM     73  N   ASP    24      -3.082  13.775   6.446  1.00  0.00              
ATOM     74  CA  ASP    24      -2.251  14.934   6.015  1.00  0.00              
ATOM     75  C   ASP    24      -1.914  14.667   4.538  1.00  0.00              
ATOM     76  O   ASP    24      -1.594  15.560   3.781  1.00  0.00              
ATOM     77  N   ILE    25      -2.072  13.415   4.178  1.00  0.00              
ATOM     78  CA  ILE    25      -1.779  12.927   2.797  1.00  0.00              
ATOM     79  C   ILE    25      -3.062  12.692   2.003  1.00  0.00              
ATOM     80  O   ILE    25      -4.140  12.687   2.552  1.00  0.00              
ATOM     81  N   GLY    26      -2.897  12.483   0.727  1.00  0.00              
ATOM     82  CA  GLY    26      -4.054  12.194  -0.169  1.00  0.00              
ATOM     83  C   GLY    26      -3.580  11.017  -1.013  1.00  0.00              
ATOM     84  O   GLY    26      -2.390  10.947  -1.308  1.00  0.00              
ATOM     85  N   HIS    27      -4.480  10.174  -1.438  1.00  0.00              
ATOM     86  CA  HIS    27      -4.047   8.987  -2.231  1.00  0.00              
ATOM     87  C   HIS    27      -4.130   9.265  -3.731  1.00  0.00              
ATOM     88  O   HIS    27      -4.778  10.198  -4.171  1.00  0.00              
ATOM     89  N   LEU    28      -3.444   8.450  -4.484  1.00  0.00              
ATOM     90  CA  LEU    28      -3.424   8.625  -5.966  1.00  0.00              
ATOM     91  C   LEU    28      -4.122   7.435  -6.636  1.00  0.00              
ATOM     92  O   LEU    28      -5.314   7.479  -6.854  1.00  0.00              
ATOM     93  N   VAL    29      -3.395   6.389  -6.923  1.00  0.00              
ATOM     94  CA  VAL    29      -4.033   5.195  -7.566  1.00  0.00              
ATOM     95  C   VAL    29      -3.911   4.041  -6.578  1.00  0.00              
ATOM     96  O   VAL    29      -2.944   3.969  -5.867  1.00  0.00              
ATOM    141  N   PRO    45      -1.320  -2.732  -3.744  1.00  0.00              
ATOM    142  CA  PRO    45      -0.323  -1.690  -4.111  1.00  0.00              
ATOM    143  C   PRO    45      -1.004  -0.410  -4.618  1.00  0.00              
ATOM    144  O   PRO    45      -1.647  -0.426  -5.658  1.00  0.00              
ATOM    145  N   ARG    46      -0.845   0.660  -3.867  1.00  0.00              
ATOM    146  CA  ARG    46      -1.460   1.974  -4.265  1.00  0.00              
ATOM    147  C   ARG    46      -0.393   3.087  -4.109  1.00  0.00              
ATOM    148  O   ARG    46       0.601   2.859  -3.440  1.00  0.00              
ATOM    149  N   ARG    47      -0.607   4.267  -4.662  1.00  0.00              
ATOM    150  CA  ARG    47       0.439   5.348  -4.558  1.00  0.00              
ATOM    151  C   ARG    47      -0.106   6.645  -3.917  1.00  0.00              
ATOM    152  O   ARG    47      -1.307   6.826  -3.848  1.00  0.00              
ATOM    153  N   VAL    48       0.791   7.532  -3.500  1.00  0.00              
ATOM    154  CA  VAL    48       0.373   8.840  -2.860  1.00  0.00              
ATOM    155  C   VAL    48       0.704  10.053  -3.762  1.00  0.00              
ATOM    156  O   VAL    48      -0.146  10.484  -4.514  1.00  0.00              
ATOM    157  N   LEU    49       1.926  10.578  -3.630  1.00  0.00              
ATOM    158  CA  LEU    49       2.411  11.772  -4.428  1.00  0.00              
ATOM    159  C   LEU    49       3.546  12.484  -3.663  1.00  0.00              
ATOM    160  O   LEU    49       3.822  12.167  -2.517  1.00  0.00              
ATOM    161  N   VAL    50       4.150  13.446  -4.317  1.00  0.00              
ATOM    162  CA  VAL    50       5.253  14.224  -3.708  1.00  0.00              
ATOM    163  C   VAL    50       4.743  15.509  -3.034  1.00  0.00              
ATOM    164  O   VAL    50       4.721  16.573  -3.620  1.00  0.00              
ATOM    165  N   HIS    51       4.267  15.371  -1.825  1.00  0.00              
ATOM    166  CA  HIS    51       3.812  16.582  -1.081  1.00  0.00              
ATOM    167  C   HIS    51       4.921  16.874  -0.077  1.00  0.00              
ATOM    168  O   HIS    51       5.656  15.966   0.268  1.00  0.00              
ATOM    169  N   GLU    52       5.021  18.096   0.382  1.00  0.00              
ATOM    170  CA  GLU    52       6.110  18.443   1.349  1.00  0.00              
ATOM    171  C   GLU    52       5.600  19.229   2.566  1.00  0.00              
ATOM    172  O   GLU    52       4.416  19.298   2.824  1.00  0.00              
ATOM    173  N   ASP    53       6.559  19.765   3.284  1.00  0.00              
ATOM    174  CA  ASP    53       6.321  20.594   4.512  1.00  0.00              
ATOM    175  C   ASP    53       5.883  19.748   5.700  1.00  0.00              
ATOM    176  O   ASP    53       6.588  19.652   6.683  1.00  0.00              
ATOM    177  N   ASP    54       4.778  19.081   5.572  1.00  0.00              
ATOM    178  CA  ASP    54       4.294  18.262   6.725  1.00  0.00              
ATOM    179  C   ASP    54       4.748  16.809   6.618  1.00  0.00              
ATOM    180  O   ASP    54       4.404  15.995   7.463  1.00  0.00              
ATOM    181  N   LEU    55       5.548  16.529   5.619  1.00  0.00              
ATOM    182  CA  LEU    55       6.051  15.204   5.366  1.00  0.00              
ATOM    183  C   LEU    55       6.501  14.500   6.650  1.00  0.00              
ATOM    184  O   LEU    55       6.062  13.418   6.938  1.00  0.00              
ATOM    185  N   ALA    56       7.370  15.139   7.379  1.00  0.00              
ATOM    186  CA  ALA    56       7.872  14.551   8.660  1.00  0.00              
ATOM    187  C   ALA    56       6.852  13.627   9.337  1.00  0.00              
ATOM    188  O   ALA    56       7.142  12.477   9.573  1.00  0.00              
ATOM    189  N   GLY    57       5.672  14.117   9.598  1.00  0.00              
ATOM    190  CA  GLY    57       4.682  13.236  10.291  1.00  0.00              
ATOM    191  C   GLY    57       4.284  12.054   9.416  1.00  0.00              
ATOM    192  O   GLY    57       4.125  10.953   9.897  1.00  0.00              
ATOM    193  N   ALA    58       4.159  12.309   8.152  1.00  0.00              
ATOM    194  CA  ALA    58       3.770  11.221   7.224  1.00  0.00              
ATOM    195  C   ALA    58       4.927  10.233   7.079  1.00  0.00              
ATOM    196  O   ALA    58       4.751   9.050   7.309  1.00  0.00              
ATOM    197  N   ARG    59       6.076  10.745   6.709  1.00  0.00              
ATOM    198  CA  ARG    59       7.257   9.862   6.538  1.00  0.00              
ATOM    199  C   ARG    59       7.500   9.118   7.872  1.00  0.00              
ATOM    200  O   ARG    59       7.758   7.930   7.885  1.00  0.00              
ATOM    201  N   ARG    60       7.368   9.831   8.968  1.00  0.00              
ATOM    202  CA  ARG    60       7.564   9.195  10.310  1.00  0.00              
ATOM    203  C   ARG    60       6.521   8.083  10.499  1.00  0.00              
ATOM    204  O   ARG    60       6.867   6.946  10.761  1.00  0.00              
ATOM    205  N   LEU    61       5.270   8.463  10.343  1.00  0.00              
ATOM    206  CA  LEU    61       4.126   7.491  10.469  1.00  0.00              
ATOM    207  C   LEU    61       4.379   6.298   9.567  1.00  0.00              
ATOM    208  O   LEU    61       3.797   5.257   9.729  1.00  0.00              
ATOM    209  N   LEU    62       5.196   6.518   8.595  1.00  0.00              
ATOM    210  CA  LEU    62       5.543   5.414   7.643  1.00  0.00              
ATOM    211  C   LEU    62       6.916   4.757   7.912  1.00  0.00              
ATOM    212  O   LEU    62       7.157   3.678   7.403  1.00  0.00              
ATOM    213  N   THR    63       7.779   5.376   8.681  1.00  0.00              
ATOM    214  CA  THR    63       9.125   4.751   8.925  1.00  0.00              
ATOM    215  C   THR    63       9.226   4.066  10.291  1.00  0.00              
ATOM    216  O   THR    63       9.546   2.900  10.354  1.00  0.00              
ATOM    217  N   ASP    64       8.985   4.806  11.345  1.00  0.00              
ATOM    218  CA  ASP    64       9.072   4.226  12.737  1.00  0.00              
ATOM    219  C   ASP    64       8.539   2.787  12.820  1.00  0.00              
ATOM    220  O   ASP    64       8.971   2.010  13.650  1.00  0.00              
ATOM    221  N   ALA    65       7.592   2.500  11.979  1.00  0.00              
ATOM    222  CA  ALA    65       6.963   1.147  11.944  1.00  0.00              
ATOM    223  C   ALA    65       7.290   0.421  10.638  1.00  0.00              
ATOM    224  O   ALA    65       7.048  -0.765  10.514  1.00  0.00              
ATOM    225  N   GLY    66       7.809   1.167   9.696  1.00  0.00              
ATOM    226  CA  GLY    66       8.136   0.605   8.357  1.00  0.00              
ATOM    227  C   GLY    66       6.827   0.134   7.725  1.00  0.00              
ATOM    228  O   GLY    66       6.720  -0.966   7.212  1.00  0.00              
ATOM    229  N   LEU    67       5.845   1.001   7.800  1.00  0.00              
ATOM    230  CA  LEU    67       4.509   0.702   7.230  1.00  0.00              
ATOM    231  C   LEU    67       4.655   0.607   5.706  1.00  0.00              
ATOM    232  O   LEU    67       4.477   1.582   4.993  1.00  0.00              
ATOM    233  N   ALA    68       5.096  -0.561   5.309  1.00  0.00              
ATOM    234  CA  ALA    68       5.337  -0.945   3.883  1.00  0.00              
ATOM    235  C   ALA    68       5.145   0.187   2.854  1.00  0.00              
ATOM    236  O   ALA    68       4.260   0.126   2.013  1.00  0.00              
END
