
#######################################################
#                                                     #
#                        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_5-D1
# Molecule2: number of CA atoms   46 (  372),  selected   46 , name T0363_D1.pdb
# PARAMETERS: T0363TS239_5-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           -
LGA    Q      12      I      13          2.538
LGA    I      13      N      14          1.977
LGA    N      14      I      15          2.090
LGA    I      15      E      16          0.701
LGA    E      16      I      17          3.842
LGA    I      17      A      18          1.330
LGA    A      18      -       -           -
LGA    Y      19      -       -           -
LGA    A      20      -       -           -
LGA    F      21      Y      19          2.325
LGA    P      22      A      20          2.414
LGA    E      23      F      21          1.841
LGA    R      24      P      22           #
LGA    -       -      E      23           -
LGA    -       -      R      24           -
LGA    Y      25      Y      25           #
LGA    Y      26      Y      26          3.232
LGA    L      27      -       -           -
LGA    K      28      L      27          2.419
LGA    S      29      K      28          3.271
LGA    F      30      S      29          1.688
LGA    Q      31      F      30          2.053
LGA    V      32      Q      31          2.726
LGA    D      33      V      32          1.851
LGA    E      34      D      33          2.322
LGA    -       -      E      34           -
LGA    G      35      G      35          5.016
LGA    I      36      I      36          2.852
LGA    T      37      T      37          1.339
LGA    V      38      V      38          1.201
LGA    Q      39      Q      39          1.522
LGA    T      40      T      40          1.462
LGA    A      41      A      41          1.355
LGA    I      42      I      42          1.770
LGA    T      43      T      43          1.584
LGA    Q      44      Q      44          1.165
LGA    I      47      S      45          2.078
LGA    L      48      G      46          4.188
LGA    S      49      -       -           -
LGA    Q      50      I      47          5.438
LGA    F      51      L      48          5.855
LGA    P      52      S      49          2.349
LGA    E      53      Q      50          1.749
LGA    I      54      F      51          3.933
LGA    D      55      P      52          4.135
LGA    -       -      E      53           -
LGA    L      56      I      54          4.113
LGA    -       -      D      55           -
LGA    -       -      L      56           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   43   46    5.0     36    2.84    30.56     51.616     1.225

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.671613 * X  +   0.740116 * Y  +   0.034119 * Z  +  14.545582
  Y_new =  -0.326537 * X  +  -0.337022 * Y  +   0.883057 * Z  +  31.283585
  Z_new =   0.665064 * X  +   0.581931 * Y  +   0.468024 * Z  + -21.742374 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.893463   -2.248129  [ DEG:    51.1917   -128.8083 ]
  Theta =  -0.727579   -2.414013  [ DEG:   -41.6872   -138.3128 ]
  Phi   =  -2.689047    0.452546  [ DEG:  -154.0710     25.9290 ]
 
# 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_5-D1                               
REMARK     2: T0363_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0363TS239_5-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   2.84   30.56  51.616
REMARK  ---------------------------------------------------------- 
MOLECULE T0363TS239_5-D1
PFRMAT TS
TARGET T0363
MODEL 5
PARENT 1fm0_D
ATOM      1  N   GLN    12      15.751   5.496   6.196  1.00  9.99
ATOM      2  CA  GLN    12      17.130   5.981   5.896  1.00  9.99
ATOM      3  C   GLN    12      17.418   7.253   6.672  1.00  9.99
ATOM      4  O   GLN    12      16.523   7.782   7.330  1.00  9.99
ATOM      5  CB  GLN    12      17.277   6.317   4.408  1.00  9.99
ATOM      6  N   ILE    13      18.684   7.680   6.660  1.00  9.99
ATOM      7  CA  ILE    13      19.038   9.035   7.115  1.00  9.99
ATOM      8  C   ILE    13      19.314  10.052   5.955  1.00  9.99
ATOM      9  O   ILE    13      20.106   9.766   5.045  1.00  9.99
ATOM     10  CB  ILE    13      20.198   8.992   8.135  1.00  9.99
ATOM     11  N   ASN    14      18.627  11.225   6.009  1.00  9.99
ATOM     12  CA  ASN    14      18.756  12.323   5.004  1.00  9.99
ATOM     13  C   ASN    14      19.840  13.300   5.477  1.00  9.99
ATOM     14  O   ASN    14      19.795  13.742   6.634  1.00  9.99
ATOM     15  CB  ASN    14      17.441  13.102   4.800  1.00  9.99
ATOM     16  N   ILE    15      20.795  13.607   4.594  1.00  9.99
ATOM     17  CA  ILE    15      21.938  14.511   4.886  1.00  9.99
ATOM     18  C   ILE    15      21.902  15.727   3.949  1.00  9.99
ATOM     19  O   ILE    15      21.856  15.582   2.718  1.00  9.99
ATOM     20  CB  ILE    15      23.311  13.785   4.749  1.00  9.99
ATOM     21  N   GLU    16      21.889  16.920   4.555  1.00  9.99
ATOM     22  CA  GLU    16      21.875  18.217   3.864  1.00  9.99
ATOM     23  C   GLU    16      23.207  18.974   4.046  1.00  9.99
ATOM     24  O   GLU    16      23.858  18.845   5.082  1.00  9.99
ATOM     25  CB  GLU    16      20.735  19.108   4.389  1.00  9.99
ATOM     26  N   ILE    17      23.573  19.771   3.030  1.00  9.99
ATOM     27  CA  ILE    17      24.812  20.572   3.021  1.00  9.99
ATOM     28  C   ILE    17      24.513  22.043   2.673  1.00  9.99
ATOM     29  O   ILE    17      23.586  22.315   1.895  1.00  9.99
ATOM     30  CB  ILE    17      25.812  19.997   2.003  1.00  9.99
ATOM     31  N   ALA    18      25.308  22.978   3.212  1.00  9.99
ATOM     32  CA  ALA    18      25.132  24.423   2.963  1.00  9.99
ATOM     33  C   ALA    18      26.441  25.173   2.682  1.00  9.99
ATOM     34  O   ALA    18      27.531  24.737   3.086  1.00  9.99
ATOM     35  CB  ALA    18      24.368  25.080   4.136  1.00  9.99
ATOM     36  N   TYR    19      26.320  26.292   1.957  1.00  9.99
ATOM     37  CA  TYR    19      27.416  27.228   1.683  1.00  9.99
ATOM     38  C   TYR    19      28.667  26.540   1.092  1.00  9.99
ATOM     39  O   TYR    19      28.528  25.737   0.163  1.00  9.99
ATOM     40  CB  TYR    19      27.721  28.082   2.925  1.00  9.99
ATOM     41  N   ALA    20      29.866  26.835   1.583  1.00  9.99
ATOM     42  CA  ALA    20      31.102  26.247   1.022  1.00  9.99
ATOM     43  C   ALA    20      31.100  24.721   1.056  1.00  9.99
ATOM     44  O   ALA    20      31.723  24.072   0.197  1.00  9.99
ATOM     45  CB  ALA    20      32.348  26.741   1.782  1.00  9.99
ATOM     46  N   PHE    21      30.495  24.137   2.098  1.00  9.99
ATOM     47  CA  PHE    21      30.434  22.681   2.208  1.00  9.99
ATOM     48  C   PHE    21      29.653  22.093   1.020  1.00  9.99
ATOM     49  O   PHE    21      30.114  21.152   0.353  1.00  9.99
ATOM     50  CB  PHE    21      29.858  22.231   3.593  1.00  9.99
ATOM     51  N   PRO    22      28.462  22.650   0.768  1.00  9.99
ATOM     52  CA  PRO    22      27.620  22.272  -0.372  1.00  9.99
ATOM     53  C   PRO    22      28.354  22.388  -1.714  1.00  9.99
ATOM     54  O   PRO    22      28.279  21.481  -2.565  1.00  9.99
ATOM     55  CB  PRO    22      26.362  23.155  -0.379  1.00  9.99
ATOM     56  N   GLU    23      29.060  23.504  -1.899  1.00  9.99
ATOM     57  CA  GLU    23      29.808  23.752  -3.145  1.00  9.99
ATOM     58  C   GLU    23      30.888  22.678  -3.375  1.00  9.99
ATOM     59  O   GLU    23      31.010  22.143  -4.487  1.00  9.99
ATOM     60  CB  GLU    23      30.439  25.156  -3.137  1.00  9.99
ATOM     61  N   ARG    24      31.625  22.322  -2.327  1.00  9.99
ATOM     62  CA  ARG    24      32.714  21.352  -2.466  1.00  9.99
ATOM     63  C   ARG    24      32.206  19.907  -2.606  1.00  9.99
ATOM     64  O   ARG    24      32.726  19.129  -3.432  1.00  9.99
ATOM     65  CB  ARG    24      33.730  21.508  -1.326  1.00  9.99
ATOM     66  N   TYR    25      31.195  19.507  -1.828  1.00  9.99
ATOM     67  CA  TYR    25      30.695  18.124  -1.968  1.00  9.99
ATOM     68  C   TYR    25      29.973  17.925  -3.314  1.00  9.99
ATOM     69  O   TYR    25      29.924  16.808  -3.837  1.00  9.99
ATOM     70  CB  TYR    25      29.846  17.601  -0.771  1.00  9.99
ATOM     71  N   TYR    26      29.404  19.000  -3.874  1.00  9.99
ATOM     72  CA  TYR    26      28.798  18.918  -5.196  1.00  9.99
ATOM     73  C   TYR    26      27.353  18.467  -5.301  1.00  9.99
ATOM     74  O   TYR    26      26.884  18.153  -6.411  1.00  9.99
ATOM     75  CB  TYR    26      29.683  17.991  -6.046  1.00  9.99
ATOM     76  N   LEU    27      26.663  18.429  -4.165  1.00  9.99
ATOM     77  CA  LEU    27      25.247  18.089  -4.106  1.00  9.99
ATOM     78  C   LEU    27      24.640  18.824  -2.908  1.00  9.99
ATOM     79  O   LEU    27      25.347  19.131  -1.946  1.00  9.99
ATOM     80  CB  LEU    27      25.055  16.549  -4.020  1.00  9.99
ATOM     81  N   LYS    28      23.332  19.092  -2.959  1.00  9.99
ATOM     82  CA  LYS    28      22.622  19.768  -1.871  1.00  9.99
ATOM     83  C   LYS    28      22.118  18.801  -0.787  1.00  9.99
ATOM     84  O   LYS    28      21.885  19.218   0.371  1.00  9.99
ATOM     85  CB  LYS    28      21.392  20.528  -2.407  1.00  9.99
ATOM     86  N   SER    29      21.949  17.526  -1.147  1.00  9.99
ATOM     87  CA  SER    29      21.300  16.556  -0.265  1.00  9.99
ATOM     88  C   SER    29      21.550  15.139  -0.753  1.00  9.99
ATOM     89  O   SER    29      21.626  14.911  -1.970  1.00  9.99
ATOM     90  CB  SER    29      19.788  16.812  -0.223  1.00  9.99
ATOM     91  N   PHE    30      21.644  14.190   0.175  1.00  9.99
ATOM     92  CA  PHE    30      21.754  12.766  -0.183  1.00  9.99
ATOM     93  C   PHE    30      21.201  11.884   0.944  1.00  9.99
ATOM     94  O   PHE    30      20.913  12.360   2.042  1.00  9.99
ATOM     95  CB  PHE    30      23.203  12.402  -0.560  1.00  9.99
ATOM     96  N   GLN    31      21.013  10.599   0.661  1.00  9.99
ATOM     97  CA  GLN    31      20.483   9.640   1.637  1.00  9.99
ATOM     98  C   GLN    31      21.515   8.574   1.972  1.00  9.99
ATOM     99  O   GLN    31      22.280   8.160   1.093  1.00  9.99
ATOM    100  CB  GLN    31      19.252   8.929   1.051  1.00  9.99
ATOM    101  N   VAL    32      21.532   8.135   3.232  1.00  9.99
ATOM    102  CA  VAL    32      22.416   7.071   3.704  1.00  9.99
ATOM    103  C   VAL    32      21.626   6.070   4.576  1.00  9.99
ATOM    104  O   VAL    32      20.677   6.434   5.265  1.00  9.99
ATOM    105  CB  VAL    32      23.588   7.652   4.544  1.00  9.99
ATOM    106  N   ASP    33      21.978   4.787   4.539  1.00  9.99
ATOM    107  CA  ASP    33      21.317   3.823   5.425  1.00  9.99
ATOM    108  C   ASP    33      21.557   4.201   6.905  1.00  9.99
ATOM    109  O   ASP    33      22.506   4.922   7.231  1.00  9.99
ATOM    110  CB  ASP    33      21.814   2.436   5.157  1.00  9.99
ATOM    111  N   GLU    34      23.062   2.992   9.440  1.00  9.99
ATOM    112  CA  GLU    34      24.085   2.102   9.988  1.00  9.99
ATOM    113  C   GLU    34      25.237   2.827  10.678  1.00  9.99
ATOM    114  O   GLU    34      26.371   2.360  10.606  1.00  9.99
ATOM    115  CB  GLU    34      24.716   1.274   8.869  1.00  9.99
ATOM    116  N   GLY    35      24.976   3.963  11.315  1.00  9.99
ATOM    117  CA  GLY    35      26.037   4.684  12.017  1.00  9.99
ATOM    118  C   GLY    35      25.562   5.114  13.407  1.00  9.99
ATOM    119  O   GLY    35      24.484   5.690  13.540  1.00  9.99
ATOM    120  N   ILE    36      26.358   4.826  14.442  1.00  9.99
ATOM    121  CA  ILE    36      25.943   5.130  15.818  1.00  9.99
ATOM    122  C   ILE    36      25.824   6.624  16.175  1.00  9.99
ATOM    123  O   ILE    36      24.964   6.985  16.968  1.00  9.99
ATOM    124  CB  ILE    36      27.031   4.454  16.671  1.00  9.99
ATOM    125  N   THR    37      26.650   7.470  15.563  1.00  9.99
ATOM    126  CA  THR    37      26.707   8.902  15.891  1.00  9.99
ATOM    127  C   THR    37      26.928   9.786  14.668  1.00  9.99
ATOM    128  O   THR    37      27.273   9.303  13.583  1.00  9.99
ATOM    129  CB  THR    37      27.921   9.161  16.786  1.00  9.99
ATOM    130  N   VAL    38      26.736  11.095  14.866  1.00  9.99
ATOM    131  CA  VAL    38      27.051  12.089  13.837  1.00  9.99
ATOM    132  C   VAL    38      28.523  11.942  13.377  1.00  9.99
ATOM    133  O   VAL    38      28.830  12.013  12.180  1.00  9.99
ATOM    134  CB  VAL    38      26.776  13.526  14.375  1.00  9.99
ATOM    135  N   GLN    39      29.446  11.781  14.331  1.00  9.99
ATOM    136  CA  GLN    39      30.879  11.638  13.991  1.00  9.99
ATOM    137  C   GLN    39      31.162  10.421  13.100  1.00  9.99
ATOM    138  O   GLN    39      31.949  10.517  12.148  1.00  9.99
ATOM    139  CB  GLN    39      31.734  11.570  15.272  1.00  9.99
ATOM    140  N   THR    40      30.552   9.277  13.409  1.00  9.99
ATOM    141  CA  THR    40      30.728   8.083  12.569  1.00  9.99
ATOM    142  C   THR    40      30.223   8.326  11.138  1.00  9.99
ATOM    143  O   THR    40      30.861   7.902  10.173  1.00  9.99
ATOM    144  CB  THR    40      30.064   6.860  13.200  1.00  9.99
ATOM    145  N   ALA    41      29.071   9.005  11.012  1.00  9.99
ATOM    146  CA  ALA    41      28.554   9.392   9.687  1.00  9.99
ATOM    147  C   ALA    41      29.523  10.366   8.954  1.00  9.99
ATOM    148  O   ALA    41      29.806  10.190   7.768  1.00  9.99
ATOM    149  CB  ALA    41      27.152  10.009   9.828  1.00  9.99
ATOM    150  N   ILE    42      30.015  11.384   9.666  1.00  9.99
ATOM    151  CA  ILE    42      30.976  12.347   9.099  1.00  9.99
ATOM    152  C   ILE    42      32.211  11.618   8.530  1.00  9.99
ATOM    153  O   ILE    42      32.651  11.876   7.385  1.00  9.99
ATOM    154  CB  ILE    42      31.401  13.392  10.152  1.00  9.99
ATOM    155  N   THR    43      32.763  10.680   9.306  1.00  9.99
ATOM    156  CA  THR    43      33.960   9.919   8.863  1.00  9.99
ATOM    157  C   THR    43      33.647   9.083   7.597  1.00  9.99
ATOM    158  O   THR    43      34.454   9.005   6.674  1.00  9.99
ATOM    159  CB  THR    43      34.491   8.994   9.981  1.00  9.99
ATOM    160  N   GLN    44      32.492   8.412   7.582  1.00  9.99
ATOM    161  CA  GLN    44      32.080   7.629   6.409  1.00  9.99
ATOM    162  C   GLN    44      31.984   8.492   5.141  1.00  9.99
ATOM    163  O   GLN    44      32.481   8.104   4.067  1.00  9.99
ATOM    164  CB  GLN    44      30.728   6.937   6.680  1.00  9.99
ATOM    165  N   ILE    47      31.339   9.655   5.263  1.00  9.99
ATOM    166  CA  ILE    47      31.177  10.539   4.103  1.00  9.99
ATOM    167  C   ILE    47      32.527  11.141   3.648  1.00  9.99
ATOM    168  O   ILE    47      32.801  11.236   2.430  1.00  9.99
ATOM    169  CB  ILE    47      30.183  11.664   4.414  1.00  9.99
ATOM    170  N   LEU    48      33.382  11.533   4.605  1.00  9.99
ATOM    171  CA  LEU    48      34.712  12.065   4.272  1.00  9.99
ATOM    172  C   LEU    48      35.555  11.050   3.481  1.00  9.99
ATOM    173  O   LEU    48      36.409  11.431   2.663  1.00  9.99
ATOM    174  CB  LEU    48      35.458  12.516   5.540  1.00  9.99
ATOM    175  N   SER    49      35.320   9.756   3.712  1.00  9.99
ATOM    176  CA  SER    49      36.109   8.715   3.086  1.00  9.99
ATOM    177  C   SER    49      35.714   8.424   1.638  1.00  9.99
ATOM    178  O   SER    49      36.390   7.612   0.990  1.00  9.99
ATOM    179  CB  SER    49      36.050   7.444   3.928  1.00  9.99
ATOM    180  N   GLN    50      34.671   9.089   1.114  1.00  9.99
ATOM    181  CA  GLN    50      34.184   8.797  -0.251  1.00  9.99
ATOM    182  C   GLN    50      35.061   9.353  -1.370  1.00  9.99
ATOM    183  O   GLN    50      35.126   8.755  -2.459  1.00  9.99
ATOM    184  CB  GLN    50      32.726   9.253  -0.433  1.00  9.99
ATOM    185  N   PHE    51      35.727  10.483  -1.119  1.00  9.99
ATOM    186  CA  PHE    51      36.600  11.133  -2.104  1.00  9.99
ATOM    187  C   PHE    51      37.462  12.217  -1.477  1.00  9.99
ATOM    188  O   PHE    51      37.184  12.662  -0.372  1.00  9.99
ATOM    189  CB  PHE    51      35.807  11.756  -3.236  1.00  9.99
ATOM    190  N   PRO    52      38.474  12.699  -2.211  1.00  9.99
ATOM    191  CA  PRO    52      39.346  13.752  -1.707  1.00  9.99
ATOM    192  C   PRO    52      38.573  15.071  -1.502  1.00  9.99
ATOM    193  O   PRO    52      38.852  15.800  -0.550  1.00  9.99
ATOM    194  CB  PRO    52      40.546  14.008  -2.637  1.00  9.99
ATOM    195  N   GLU    53      37.608  15.371  -2.382  1.00  9.99
ATOM    196  CA  GLU    53      36.780  16.586  -2.236  1.00  9.99
ATOM    197  C   GLU    53      35.873  16.488  -1.003  1.00  9.99
ATOM    198  O   GLU    53      35.713  17.474  -0.280  1.00  9.99
ATOM    199  CB  GLU    53      35.916  16.853  -3.477  1.00  9.99
ATOM    200  N   ILE    54      35.250  15.323  -0.790  1.00  9.99
ATOM    201  CA  ILE    54      34.397  15.122   0.391  1.00  9.99
ATOM    202  C   ILE    54      35.226  15.212   1.692  1.00  9.99
ATOM    203  O   ILE    54      34.769  15.770   2.683  1.00  9.99
ATOM    204  CB  ILE    54      33.739  13.738   0.347  1.00  9.99
ATOM    205  N   ASP    55      36.466  14.698   1.669  1.00  9.99
ATOM    206  CA  ASP    55      37.341  14.794   2.852  1.00  9.99
ATOM    207  C   ASP    55      37.696  16.253   3.184  1.00  9.99
ATOM    208  O   ASP    55      37.660  16.669   4.345  1.00  9.99
ATOM    209  CB  ASP    55      38.628  13.967   2.650  1.00  9.99
ATOM    210  N   LEU    56      34.542  18.044   4.716  1.00  9.99
ATOM    211  CA  LEU    56      34.052  17.542   5.996  1.00  9.99
ATOM    212  C   LEU    56      35.096  17.318   7.097  1.00  9.99
ATOM    213  O   LEU    56      34.736  16.919   8.194  1.00  9.99
ATOM    214  CB  LEU    56      33.240  16.249   5.753  1.00  9.99
TER
END
