
#######################################################
#                                                     #
#                        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   43 (  214),  selected   43 , name T0363TS239_3-D1
# Molecule2: number of CA atoms   46 (  372),  selected   46 , name T0363_D1.pdb
# PARAMETERS: T0363TS239_3-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          1.005
LGA    I      13      I      13          1.815
LGA    N      14      N      14          0.612
LGA    I      15      I      15          0.826
LGA    E      16      E      16          2.417
LGA    I      17      I      17          2.491
LGA    A      18      A      18          2.847
LGA    Y      19      Y      19          2.879
LGA    A      20      A      20          1.912
LGA    F      21      F      21          3.776
LGA    P      22      P      22          3.100
LGA    E      23      E      23           -
LGA    R      24      R      24          3.729
LGA    Y      25      Y      25          4.638
LGA    Y      26      Y      26          5.905
LGA    L      27      -       -           -
LGA    K      28      L      27           #
LGA    -       -      K      28           -
LGA    S      29      S      29          1.132
LGA    F      30      F      30          1.136
LGA    Q      31      Q      31          1.118
LGA    V      32      V      32          1.174
LGA    D      33      D      33          1.173
LGA    E      34      E      34          2.155
LGA    G      35      G      35          0.719
LGA    I      36      I      36          0.410
LGA    T      37      T      37          0.218
LGA    V      38      V      38          0.272
LGA    Q      39      Q      39          0.676
LGA    T      40      T      40          0.966
LGA    A      41      A      41          1.014
LGA    I      42      I      42          0.762
LGA    T      43      T      43          1.124
LGA    Q      44      Q      44          2.314
LGA    I      47      S      45          2.451
LGA    L      48      G      46          1.859
LGA    S      49      -       -           -
LGA    Q      50      I      47           #
LGA    F      51      L      48           #
LGA    P      52      S      49          2.975
LGA    E      53      Q      50          1.349
LGA    I      54      F      51          2.827
LGA    D      55      -       -           -
LGA    L      56      P      52          1.853
LGA    -       -      E      53           -
LGA    -       -      I      54           -
LGA    -       -      D      55           -
LGA    -       -      L      56           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   43   46    5.0     36    2.27    83.33     57.783     1.522

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.489214 * X  +  -0.860045 * Y  +  -0.144885 * Z  +  50.916157
  Y_new =   0.798272 * X  +   0.374627 * Y  +   0.471611 * Z  + -26.117695
  Z_new =  -0.351329 * X  +  -0.346376 * Y  +   0.869823 * Z  +  32.514282 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.378966    2.762626  [ DEG:   -21.7132    158.2868 ]
  Theta =   0.358990    2.782603  [ DEG:    20.5686    159.4314 ]
  Phi   =   1.020988   -2.120605  [ DEG:    58.4983   -121.5017 ]
 
# 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: T0363TS239_3-D1                               
REMARK     2: T0363_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0363TS239_3-D1.T0363_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   43   46   5.0   36   2.27   83.33  57.783
REMARK  ---------------------------------------------------------- 
MOLECULE T0363TS239_3-D1
PFRMAT TS
TARGET T0363
MODEL 3
PARENT 1vjk_A
ATOM      1  N   GLN    12      17.465   1.399   9.432  1.00  9.99
ATOM      2  CA  GLN    12      18.172   2.507   8.694  1.00  9.99
ATOM      3  C   GLN    12      17.733   3.908   9.151  1.00  9.99
ATOM      4  O   GLN    12      16.582   4.119   9.574  1.00  9.99
ATOM      5  CB  GLN    12      17.945   2.357   7.186  1.00  9.99
ATOM      6  N   ILE    13      18.668   4.855   9.074  1.00  9.99
ATOM      7  CA  ILE    13      18.419   6.266   9.382  1.00  9.99
ATOM      8  C   ILE    13      18.730   7.045   8.091  1.00  9.99
ATOM      9  O   ILE    13      19.862   6.984   7.604  1.00  9.99
ATOM     10  CB  ILE    13      19.330   6.708  10.550  1.00  9.99
ATOM     11  N   ASN    14      17.741   7.741   7.531  1.00  9.99
ATOM     12  CA  ASN    14      17.959   8.495   6.305  1.00  9.99
ATOM     13  C   ASN    14      18.036   9.969   6.624  1.00  9.99
ATOM     14  O   ASN    14      17.070  10.545   7.175  1.00  9.99
ATOM     15  CB  ASN    14      16.861   8.231   5.266  1.00  9.99
ATOM     16  N   ILE    15      19.168  10.583   6.310  1.00  9.99
ATOM     17  CA  ILE    15      19.364  12.004   6.578  1.00  9.99
ATOM     18  C   ILE    15      19.457  12.762   5.270  1.00  9.99
ATOM     19  O   ILE    15      19.876  12.208   4.226  1.00  9.99
ATOM     20  CB  ILE    15      20.606  12.263   7.470  1.00  9.99
ATOM     21  N   GLU    16      19.071  14.020   5.290  1.00  9.99
ATOM     22  CA  GLU    16      19.159  14.890   4.145  1.00  9.99
ATOM     23  C   GLU    16      20.377  15.750   4.337  1.00  9.99
ATOM     24  O   GLU    16      20.431  16.543   5.288  1.00  9.99
ATOM     25  CB  GLU    16      17.911  15.771   4.052  1.00  9.99
ATOM     26  N   ILE    17      21.354  15.621   3.461  1.00  9.99
ATOM     27  CA  ILE    17      22.571  16.415   3.518  1.00  9.99
ATOM     28  C   ILE    17      22.475  17.580   2.564  1.00  9.99
ATOM     29  O   ILE    17      22.170  17.371   1.389  1.00  9.99
ATOM     30  CB  ILE    17      23.833  15.571   3.204  1.00  9.99
ATOM     31  N   ALA    18      22.700  18.800   3.068  1.00  9.99
ATOM     32  CA  ALA    18      22.676  20.003   2.231  1.00  9.99
ATOM     33  C   ALA    18      24.083  20.556   2.180  1.00  9.99
ATOM     34  O   ALA    18      24.673  20.889   3.223  1.00  9.99
ATOM     35  CB  ALA    18      21.693  21.055   2.774  1.00  9.99
ATOM     36  N   TYR    19      24.629  20.649   0.979  1.00  9.99
ATOM     37  CA  TYR    19      25.960  21.222   0.770  1.00  9.99
ATOM     38  C   TYR    19      25.854  22.680   0.427  1.00  9.99
ATOM     39  O   TYR    19      24.911  23.107  -0.263  1.00  9.99
ATOM     40  CB  TYR    19      26.647  20.481  -0.390  1.00  9.99
ATOM     41  N   ALA    20      26.857  23.443   0.878  1.00  9.99
ATOM     42  CA  ALA    20      26.888  24.873   0.647  1.00  9.99
ATOM     43  C   ALA    20      28.158  25.322  -0.021  1.00  9.99
ATOM     44  O   ALA    20      29.222  24.740   0.179  1.00  9.99
ATOM     45  CB  ALA    20      26.740  25.617   1.988  1.00  9.99
ATOM     46  N   PHE    21      28.044  26.404  -0.790  1.00  9.99
ATOM     47  CA  PHE    21      29.199  27.080  -1.374  1.00  9.99
ATOM     48  C   PHE    21      30.068  26.080  -2.153  1.00  9.99
ATOM     49  O   PHE    21      29.528  25.313  -2.961  1.00  9.99
ATOM     50  CB  PHE    21      29.986  27.842  -0.310  1.00  9.99
ATOM     51  N   PRO    22      31.389  26.070  -1.937  1.00  9.99
ATOM     52  CA  PRO    22      32.226  25.241  -2.827  1.00  9.99
ATOM     53  C   PRO    22      31.976  23.761  -2.650  1.00  9.99
ATOM     54  O   PRO    22      32.296  22.969  -3.533  1.00  9.99
ATOM     55  CB  PRO    22      33.713  25.571  -2.695  1.00  9.99
ATOM     56  N   GLU    23      31.371  23.373  -1.529  1.00  9.99
ATOM     57  CA  GLU    23      31.104  21.946  -1.276  1.00  9.99
ATOM     58  C   GLU    23      30.009  21.401  -2.162  1.00  9.99
ATOM     59  O   GLU    23      29.922  20.185  -2.341  1.00  9.99
ATOM     60  CB  GLU    23      30.881  21.713   0.227  1.00  9.99
ATOM     61  N   ARG    24      29.216  22.288  -2.759  1.00  9.99
ATOM     62  CA  ARG    24      28.272  21.874  -3.803  1.00  9.99
ATOM     63  C   ARG    24      29.022  21.345  -5.013  1.00  9.99
ATOM     64  O   ARG    24      28.543  20.406  -5.666  1.00  9.99
ATOM     65  CB  ARG    24      27.385  23.052  -4.222  1.00  9.99
ATOM     66  N   TYR    25      30.168  21.950  -5.358  1.00  9.99
ATOM     67  CA  TYR    25      30.965  21.428  -6.450  1.00  9.99
ATOM     68  C   TYR    25      31.684  20.177  -6.095  1.00  9.99
ATOM     69  O   TYR    25      31.785  19.294  -6.932  1.00  9.99
ATOM     70  CB  TYR    25      31.980  22.438  -6.986  1.00  9.99
ATOM     71  N   TYR    26      32.201  20.079  -4.866  1.00  9.99
ATOM     72  CA  TYR    26      32.881  18.845  -4.471  1.00  9.99
ATOM     73  C   TYR    26      31.930  17.653  -4.432  1.00  9.99
ATOM     74  O   TYR    26      32.310  16.543  -4.801  1.00  9.99
ATOM     75  CB  TYR    26      33.532  19.004  -3.095  1.00  9.99
ATOM     76  N   LEU    27      30.704  17.868  -3.941  1.00  9.99
ATOM     77  CA  LEU    27      29.728  16.788  -3.889  1.00  9.99
ATOM     78  C   LEU    27      29.090  16.515  -5.246  1.00  9.99
ATOM     79  O   LEU    27      28.554  15.422  -5.476  1.00  9.99
ATOM     80  CB  LEU    27      28.619  17.072  -2.841  1.00  9.99
ATOM     81  N   LYS    28      29.103  17.515  -6.125  1.00  9.99
ATOM     82  CA  LYS    28      28.422  17.401  -7.418  1.00  9.99
ATOM     83  C   LYS    28      26.913  17.592  -7.388  1.00  9.99
ATOM     84  O   LYS    28      26.255  17.468  -8.435  1.00  9.99
ATOM     85  CB  LYS    28      28.765  16.027  -8.017  1.00  9.99
ATOM     86  N   SER    29      20.272  12.564  -0.100  1.00  9.99
ATOM     87  CA  SER    29      19.806  11.724   0.976  1.00  9.99
ATOM     88  C   SER    29      20.794  10.626   1.222  1.00  9.99
ATOM     89  O   SER    29      21.186   9.909   0.276  1.00  9.99
ATOM     90  CB  SER    29      18.441  11.131   0.647  1.00  9.99
ATOM     91  N   PHE    30      21.177  10.430   2.471  1.00  9.99
ATOM     92  CA  PHE    30      22.126   9.400   2.817  1.00  9.99
ATOM     93  C   PHE    30      21.522   8.460   3.846  1.00  9.99
ATOM     94  O   PHE    30      21.172   8.867   4.973  1.00  9.99
ATOM     95  CB  PHE    30      23.454  10.011   3.327  1.00  9.99
ATOM     96  N   GLN    31      21.366   7.206   3.457  1.00  9.99
ATOM     97  CA  GLN    31      20.883   6.157   4.345  1.00  9.99
ATOM     98  C   GLN    31      22.063   5.599   5.138  1.00  9.99
ATOM     99  O   GLN    31      23.094   5.235   4.567  1.00  9.99
ATOM    100  CB  GLN    31      20.202   5.060   3.538  1.00  9.99
ATOM    101  N   VAL    32      21.904   5.556   6.459  1.00  9.99
ATOM    102  CA  VAL    32      22.944   5.137   7.371  1.00  9.99
ATOM    103  C   VAL    32      22.418   4.013   8.243  1.00  9.99
ATOM    104  O   VAL    32      21.219   3.932   8.467  1.00  9.99
ATOM    105  CB  VAL    32      23.380   6.322   8.257  1.00  9.99
ATOM    106  N   ASP    33      23.291   3.129   8.735  1.00  9.99
ATOM    107  CA  ASP    33      22.848   2.058   9.625  1.00  9.99
ATOM    108  C   ASP    33      22.347   2.588  10.959  1.00  9.99
ATOM    109  O   ASP    33      22.732   3.675  11.405  1.00  9.99
ATOM    110  CB  ASP    33      24.111   1.198   9.826  1.00  9.99
ATOM    111  N   GLU    34      21.483   1.801  11.584  1.00  9.99
ATOM    112  CA  GLU    34      21.027   2.046  12.935  1.00  9.99
ATOM    113  C   GLU    34      22.200   2.445  13.838  1.00  9.99
ATOM    114  O   GLU    34      23.262   1.833  13.789  1.00  9.99
ATOM    115  CB  GLU    34      20.351   0.779  13.467  1.00  9.99
ATOM    116  N   GLY    35      21.987   3.489  14.638  1.00  9.99
ATOM    117  CA  GLY    35      22.982   3.940  15.602  1.00  9.99
ATOM    118  C   GLY    35      23.988   4.920  15.028  1.00  9.99
ATOM    119  O   GLY    35      24.921   5.355  15.725  1.00  9.99
ATOM    120  N   ILE    36      23.821   5.284  13.763  1.00  9.99
ATOM    121  CA  ILE    36      24.779   6.174  13.133  1.00  9.99
ATOM    122  C   ILE    36      24.924   7.471  13.869  1.00  9.99
ATOM    123  O   ILE    36      23.943   8.058  14.354  1.00  9.99
ATOM    124  CB  ILE    36      24.369   6.458  11.671  1.00  9.99
ATOM    125  N   THR    37      26.173   7.931  13.910  1.00  9.99
ATOM    126  CA  THR    37      26.542   9.187  14.534  1.00  9.99
ATOM    127  C   THR    37      27.031  10.183  13.487  1.00  9.99
ATOM    128  O   THR    37      27.358   9.818  12.346  1.00  9.99
ATOM    129  CB  THR    37      27.664   8.950  15.534  1.00  9.99
ATOM    130  N   VAL    38      27.140  11.452  13.863  1.00  9.99
ATOM    131  CA  VAL    38      27.696  12.466  12.966  1.00  9.99
ATOM    132  C   VAL    38      29.034  12.019  12.346  1.00  9.99
ATOM    133  O   VAL    38      29.250  12.157  11.121  1.00  9.99
ATOM    134  CB  VAL    38      27.811  13.827  13.685  1.00  9.99
ATOM    135  N   GLN    39      29.933  11.445  13.159  1.00  9.99
ATOM    136  CA  GLN    39      31.217  11.015  12.601  1.00  9.99
ATOM    137  C   GLN    39      31.053   9.951  11.484  1.00  9.99
ATOM    138  O   GLN    39      31.851   9.916  10.533  1.00  9.99
ATOM    139  CB  GLN    39      32.163  10.529  13.714  1.00  9.99
ATOM    140  N   THR    40      30.032   9.095  11.606  1.00  9.99
ATOM    141  CA  THR    40      29.795   8.057  10.577  1.00  9.99
ATOM    142  C   THR    40      29.304   8.698   9.315  1.00  9.99
ATOM    143  O   THR    40      29.691   8.275   8.217  1.00  9.99
ATOM    144  CB  THR    40      28.793   7.011  11.058  1.00  9.99
ATOM    145  N   ALA    41      28.476   9.721   9.445  1.00  9.99
ATOM    146  CA  ALA    41      28.013  10.454   8.267  1.00  9.99
ATOM    147  C   ALA    41      29.174  11.151   7.548  1.00  9.99
ATOM    148  O   ALA    41      29.261  11.084   6.308  1.00  9.99
ATOM    149  CB  ALA    41      26.957  11.477   8.677  1.00  9.99
ATOM    150  N   ILE    42      30.084  11.764   8.305  1.00  9.99
ATOM    151  CA  ILE    42      31.249  12.398   7.700  1.00  9.99
ATOM    152  C   ILE    42      32.063  11.366   6.925  1.00  9.99
ATOM    153  O   ILE    42      32.499  11.627   5.774  1.00  9.99
ATOM    154  CB  ILE    42      32.086  13.096   8.775  1.00  9.99
ATOM    155  N   THR    43      32.279  10.176   7.514  1.00  9.99
ATOM    156  CA  THR    43      32.995   9.137   6.765  1.00  9.99
ATOM    157  C   THR    43      32.291   8.703   5.501  1.00  9.99
ATOM    158  O   THR    43      32.961   8.416   4.485  1.00  9.99
ATOM    159  CB  THR    43      33.322   7.948   7.662  1.00  9.99
ATOM    160  N   GLN    44      30.968   8.651   5.531  1.00  9.99
ATOM    161  CA  GLN    44      30.219   8.270   4.348  1.00  9.99
ATOM    162  C   GLN    44      30.292   9.356   3.274  1.00  9.99
ATOM    163  O   GLN    44      30.385   9.020   2.088  1.00  9.99
ATOM    164  CB  GLN    44      28.759   7.934   4.711  1.00  9.99
ATOM    165  N   ILE    47      30.271  10.646   3.660  1.00  9.99
ATOM    166  CA  ILE    47      30.430  11.723   2.674  1.00  9.99
ATOM    167  C   ILE    47      31.774  11.577   1.958  1.00  9.99
ATOM    168  O   ILE    47      31.837  11.666   0.713  1.00  9.99
ATOM    169  CB  ILE    47      30.282  13.093   3.354  1.00  9.99
ATOM    170  N   LEU    48      32.820  11.306   2.733  1.00  9.99
ATOM    171  CA  LEU    48      34.162  11.107   2.174  1.00  9.99
ATOM    172  C   LEU    48      34.238   9.878   1.256  1.00  9.99
ATOM    173  O   LEU    48      34.970   9.900   0.239  1.00  9.99
ATOM    174  CB  LEU    48      35.192  11.002   3.293  1.00  9.99
ATOM    175  N   SER    49      33.494   8.828   1.592  1.00  9.99
ATOM    176  CA  SER    49      33.462   7.623   0.780  1.00  9.99
ATOM    177  C   SER    49      32.746   7.874  -0.545  1.00  9.99
ATOM    178  O   SER    49      33.160   7.349  -1.589  1.00  9.99
ATOM    179  CB  SER    49      32.767   6.499   1.552  1.00  9.99
ATOM    180  N   GLN    50      31.664   8.649  -0.524  1.00  9.99
ATOM    181  CA  GLN    50      30.911   8.919  -1.737  1.00  9.99
ATOM    182  C   GLN    50      31.606   9.927  -2.639  1.00  9.99
ATOM    183  O   GLN    50      31.449   9.909  -3.858  1.00  9.99
ATOM    184  CB  GLN    50      29.541   9.471  -1.376  1.00  9.99
ATOM    185  N   PHE    51      32.308  10.860  -2.012  1.00  9.99
ATOM    186  CA  PHE    51      32.869  12.006  -2.717  1.00  9.99
ATOM    187  C   PHE    51      34.298  12.193  -2.278  1.00  9.99
ATOM    188  O   PHE    51      34.581  12.934  -1.304  1.00  9.99
ATOM    189  CB  PHE    51      32.063  13.277  -2.399  1.00  9.99
ATOM    190  N   PRO    52      35.210  11.549  -3.006  1.00  9.99
ATOM    191  CA  PRO    52      36.603  11.453  -2.566  1.00  9.99
ATOM    192  C   PRO    52      37.293  12.797  -2.382  1.00  9.99
ATOM    193  O   PRO    52      38.254  12.879  -1.622  1.00  9.99
ATOM    194  CB  PRO    52      37.413  10.563  -3.500  1.00  9.99
ATOM    195  N   GLU    53      36.804  13.843  -3.044  1.00  9.99
ATOM    196  CA  GLU    53      37.428  15.175  -2.878  1.00  9.99
ATOM    197  C   GLU    53      37.279  15.699  -1.450  1.00  9.99
ATOM    198  O   GLU    53      38.032  16.591  -1.035  1.00  9.99
ATOM    199  CB  GLU    53      36.889  16.180  -3.892  1.00  9.99
ATOM    200  N   ILE    54      36.341  15.139  -0.668  1.00  9.99
ATOM    201  CA  ILE    54      36.207  15.534   0.733  1.00  9.99
ATOM    202  C   ILE    54      37.238  14.891   1.659  1.00  9.99
ATOM    203  O   ILE    54      37.369  15.296   2.822  1.00  9.99
ATOM    204  CB  ILE    54      34.808  15.188   1.282  1.00  9.99
ATOM    205  N   ASP    55      37.956  13.879   1.179  1.00  9.99
ATOM    206  CA  ASP    55      38.927  13.197   2.047  1.00  9.99
ATOM    207  C   ASP    55      39.996  14.169   2.543  1.00  9.99
ATOM    208  O   ASP    55      40.469  14.036   3.681  1.00  9.99
ATOM    209  CB  ASP    55      39.576  12.013   1.319  1.00  9.99
ATOM    210  N   LEU    56      40.335  15.143   1.697  1.00  9.99
ATOM    211  CA  LEU    56      41.419  16.109   1.923  1.00  9.99
ATOM    212  C   LEU    56      40.925  17.354   2.693  1.00  9.99
ATOM    213  O   LEU    56      41.726  18.243   3.048  1.00  9.99
ATOM    214  CB  LEU    56      42.014  16.528   0.565  1.00  9.99
TER
END
