
#######################################################
#                                                     #
#                        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   40 (  199),  selected   40 , name T0363TS261_1-D1
# Molecule2: number of CA atoms   46 (  372),  selected   46 , name T0363_D1.pdb
# PARAMETERS: T0363TS261_1-D1.T0363_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      N      11           -
LGA    Q      12      Q      12          1.280
LGA    I      13      I      13          1.778
LGA    N      14      N      14          1.015
LGA    I      15      I      15          0.925
LGA    E      16      E      16          1.808
LGA    I      17      I      17          1.681
LGA    A      18      A      18          1.765
LGA    Y      19      Y      19          1.529
LGA    A      20      A      20          1.118
LGA    F      21      F      21          3.263
LGA    P      22      P      22          4.858
LGA    -       -      E      23           -
LGA    -       -      R      24           -
LGA    E      23      Y      25          2.482
LGA    R      24      Y      26          3.982
LGA    -       -      L      27           -
LGA    Y      25      K      28          0.742
LGA    S      29      S      29          0.567
LGA    F      30      F      30          1.669
LGA    Q      31      Q      31          1.704
LGA    V      32      V      32          1.520
LGA    D      33      D      33          1.187
LGA    E      34      E      34          1.717
LGA    G      35      G      35          0.427
LGA    I      36      I      36          0.862
LGA    T      37      T      37          0.791
LGA    V      38      V      38          0.578
LGA    Q      39      Q      39          1.186
LGA    T      40      T      40          0.890
LGA    A      41      A      41          1.167
LGA    I      42      I      42          1.632
LGA    T      43      T      43          1.024
LGA    Q      44      Q      44          1.540
LGA    I      47      S      45          2.828
LGA    L      48      G      46          3.407
LGA    S      49      -       -           -
LGA    Q      50      I      47          5.414
LGA    F      51      L      48          5.225
LGA    P      52      S      49          1.558
LGA    -       -      Q      50           -
LGA    -       -      F      51           -
LGA    -       -      P      52           -
LGA    -       -      E      53           -
LGA    -       -      I      54           -
LGA    -       -      D      55           -
LGA    E      53      L      56           #
LGA    I      54      -       -           -
LGA    D      55      -       -           -
LGA    L      56      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   40   46    5.0     35    2.26    77.14     64.701     1.482

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.547763 * X  +  -0.799073 * Y  +  -0.247868 * Z  +  47.050343
  Y_new =   0.783998 * X  +   0.386830 * Y  +   0.485499 * Z  + -26.151211
  Z_new =  -0.292066 * X  +  -0.460266 * Y  +   0.838363 * Z  +  36.203682 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.502079    2.639513  [ DEG:   -28.7670    151.2330 ]
  Theta =   0.296387    2.845206  [ DEG:    16.9817    163.0183 ]
  Phi   =   0.960958   -2.180635  [ DEG:    55.0588   -124.9412 ]
 
# 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: T0363TS261_1-D1                               
REMARK     2: T0363_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0363TS261_1-D1.T0363_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   40   46   5.0   35   2.26   77.14  64.701
REMARK  ---------------------------------------------------------- 
MOLECULE T0363TS261_1-D1
PFRMAT TS
TARGET T0363
MODEL  1
PARENT 1vjk_A
ATOM      1  N   GLN    12      17.505   1.713   8.643  1.00  5.75
ATOM      2  CA  GLN    12      18.325   2.797   7.993  1.00  5.75
ATOM      3  C   GLN    12      17.859   4.212   8.375  1.00  5.75
ATOM      4  O   GLN    12      16.668   4.451   8.640  1.00  5.75
ATOM      5  CB  GLN    12      18.295   2.632   6.471  1.00  5.75
ATOM      6  N   ILE    13      18.816   5.140   8.412  1.00  5.16
ATOM      7  CA  ILE    13      18.559   6.559   8.670  1.00  5.16
ATOM      8  C   ILE    13      19.052   7.315   7.423  1.00  5.16
ATOM      9  O   ILE    13      20.237   7.226   7.090  1.00  5.16
ATOM     10  CB  ILE    13      19.317   6.998   9.943  1.00  5.16
ATOM     11  N   ASN    14      18.161   8.023   6.731  1.00  6.13
ATOM     12  CA  ASN    14      18.553   8.757   5.536  1.00  6.13
ATOM     13  C   ASN    14      18.619  10.233   5.848  1.00  6.13
ATOM     14  O   ASN    14      17.601  10.835   6.261  1.00  6.13
ATOM     15  CB  ASN    14      17.596   8.501   4.365  1.00  6.13
ATOM     16  N   ILE    15      19.795  10.821   5.679  1.00  4.92
ATOM     17  CA  ILE    15      19.984  12.241   5.956  1.00  4.92
ATOM     18  C   ILE    15      20.264  12.980   4.664  1.00  4.92
ATOM     19  O   ILE    15      20.805  12.405   3.690  1.00  4.92
ATOM     20  CB  ILE    15      21.103  12.487   7.001  1.00  4.92
ATOM     21  N   GLU    16      19.904  14.246   4.620  1.00  3.55
ATOM     22  CA  GLU    16      20.160  15.099   3.488  1.00  3.55
ATOM     23  C   GLU    16      21.360  15.938   3.830  1.00  3.55
ATOM     24  O   GLU    16      21.306  16.742   4.771  1.00  3.55
ATOM     25  CB  GLU    16      18.955  16.003   3.223  1.00  3.55
ATOM     26  N   ILE    17      22.441  15.779   3.091  1.00  5.76
ATOM     27  CA  ILE    17      23.656  16.549   3.299  1.00  5.76
ATOM     28  C   ILE    17      23.711  17.703   2.330  1.00  5.76
ATOM     29  O   ILE    17      23.559  17.485   1.127  1.00  5.76
ATOM     30  CB  ILE    17      24.931  15.677   3.163  1.00  5.76
ATOM     31  N   ALA    18      23.894  18.925   2.847  1.00  5.25
ATOM     32  CA  ALA    18      24.005  20.118   2.002  1.00  5.25
ATOM     33  C   ALA    18      25.418  20.642   2.130  1.00  5.25
ATOM     34  O   ALA    18      25.873  20.978   3.238  1.00  5.25
ATOM     35  CB  ALA    18      22.981  21.196   2.400  1.00  5.25
ATOM     36  N   TYR    19      26.118  20.710   1.010  1.00  3.43
ATOM     37  CA  TYR    19      27.477  21.254   0.972  1.00  3.43
ATOM     38  C   TYR    19      27.448  22.708   0.603  1.00  3.43
ATOM     39  O   TYR    19      26.613  23.145  -0.209  1.00  3.43
ATOM     40  CB  TYR    19      28.295  20.485  -0.080  1.00  3.43
ATOM     41  N   ALA    20      28.398  23.457   1.175  1.00  5.54
ATOM     42  CA  ALA    20      28.490  24.883   0.935  1.00  5.54
ATOM     43  C   ALA    20      29.846  25.299   0.436  1.00  5.54
ATOM     44  O   ALA    20      30.862  24.699   0.779  1.00  5.54
ATOM     45  CB  ALA    20      28.183  25.648   2.238  1.00  5.54
ATOM     46  N   PHE    21      29.856  26.374  -0.353  1.00  6.11
ATOM     47  CA  PHE    21      31.092  27.019  -0.787  1.00  6.11
ATOM     48  C   PHE    21      32.035  25.993  -1.435  1.00  6.11
ATOM     49  O   PHE    21      31.589  25.226  -2.299  1.00  6.11
ATOM     50  CB  PHE    21      31.748  27.779   0.364  1.00  6.11
ATOM     51  N   PRO    22      33.316  25.960  -1.046  1.00  5.30
ATOM     52  CA  PRO    22      34.244  25.103  -1.811  1.00  5.30
ATOM     53  C   PRO    22      33.942  23.630  -1.652  1.00  5.30
ATOM     54  O   PRO    22      34.359  22.821  -2.478  1.00  5.30
ATOM     55  CB  PRO    22      35.708  25.406  -1.487  1.00  5.30
ATOM     56  N   GLU    23      25.827  19.717  -4.876  1.00  5.06
ATOM     57  CA  GLU    23      25.431  20.709  -3.901  1.00  5.06
ATOM     58  C   GLU    23      24.795  20.042  -2.692  1.00  5.06
ATOM     59  O   GLU    23      24.857  20.556  -1.576  1.00  5.06
ATOM     60  CB  GLU    23      24.463  21.718  -4.522  1.00  5.06
ATOM     61  N   ARG    24      24.219  18.859  -2.899  1.00  4.23
ATOM     62  CA  ARG    24      23.547  18.122  -1.839  1.00  4.23
ATOM     63  C   ARG    24      23.490  16.669  -2.212  1.00  4.23
ATOM     64  O   ARG    24      23.586  16.308  -3.390  1.00  4.23
ATOM     65  CB  ARG    24      22.151  18.672  -1.544  1.00  4.23
ATOM     66  N   TYR    25      23.328  15.818  -1.206  1.00  8.08
ATOM     67  CA  TYR    25      23.225  14.390  -1.426  1.00  8.08
ATOM     68  C   TYR    25      22.545  13.724  -0.263  1.00  8.08
ATOM     69  O   TYR    25      22.703  14.158   0.885  1.00  8.08
ATOM     70  CB  TYR    25      24.570  13.700  -1.832  1.00  8.08
ATOM     71  N   SER    29      21.772  12.697  -0.549  1.00  4.00
ATOM     72  CA  SER    29      21.151  11.881   0.464  1.00  4.00
ATOM     73  C   SER    29      22.075  10.767   0.849  1.00  4.00
ATOM     74  O   SER    29      22.573  10.030  -0.030  1.00  4.00
ATOM     75  CB  SER    29      19.829  11.310  -0.036  1.00  4.00
ATOM     76  N   PHE    30      22.287  10.579   2.140  1.00  5.28
ATOM     77  CA  PHE    30      23.161   9.536   2.617  1.00  5.28
ATOM     78  C   PHE    30      22.407   8.621   3.568  1.00  5.28
ATOM     79  O   PHE    30      21.921   9.049   4.635  1.00  5.28
ATOM     80  CB  PHE    30      24.423  10.127   3.292  1.00  5.28
ATOM     81  N   GLN    31      22.277   7.365   3.174  1.00  5.39
ATOM     82  CA  GLN    31      21.660   6.337   4.002  1.00  5.39
ATOM     83  C   GLN    31      22.713   5.767   4.949  1.00  5.39
ATOM     84  O   GLN    31      23.803   5.376   4.522  1.00  5.39
ATOM     85  CB  GLN    31      21.068   5.244   3.123  1.00  5.39
ATOM     86  N   VAL    32      22.381   5.744   6.238  1.00  5.59
ATOM     87  CA  VAL    32      23.284   5.317   7.283  1.00  5.59
ATOM     88  C   VAL    32      22.624   4.214   8.089  1.00  5.59
ATOM     89  O   VAL    32      21.404   4.160   8.155  1.00  5.59
ATOM     90  CB  VAL    32      23.625   6.504   8.207  1.00  5.59
ATOM     91  N   ASP    33      23.406   3.320   8.702  1.00  4.56
ATOM     92  CA  ASP    33      22.828   2.269   9.536  1.00  4.56
ATOM     93  C   ASP    33      22.168   2.827  10.787  1.00  4.56
ATOM     94  O   ASP    33      22.513   3.911  11.269  1.00  4.56
ATOM     95  CB  ASP    33      24.035   1.388   9.910  1.00  4.56
ATOM     96  N   GLU    34      21.212   2.065  11.301  1.00  3.83
ATOM     97  CA  GLU    34      20.588   2.335  12.577  1.00  3.83
ATOM     98  C   GLU    34      21.640   2.723  13.623  1.00  3.83
ATOM     99  O   GLU    34      22.687   2.090  13.721  1.00  3.83
ATOM    100  CB  GLU    34      19.822   1.089  13.029  1.00  3.83
ATOM    101  N   GLY    35      21.346   3.781  14.377  1.00  3.60
ATOM    102  CA  GLY    35      22.216   4.225  15.459  1.00  3.60
ATOM    103  C   GLY    35      23.309   5.178  15.012  1.00  3.60
ATOM    104  O   GLY    35      24.151   5.603  15.821  1.00  3.60
ATOM    105  N   ILE    36      23.316   5.528  13.733  1.00  4.23
ATOM    106  CA  ILE    36      24.367   6.392  13.226  1.00  4.23
ATOM    107  C   ILE    36      24.442   7.695  13.961  1.00  4.23
ATOM    108  O   ILE    36      23.418   8.308  14.307  1.00  4.23
ATOM    109  CB  ILE    36      24.160   6.665  11.719  1.00  4.23
ATOM    110  N   THR    37      25.684   8.131  14.161  1.00  2.45
ATOM    111  CA  THR    37      25.994   9.387  14.816  1.00  2.45
ATOM    112  C   THR    37      26.638  10.360  13.832  1.00  2.45
ATOM    113  O   THR    37      27.104   9.974  12.747  1.00  2.45
ATOM    114  CB  THR    37      26.970   9.142  15.957  1.00  2.45
ATOM    115  N   VAL    38      26.723  11.632  14.206  1.00  4.41
ATOM    116  CA  VAL    38      27.413  12.622  13.379  1.00  4.41
ATOM    117  C   VAL    38      28.812  12.142  12.945  1.00  4.41
ATOM    118  O   VAL    38      29.188  12.260  11.758  1.00  4.41
ATOM    119  CB  VAL    38      27.461  13.990  14.094  1.00  4.41
ATOM    120  N   GLN    39      29.583  11.561  13.875  1.00  6.71
ATOM    121  CA  GLN    39      30.920  11.099  13.495  1.00  6.71
ATOM    122  C   GLN    39      30.882  10.025  12.378  1.00  6.71
ATOM    123  O   GLN    39      31.797   9.961  11.540  1.00  6.71
ATOM    124  CB  GLN    39      31.701  10.609  14.728  1.00  6.71
ATOM    125  N   THR    40      29.836   9.190  12.373  1.00  5.67
ATOM    126  CA  THR    40      29.715   8.143  11.333  1.00  5.67
ATOM    127  C   THR    40      29.407   8.777  10.010  1.00  5.67
ATOM    128  O   THR    40      29.925   8.333   8.977  1.00  5.67
ATOM    129  CB  THR    40      28.636   7.124  11.688  1.00  5.67
ATOM    130  N   ALA    41      28.591   9.818  10.020  1.00  9.02
ATOM    131  CA  ALA    41      28.302  10.545   8.783  1.00  9.02
ATOM    132  C   ALA    41      29.562  11.210   8.216  1.00  9.02
ATOM    133  O   ALA    41      29.809  11.125   6.999  1.00  9.02
ATOM    134  CB  ALA    41      27.222  11.593   9.041  1.00  9.02
ATOM    135  N   ILE    42      30.377  11.815   9.080  1.00  5.33
ATOM    136  CA  ILE    42      31.624  12.418   8.627  1.00  5.33
ATOM    137  C   ILE    42      32.511  11.360   7.977  1.00  5.33
ATOM    138  O   ILE    42      33.100  11.598   6.890  1.00  5.33
ATOM    139  CB  ILE    42      32.328  13.114   9.796  1.00  5.33
ATOM    140  N   THR    43      32.623  10.174   8.601  1.00  3.43
ATOM    141  CA  THR    43      33.409   9.111   7.963  1.00  3.43
ATOM    142  C   THR    43      32.868   8.675   6.622  1.00  3.43
ATOM    143  O   THR    43      33.660   8.362   5.706  1.00  3.43
ATOM    144  CB  THR    43      33.590   7.928   8.908  1.00  3.43
ATOM    145  N   GLN    44      31.552   8.650   6.479  1.00  4.05
ATOM    146  CA  GLN    44      30.957   8.268   5.212  1.00  4.05
ATOM    147  C   GLN    44      31.193   9.338   4.145  1.00  4.05
ATOM    148  O   GLN    44      31.434   8.985   2.985  1.00  4.05
ATOM    149  CB  GLN    44      29.455   7.965   5.382  1.00  4.05
ATOM    150  N   ILE    47      31.149  10.634   4.512  1.00  5.62
ATOM    151  CA  ILE    47      31.458  11.694   3.544  1.00  5.62
ATOM    152  C   ILE    47      32.881  11.513   3.013  1.00  5.62
ATOM    153  O   ILE    47      33.108  11.584   1.786  1.00  5.62
ATOM    154  CB  ILE    47      31.251  13.075   4.185  1.00  5.62
ATOM    155  N   LEU    48      33.810  11.232   3.922  1.00  4.21
ATOM    156  CA  LEU    48      35.209  10.999   3.546  1.00  4.21
ATOM    157  C   LEU    48      35.380   9.757   2.658  1.00  4.21
ATOM    158  O   LEU    48      36.239   9.752   1.746  1.00  4.21
ATOM    159  CB  LEU    48      36.081  10.889   4.792  1.00  4.21
ATOM    160  N   SER    49      34.576   8.727   2.904  1.00  4.45
ATOM    161  CA  SER    49      34.626   7.513   2.107  1.00  4.45
ATOM    162  C   SER    49      34.095   7.760   0.698  1.00  4.45
ATOM    163  O   SER    49      34.632   7.213  -0.278  1.00  4.45
ATOM    164  CB  SER    49      33.812   6.412   2.792  1.00  4.45
ATOM    165  N   GLN    50      33.036   8.556   0.568  1.00  4.98
ATOM    166  CA  GLN    50      32.454   8.825  -0.736  1.00  4.98
ATOM    167  C   GLN    50      33.283   9.808  -1.549  1.00  4.98
ATOM    168  O   GLN    50      33.287   9.777  -2.778  1.00  4.98
ATOM    169  CB  GLN    50      31.061   9.408  -0.565  1.00  4.98
ATOM    170  N   PHE    51      33.916  10.735  -0.845  1.00  3.34
ATOM    171  CA  PHE    51      34.589  11.861  -1.481  1.00  3.34
ATOM    172  C   PHE    51      35.952  12.025  -0.861  1.00  3.34
ATOM    173  O   PHE    51      36.120  12.773   0.134  1.00  3.34
ATOM    174  CB  PHE    51      33.775  13.150  -1.285  1.00  3.34
ATOM    175  N   PRO    52      36.937  11.354  -1.456  1.00  2.69
ATOM    176  CA  PRO    52      38.258  11.237  -0.835  1.00  2.69
ATOM    177  C   PRO    52      38.947  12.569  -0.576  1.00  2.69
ATOM    178  O   PRO    52      39.801  12.643   0.303  1.00  2.69
ATOM    179  CB  PRO    52      39.166  10.319  -1.646  1.00  2.69
ATOM    180  N   GLU    53      34.296  19.913  15.821  1.00  4.50
ATOM    181  CA  GLU    53      33.181  19.468  16.624  1.00  4.50
ATOM    182  C   GLU    53      32.455  20.701  17.116  1.00  4.50
ATOM    183  O   GLU    53      33.058  21.553  17.810  1.00  4.50
ATOM    184  CB  GLU    53      33.666  18.608  17.779  1.00  4.50
ATOM    185  N   ILE    54      31.177  20.808  16.774  1.00  4.84
ATOM    186  CA  ILE    54      30.414  22.022  17.007  1.00  4.84
ATOM    187  C   ILE    54      31.013  23.186  16.249  1.00  4.84
ATOM    188  O   ILE    54      31.606  23.022  15.165  1.00  4.84
ATOM    189  CB  ILE    54      30.359  22.308  18.518  1.00  4.84
ATOM    190  N   ASP    55      30.895  24.378  16.816  1.00  5.42
ATOM    191  CA  ASP    55      31.524  25.533  16.227  1.00  5.42
ATOM    192  C   ASP    55      33.033  25.498  16.494  1.00  5.42
ATOM    193  O   ASP    55      33.473  25.337  17.645  1.00  5.42
ATOM    194  CB  ASP    55      30.918  26.830  16.766  1.00  5.42
ATOM    195  N   LEU    56      33.818  25.648  15.428  1.00  4.07
ATOM    196  CA  LEU    56      35.267  25.669  15.525  1.00  4.07
ATOM    197  C   LEU    56      35.864  26.424  14.354  1.00  4.07
ATOM    198  O   LEU    56      35.866  25.942  13.233  1.00  4.07
ATOM    199  CB  LEU    56      35.804  24.235  15.612  1.00  4.07
TER
END
