
#######################################################
#                                                     #
#                        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   45 (  223),  selected   45 , name T0363TS102_5-D1
# Molecule2: number of CA atoms   46 (  372),  selected   46 , name T0363_D1.pdb
# PARAMETERS: T0363TS102_5-D1.T0363_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

# WARNING! The change of the parameter DIST cutoff may give you better result.

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      N      11           -
LGA    Q      12      Q      12           #
LGA    I      13      I      13           -
LGA    N      14      N      14           -
LGA    I      15      I      15           -
LGA    E      16      E      16           -
LGA    I      17      I      17           #
LGA    A      18      -       -           -
LGA    Y      19      -       -           -
LGA    A      20      A      18           #
LGA    -       -      Y      19           -
LGA    F      21      A      20          3.628
LGA    P      22      F      21          3.674
LGA    -       -      P      22           -
LGA    E      23      E      23           #
LGA    R      24      R      24          4.772
LGA    Y      25      Y      25           #
LGA    Y      26      Y      26          2.973
LGA    L      27      L      27          4.670
LGA    K      28      K      28          3.539
LGA    S      29      S      29          0.701
LGA    F      30      F      30          3.955
LGA    Q      31      Q      31          2.964
LGA    V      32      -       -           -
LGA    D      33      -       -           -
LGA    E      34      -       -           -
LGA    G      35      V      32           #
LGA    I      36      D      33          3.577
LGA    T      37      E      34          2.558
LGA    -       -      G      35           -
LGA    V      38      I      36          3.434
LGA    Q      39      T      37          4.613
LGA    -       -      V      38           -
LGA    -       -      Q      39           -
LGA    T      40      T      40          1.098
LGA    A      41      A      41          3.064
LGA    I      42      I      42          4.402
LGA    -       -      T      43           -
LGA    -       -      Q      44           -
LGA    -       -      S      45           -
LGA    -       -      G      46           -
LGA    -       -      I      47           -
LGA    T      43      L      48          1.798
LGA    Q      44      S      49          3.126
LGA    S      45      Q      50          3.799
LGA    G      46      F      51          2.170
LGA    I      47      P      52          3.131
LGA    L      48      E      53          3.155
LGA    S      49      I      54          3.920
LGA    Q      50      -       -           -
LGA    F      51      D      55           #
LGA    P      52      L      56           #
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)   45   46    5.0     23    3.41    43.48     29.502     0.656

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.267750 * X  +  -0.037152 * Y  +  -0.962772 * Z  +  51.402405
  Y_new =   0.940335 * X  +   0.227825 * Y  +   0.252718 * Z  + -78.056404
  Z_new =   0.209954 * X  +  -0.972993 * Y  +   0.095936 * Z  +  31.478067 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.472515    1.669077  [ DEG:   -84.3689     95.6311 ]
  Theta =  -0.211528   -2.930065  [ DEG:   -12.1197   -167.8803 ]
  Phi   =   1.293399   -1.848194  [ DEG:    74.1063   -105.8937 ]
 
# 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: T0363TS102_5-D1                               
REMARK     2: T0363_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0363TS102_5-D1.T0363_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   45   46   5.0   23   3.41   43.48  29.502
REMARK  ---------------------------------------------------------- 
MOLECULE T0363TS102_5-D1
PFRMAT TS
TARGET T0363
MODEL 5
PARENT 2d1p_A
ATOM     16  N   GLN    12      23.548  -0.062   9.189  1.00  1.00
ATOM     17  CA  GLN    12      24.591   0.850   9.650  1.00  1.00
ATOM     18  C   GLN    12      25.292   1.427   8.429  1.00  1.00
ATOM     19  O   GLN    12      25.929   0.698   7.671  1.00  1.00
ATOM     20  CB  GLN    12      25.621   0.119  10.518  1.00  1.00
ATOM     21  N   ILE    13      25.181   2.741   8.254  1.00  1.00
ATOM     22  CA  ILE    13      25.793   3.419   7.112  1.00  1.00
ATOM     23  C   ILE    13      27.045   4.231   7.414  1.00  1.00
ATOM     24  O   ILE    13      27.201   4.804   8.487  1.00  1.00
ATOM     25  CB  ILE    13      24.778   4.360   6.453  1.00  1.00
ATOM     26  N   ASN    14      27.931   4.266   6.432  1.00  1.00
ATOM     27  CA  ASN    14      29.159   5.040   6.492  1.00  1.00
ATOM     28  C   ASN    14      29.153   5.781   5.156  1.00  1.00
ATOM     29  O   ASN    14      29.012   5.157   4.108  1.00  1.00
ATOM     30  CB  ASN    14      30.366   4.122   6.574  1.00  1.00
ATOM     31  N   ILE    15      29.281   7.102   5.188  1.00  1.00
ATOM     32  CA  ILE    15      29.294   7.884   3.951  1.00  1.00
ATOM     33  C   ILE    15      30.677   8.474   3.722  1.00  1.00
ATOM     34  O   ILE    15      31.326   8.936   4.663  1.00  1.00
ATOM     35  CB  ILE    15      28.270   9.035   4.003  1.00  1.00
ATOM     36  N   GLU    16      31.131   8.442   2.472  1.00  1.00
ATOM     37  CA  GLU    16      32.430   8.997   2.122  1.00  1.00
ATOM     38  C   GLU    16      32.218  10.215   1.220  1.00  1.00
ATOM     39  O   GLU    16      31.600  10.114   0.160  1.00  1.00
ATOM     40  CB  GLU    16      33.307   7.962   1.382  1.00  1.00
ATOM     41  N   ILE    17      32.721  11.367   1.654  1.00  1.00
ATOM     42  CA  ILE    17      32.580  12.602   0.888  1.00  1.00
ATOM     43  C   ILE    17      33.937  12.986   0.318  1.00  1.00
ATOM     44  O   ILE    17      34.915  13.116   1.054  1.00  1.00
ATOM     45  CB  ILE    17      32.031  13.736   1.782  1.00  1.00
ATOM     46  N   ALA    18      33.998  13.151  -0.997  1.00  1.00
ATOM     47  CA  ALA    18      35.249  13.491  -1.652  1.00  1.00
ATOM     48  C   ALA    18      35.206  14.828  -2.384  1.00  1.00
ATOM     49  O   ALA    18      36.174  15.186  -3.060  1.00  1.00
ATOM     50  CB  ALA    18      35.673  12.385  -2.662  1.00  1.00
ATOM     51  N   TYR    19      34.095  15.556  -2.252  1.00  1.00
ATOM     52  CA  TYR    19      33.957  16.858  -2.899  1.00  1.00
ATOM     53  C   TYR    19      33.870  18.018  -1.905  1.00  1.00
ATOM     54  O   TYR    19      33.453  17.826  -0.756  1.00  1.00
ATOM     55  CB  TYR    19      32.652  16.842  -3.718  1.00  1.00
ATOM     56  N   ALA    20      32.780  21.782  -0.014  1.00  1.00
ATOM     57  CA  ALA    20      31.519  22.333   0.484  1.00  1.00
ATOM     58  C   ALA    20      30.896  23.125  -0.674  1.00  1.00
ATOM     59  O   ALA    20      29.705  23.015  -0.938  1.00  1.00
ATOM     60  CB  ALA    20      31.788  23.240   1.682  1.00  1.00
ATOM     61  N   PHE    21      31.721  23.907  -1.366  1.00  1.00
ATOM     62  CA  PHE    21      31.282  24.692  -2.526  1.00  1.00
ATOM     63  C   PHE    21      32.245  24.426  -3.679  1.00  1.00
ATOM     64  O   PHE    21      33.468  24.474  -3.497  1.00  1.00
ATOM     65  CB  PHE    21      31.288  26.198  -2.238  1.00  1.00
ATOM     66  N   PRO    22      31.696  24.160  -4.859  1.00  1.00
ATOM     67  CA  PRO    22      32.532  23.877  -6.012  1.00  1.00
ATOM     68  C   PRO    22      31.929  22.803  -6.898  1.00  1.00
ATOM     69  O   PRO    22      31.965  22.911  -8.126  1.00  1.00
ATOM     70  CB  PRO    22      33.894  23.370  -5.504  1.00  1.00
ATOM     71  N   GLU    23      31.413  21.746  -6.268  1.00  1.00
ATOM     72  CA  GLU    23      30.751  20.642  -6.967  1.00  1.00
ATOM     73  C   GLU    23      29.546  20.292  -6.102  1.00  1.00
ATOM     74  O   GLU    23      29.421  20.790  -4.980  1.00  1.00
ATOM     75  CB  GLU    23      31.640  19.373  -7.114  1.00  1.00
ATOM     76  N   ARG    24      28.668  19.435  -6.610  1.00  1.00
ATOM     77  CA  ARG    24      27.458  19.057  -5.888  1.00  1.00
ATOM     78  C   ARG    24      27.601  17.820  -4.997  1.00  1.00
ATOM     79  O   ARG    24      26.718  17.531  -4.188  1.00  1.00
ATOM     80  CB  ARG    24      26.326  18.822  -6.897  1.00  1.00
ATOM     81  N   TYR    25      28.706  17.094  -5.135  1.00  1.00
ATOM     82  CA  TYR    25      28.900  15.865  -4.362  1.00  1.00
ATOM     83  C   TYR    25      28.612  15.952  -2.861  1.00  1.00
ATOM     84  O   TYR    25      27.855  15.141  -2.330  1.00  1.00
ATOM     85  CB  TYR    25      30.318  15.322  -4.590  1.00  1.00
ATOM     86  N   TYR    26      29.203  16.928  -2.175  1.00  1.00
ATOM     87  CA  TYR    26      28.999  17.059  -0.732  1.00  1.00
ATOM     88  C   TYR    26      27.544  17.356  -0.398  1.00  1.00
ATOM     89  O   TYR    26      27.025  16.877   0.614  1.00  1.00
ATOM     90  CB  TYR    26      29.908  18.141  -0.162  1.00  1.00
ATOM     91  N   LEU    27      24.919  15.050   1.699  1.00  1.00
ATOM     92  CA  LEU    27      24.193  15.579   2.855  1.00  1.00
ATOM     93  C   LEU    27      22.701  15.260   2.743  1.00  1.00
ATOM     94  O   LEU    27      22.063  14.881   3.728  1.00  1.00
ATOM     95  CB  LEU    27      24.378  17.094   2.977  1.00  1.00
ATOM     96  N   LYS    28      22.147  15.419   1.541  1.00  1.00
ATOM     97  CA  LYS    28      20.731  15.132   1.319  1.00  1.00
ATOM     98  C   LYS    28      20.489  13.627   1.433  1.00  1.00
ATOM     99  O   LYS    28      19.417  13.189   1.838  1.00  1.00
ATOM    100  CB  LYS    28      20.283  15.654  -0.056  1.00  1.00
ATOM    101  N   SER    29      21.500  12.841   1.084  1.00  1.00
ATOM    102  CA  SER    29      21.402  11.392   1.183  1.00  1.00
ATOM    103  C   SER    29      21.396  10.994   2.664  1.00  1.00
ATOM    104  O   SER    29      20.634  10.116   3.079  1.00  1.00
ATOM    105  CB  SER    29      22.596  10.728   0.486  1.00  1.00
ATOM    106  N   PHE    30      22.253  11.645   3.449  1.00  1.00
ATOM    107  CA  PHE    30      22.357  11.370   4.880  1.00  1.00
ATOM    108  C   PHE    30      21.036  11.636   5.588  1.00  1.00
ATOM    109  O   PHE    30      20.591  10.832   6.410  1.00  1.00
ATOM    110  CB  PHE    30      23.464  12.221   5.502  1.00  1.00
ATOM    111  N   GLN    31      18.462   8.847   4.588  1.00  1.00
ATOM    112  CA  GLN    31      18.640   7.540   5.197  1.00  1.00
ATOM    113  C   GLN    31      18.251   7.589   6.675  1.00  1.00
ATOM    114  O   GLN    31      17.615   6.669   7.182  1.00  1.00
ATOM    115  CB  GLN    31      20.086   7.048   5.023  1.00  1.00
ATOM    116  N   VAL    32      18.614   8.669   7.362  1.00  1.00
ATOM    117  CA  VAL    32      18.274   8.802   8.776  1.00  1.00
ATOM    118  C   VAL    32      16.764   8.896   8.932  1.00  1.00
ATOM    119  O   VAL    32      16.189   8.305   9.844  1.00  1.00
ATOM    120  CB  VAL    32      18.929  10.046   9.406  1.00  1.00
ATOM    121  N   ASP    33      16.126   9.628   8.025  1.00  1.00
ATOM    122  CA  ASP    33      14.679   9.776   8.048  1.00  1.00
ATOM    123  C   ASP    33      13.997   8.438   7.750  1.00  1.00
ATOM    124  O   ASP    33      12.871   8.204   8.188  1.00  1.00
ATOM    125  CB  ASP    33      14.245  10.823   7.027  1.00  1.00
ATOM    126  N   GLU    34      14.675   7.562   7.012  1.00  1.00
ATOM    127  CA  GLU    34      14.093   6.263   6.677  1.00  1.00
ATOM    128  C   GLU    34      14.390   5.186   7.727  1.00  1.00
ATOM    129  O   GLU    34      14.259   3.995   7.458  1.00  1.00
ATOM    130  CB  GLU    34      14.577   5.804   5.298  1.00  1.00
ATOM    131  N   GLY    35      14.799   5.615   8.918  1.00  1.00
ATOM    132  CA  GLY    35      15.074   4.684   9.999  1.00  1.00
ATOM    133  C   GLY    35      16.446   4.039  10.081  1.00  1.00
ATOM    134  O   GLY    35      16.686   3.224  10.974  1.00  1.00
ATOM    135  N   ILE    36      17.353   4.385   9.176  1.00  1.00
ATOM    136  CA  ILE    36      18.683   3.785   9.211  1.00  1.00
ATOM    137  C   ILE    36      19.635   4.581  10.091  1.00  1.00
ATOM    138  O   ILE    36      19.342   5.712  10.481  1.00  1.00
ATOM    139  CB  ILE    36      19.238   3.662   7.795  1.00  1.00
ATOM    140  N   THR    37      20.772   3.982  10.412  1.00  1.00
ATOM    141  CA  THR    37      21.735   4.652  11.259  1.00  1.00
ATOM    142  C   THR    37      22.957   5.107  10.485  1.00  1.00
ATOM    143  O   THR    37      23.573   4.334   9.752  1.00  1.00
ATOM    144  CB  THR    37      22.157   3.733  12.407  1.00  1.00
ATOM    145  N   VAL    38      23.293   6.379  10.651  1.00  1.00
ATOM    146  CA  VAL    38      24.455   6.949   9.994  1.00  1.00
ATOM    147  C   VAL    38      25.608   6.920  10.984  1.00  1.00
ATOM    148  O   VAL    38      25.769   7.832  11.792  1.00  1.00
ATOM    149  CB  VAL    38      24.176   8.390   9.560  1.00  1.00
ATOM    150  N   GLN    39      26.396   5.855  10.915  1.00  1.00
ATOM    151  CA  GLN    39      27.538   5.669  11.796  1.00  1.00
ATOM    152  C   GLN    39      28.514   6.840  11.698  1.00  1.00
ATOM    153  O   GLN    39      28.891   7.431  12.710  1.00  1.00
ATOM    154  CB  GLN    39      28.247   4.359  11.439  1.00  1.00
ATOM    155  N   THR    40      28.914   7.185  10.478  1.00  1.00
ATOM    156  CA  THR    40      29.852   8.286  10.300  1.00  1.00
ATOM    157  C   THR    40      29.975   8.734   8.857  1.00  1.00
ATOM    158  O   THR    40      29.527   8.055   7.933  1.00  1.00
ATOM    159  CB  THR    40      31.241   7.879  10.796  1.00  1.00
ATOM    160  N   ALA    41      30.585   9.898   8.684  1.00  1.00
ATOM    161  CA  ALA    41      30.831  10.459   7.370  1.00  1.00
ATOM    162  C   ALA    41      32.332  10.713   7.339  1.00  1.00
ATOM    163  O   ALA    41      32.868  11.409   8.197  1.00  1.00
ATOM    164  CB  ALA    41      30.072  11.795   7.164  1.00  1.00
ATOM    165  N   ILE    42      33.018  10.122   6.372  1.00  1.00
ATOM    166  CA  ILE    42      34.458  10.312   6.257  1.00  1.00
ATOM    167  C   ILE    42      34.744  11.299   5.128  1.00  1.00
ATOM    168  O   ILE    42      34.315  11.102   3.986  1.00  1.00
ATOM    169  CB  ILE    42      35.162   8.983   5.961  1.00  1.00
ATOM    170  N   THR    43      35.460  12.366   5.454  1.00  1.00
ATOM    171  CA  THR    43      35.801  13.389   4.477  1.00  1.00
ATOM    172  C   THR    43      37.249  13.201   4.042  1.00  1.00
ATOM    173  O   THR    43      38.172  13.276   4.855  1.00  1.00
ATOM    174  CB  THR    43      35.591  14.773   5.092  1.00  1.00
ATOM    175  N   GLN    44      40.180  13.675   0.416  1.00  1.00
ATOM    176  CA  GLN    44      40.436  14.419  -0.820  1.00  1.00
ATOM    177  C   GLN    44      39.841  15.829  -0.654  1.00  1.00
ATOM    178  O   GLN    44      39.952  16.409   0.429  1.00  1.00
ATOM    179  CB  GLN    44      39.797  13.684  -2.006  1.00  1.00
ATOM    180  N   SER    45      39.219  16.379  -1.703  1.00  1.00
ATOM    181  CA  SER    45      38.615  17.710  -1.607  1.00  1.00
ATOM    182  C   SER    45      37.486  17.749  -0.567  1.00  1.00
ATOM    183  O   SER    45      37.011  18.822  -0.187  1.00  1.00
ATOM    184  CB  SER    45      38.083  18.182  -2.976  1.00  1.00
ATOM    185  N   GLY    46      37.056  16.581  -0.102  1.00  1.00
ATOM    186  CA  GLY    46      36.012  16.539   0.907  1.00  1.00
ATOM    187  C   GLY    46      36.384  17.249   2.207  1.00  1.00
ATOM    188  O   GLY    46      35.500  17.672   2.960  1.00  1.00
ATOM    189  N   ILE    47      37.680  17.389   2.483  1.00  1.00
ATOM    190  CA  ILE    47      38.119  18.044   3.717  1.00  1.00
ATOM    191  C   ILE    47      37.673  19.510   3.823  1.00  1.00
ATOM    192  O   ILE    47      37.546  20.039   4.925  1.00  1.00
ATOM    193  CB  ILE    47      39.669  17.961   3.895  1.00  1.00
ATOM    194  N   LEU    48      37.424  20.159   2.688  1.00  1.00
ATOM    195  CA  LEU    48      36.980  21.555   2.695  1.00  1.00
ATOM    196  C   LEU    48      35.641  21.727   3.407  1.00  1.00
ATOM    197  O   LEU    48      35.285  22.837   3.822  1.00  1.00
ATOM    198  CB  LEU    48      36.884  22.101   1.269  1.00  1.00
ATOM    199  N   SER    49      34.898  20.633   3.556  1.00  1.00
ATOM    200  CA  SER    49      33.613  20.694   4.248  1.00  1.00
ATOM    201  C   SER    49      33.825  21.055   5.727  1.00  1.00
ATOM    202  O   SER    49      32.883  21.450   6.418  1.00  1.00
ATOM    203  CB  SER    49      32.875  19.349   4.124  1.00  1.00
ATOM    204  N   GLN    50      35.066  20.939   6.202  1.00  1.00
ATOM    205  CA  GLN    50      35.370  21.272   7.597  1.00  1.00
ATOM    206  C   GLN    50      36.065  22.636   7.736  1.00  1.00
ATOM    207  O   GLN    50      36.569  22.962   8.808  1.00  1.00
ATOM    208  CB  GLN    50      36.246  20.162   8.236  1.00  1.00
ATOM    209  N   PHE    51      36.107  23.420   6.658  1.00  1.00
ATOM    210  CA  PHE    51      36.741  24.738   6.716  1.00  1.00
ATOM    211  C   PHE    51      35.775  25.730   7.360  1.00  1.00
ATOM    212  O   PHE    51      34.806  26.166   6.736  1.00  1.00
ATOM    213  CB  PHE    51      37.126  25.241   5.322  1.00  1.00
ATOM    214  N   PRO    52      36.050  26.066   8.616  1.00  1.00
ATOM    215  CA  PRO    52      35.230  26.980   9.406  1.00  1.00
ATOM    216  C   PRO    52      35.055  28.366   8.773  1.00  1.00
ATOM    217  O   PRO    52      34.024  29.003   8.952  1.00  1.00
ATOM    218  CB  PRO    52      35.864  27.117  10.800  1.00  1.00
ATOM    219  N   GLU    53      36.052  28.825   8.025  1.00  1.00
ATOM    220  CA  GLU    53      35.991  30.154   7.424  1.00  1.00
ATOM    221  C   GLU    53      35.062  30.262   6.208  1.00  1.00
ATOM    222  O   GLU    53      34.854  31.365   5.684  1.00  1.00
ATOM    223  CB  GLU    53      37.403  30.615   7.043  1.00  1.00
ATOM    224  N   ILE    54      34.502  29.132   5.772  1.00  1.00
ATOM    225  CA  ILE    54      33.597  29.112   4.621  1.00  1.00
ATOM    226  C   ILE    54      32.476  30.133   4.840  1.00  1.00
ATOM    227  O   ILE    54      31.777  30.089   5.847  1.00  1.00
ATOM    228  CB  ILE    54      33.020  27.696   4.421  1.00  1.00
ATOM    229  N   ASP    55      32.300  31.053   3.893  1.00  1.00
ATOM    230  CA  ASP    55      31.292  32.099   4.051  1.00  1.00
ATOM    231  C   ASP    55      30.345  32.255   2.877  1.00  1.00
ATOM    232  O   ASP    55      30.554  33.100   2.012  1.00  1.00
ATOM    233  CB  ASP    55      31.980  33.445   4.305  1.00  1.00
ATOM    234  N   LEU    56      29.282  31.446   2.834  1.00  1.00
ATOM    235  CA  LEU    56      28.328  31.551   1.728  1.00  1.00
ATOM    236  C   LEU    56      27.470  32.808   1.887  1.00  1.00
ATOM    237  O   LEU    56      27.412  33.392   2.970  1.00  1.00
ATOM    238  CB  LEU    56      27.501  30.278   1.876  1.00  1.00
TER
END
