
#######################################################
#                                                     #
#                        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   46 (  232),  selected   46 , name T0363TS437_1-D1
# Molecule2: number of CA atoms   46 (  372),  selected   46 , name T0363_D1.pdb
# PARAMETERS: T0363TS437_1-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      -       -           -
LGA    I      13      -       -           -
LGA    N      14      -       -           -
LGA    I      15      -       -           -
LGA    E      16      -       -           -
LGA    I      17      -       -           -
LGA    A      18      -       -           -
LGA    Y      19      -       -           -
LGA    A      20      -       -           -
LGA    F      21      -       -           -
LGA    P      22      N      11           #
LGA    E      23      Q      12           #
LGA    R      24      I      13          1.465
LGA    Y      25      N      14          3.219
LGA    Y      26      I      15          1.768
LGA    L      27      E      16          1.148
LGA    -       -      I      17           -
LGA    -       -      A      18           -
LGA    -       -      Y      19           -
LGA    -       -      A      20           -
LGA    -       -      F      21           -
LGA    -       -      P      22           -
LGA    -       -      E      23           -
LGA    -       -      R      24           -
LGA    -       -      Y      25           -
LGA    -       -      Y      26           -
LGA    -       -      L      27           -
LGA    K      28      K      28          2.481
LGA    S      29      S      29          2.414
LGA    F      30      F      30          1.944
LGA    Q      31      Q      31          2.689
LGA    V      32      V      32          2.006
LGA    D      33      D      33          1.738
LGA    E      34      E      34          3.895
LGA    G      35      G      35          1.330
LGA    I      36      I      36          2.968
LGA    -       -      T      37           -
LGA    -       -      V      38           -
LGA    -       -      Q      39           -
LGA    T      37      T      40          4.768
LGA    V      38      A      41          1.500
LGA    Q      39      I      42          3.379
LGA    T      40      T      43          4.745
LGA    -       -      Q      44           -
LGA    -       -      S      45           -
LGA    -       -      G      46           -
LGA    A      41      I      47          1.267
LGA    I      42      L      48          3.446
LGA    -       -      S      49           -
LGA    -       -      Q      50           -
LGA    T      43      F      51          2.878
LGA    Q      44      P      52          2.223
LGA    S      45      E      53           #
LGA    G      46      I      54           #
LGA    I      47      D      55          2.302
LGA    L      48      L      56          3.318
LGA    S      49      -       -           -
LGA    Q      50      -       -           -
LGA    F      51      -       -           -
LGA    P      52      -       -           -
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)   46   46    5.0     23    2.76    52.17     33.935     0.805

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.503161 * X  +  -0.742419 * Y  +   0.442315 * Z  + -95.303276
  Y_new =  -0.836765 * X  +  -0.546465 * Y  +   0.034641 * Z  + 121.570068
  Z_new =   0.215991 * X  +  -0.387544 * Y  +  -0.896190 * Z  + -44.621048 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.733441    0.408151  [ DEG:  -156.6147     23.3853 ]
  Theta =  -0.217707   -2.923886  [ DEG:   -12.4737   -167.5263 ]
  Phi   =  -1.029409    2.112184  [ DEG:   -58.9808    121.0192 ]
 
# 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: T0363TS437_1-D1                               
REMARK     2: T0363_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0363TS437_1-D1.T0363_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   46   46   5.0   23   2.76   52.17  33.935
REMARK  ---------------------------------------------------------- 
MOLECULE T0363TS437_1-D1
PFRMAT TS
TARGET T0363
MODEL     1 REFINED
PARENT N/A
ATOM     88  N   ASN    11      25.558  20.977   4.581  1.00   .00
ATOM     89  CA  ASN    11      25.945  20.959   3.078  1.00   .00
ATOM     90  C   ASN    11      27.361  21.781   2.752  1.00   .00
ATOM     91  O   ASN    11      28.174  21.319   1.941  1.00   .00
ATOM     92  CB  ASN    11      24.716  21.521   2.304  1.00   .00
ATOM     96  N   GLN    12      27.614  22.975   3.459  1.00   .00
ATOM     97  CA  GLN    12      28.955  23.780   3.283  1.00   .00
ATOM     98  C   GLN    12      30.300  22.873   3.653  1.00   .00
ATOM     99  O   GLN    12      31.337  23.022   3.019  1.00   .00
ATOM    100  CB  GLN    12      28.824  25.038   4.175  1.00   .00
ATOM    105  N   ILE    13      30.181  21.924   4.662  1.00   .00
ATOM    106  CA  ILE    13      31.308  20.972   5.039  1.00   .00
ATOM    107  C   ILE    13      31.438  19.613   4.062  1.00   .00
ATOM    108  O   ILE    13      32.284  18.737   4.324  1.00   .00
ATOM    109  CB  ILE    13      30.956  20.546   6.510  1.00   .00
ATOM    113  N   ASN    14      30.539  19.465   2.987  1.00   .00
ATOM    114  CA  ASN    14      30.518  18.195   2.049  1.00   .00
ATOM    115  C   ASN    14      30.287  16.731   2.850  1.00   .00
ATOM    116  O   ASN    14      30.632  15.663   2.329  1.00   .00
ATOM    117  CB  ASN    14      31.759  18.242   1.105  1.00   .00
ATOM    121  N   ILE    15      29.680  16.777   4.094  1.00   .00
ATOM    122  CA  ILE    15      29.393  15.537   4.918  1.00   .00
ATOM    123  C   ILE    15      27.829  15.067   4.788  1.00   .00
ATOM    124  O   ILE    15      26.908  15.717   5.321  1.00   .00
ATOM    125  CB  ILE    15      29.800  15.894   6.394  1.00   .00
ATOM    129  N   GLU    16      27.576  13.916   4.079  1.00   .00
ATOM    130  CA  GLU    16      26.139  13.382   3.912  1.00   .00
ATOM    131  C   GLU    16      25.650  12.568   5.252  1.00   .00
ATOM    132  O   GLU    16      25.863  11.352   5.405  1.00   .00
ATOM    133  CB  GLU    16      26.137  12.513   2.624  1.00   .00
ATOM    138  N   ILE    17      25.008  13.316   6.217  1.00   .00
ATOM    139  CA  ILE    17      24.505  12.699   7.539  1.00   .00
ATOM    140  C   ILE    17      23.068  11.909   7.472  1.00   .00
ATOM    141  O   ILE    17      21.984  12.504   7.261  1.00   .00
ATOM    142  CB  ILE    17      24.455  13.892   8.574  1.00   .00
ATOM    146  N   ALA    18      23.111  10.562   7.694  1.00   .00
ATOM    147  CA  ALA    18      21.832   9.689   7.720  1.00   .00
ATOM    148  C   ALA    18      21.444   9.272   9.260  1.00   .00
ATOM    149  O   ALA    18      22.211   8.607   9.960  1.00   .00
ATOM    150  CB  ALA    18      22.114   8.461   6.824  1.00   .00
ATOM    151  N   TYR    19      20.257   9.718   9.744  1.00   .00
ATOM    152  CA  TYR    19      19.800   9.435  11.197  1.00   .00
ATOM    153  C   TYR    19      18.651   8.293  11.286  1.00   .00
ATOM    154  O   TYR    19      17.521   8.468  10.776  1.00   .00
ATOM    155  CB  TYR    19      19.317  10.824  11.735  1.00   .00
ATOM    163  N   ALA    20      18.983   7.136  11.953  1.00   .00
ATOM    164  CA  ALA    20      18.004   5.972  12.112  1.00   .00
ATOM    165  C   ALA    20      17.385   5.803  13.620  1.00   .00
ATOM    166  O   ALA    20      18.073   5.472  14.598  1.00   .00
ATOM    167  CB  ALA    20      18.766   4.700  11.697  1.00   .00
ATOM    168  N   PHE    21      16.045   5.996  13.711  1.00   .00
ATOM    169  CA  PHE    21      15.254   5.762  15.041  1.00   .00
ATOM    170  C   PHE    21      13.954   4.827  14.552  1.00   .00
ATOM    171  O   PHE    21      14.227   3.737  13.993  1.00   .00
ATOM    172  CB  PHE    21      15.081   7.173  15.722  1.00   .00
ATOM    179  N   PRO    22      12.548   5.164  14.668  1.00   .00
ATOM    180  CA  PRO    22      11.443   4.201  14.054  1.00   .00
ATOM    181  C   PRO    22      11.389   4.277  12.357  1.00   .00
ATOM    182  O   PRO    22      10.805   3.427  11.684  1.00   .00
ATOM    183  CB  PRO    22      10.198   4.771  14.760  1.00   .00
ATOM    184  CG  PRO    22      10.485   6.295  14.963  1.00   .00
ATOM    185  CD  PRO    22      12.002   6.409  15.294  1.00   .00
ATOM    186  N   GLU    23      12.057   5.327  11.781  1.00   .00
ATOM    187  CA  GLU    23      12.191   5.578  10.280  1.00   .00
ATOM    188  C   GLU    23      13.721   6.178   9.993  1.00   .00
ATOM    189  O   GLU    23      14.424   6.703  10.920  1.00   .00
ATOM    190  CB  GLU    23      11.045   6.583   9.872  1.00   .00
ATOM    195  N   ARG    24      14.193   6.081   8.718  1.00   .00
ATOM    196  CA  ARG    24      15.612   6.598   8.339  1.00   .00
ATOM    197  C   ARG    24      15.583   8.097   7.686  1.00   .00
ATOM    198  O   ARG    24      15.129   8.300   6.540  1.00   .00
ATOM    199  CB  ARG    24      16.213   5.531   7.365  1.00   .00
ATOM    206  N   TYR    25      16.082   9.129   8.440  1.00   .00
ATOM    207  CA  TYR    25      16.120  10.582   7.915  1.00   .00
ATOM    208  C   TYR    25      17.576  10.889   7.230  1.00   .00
ATOM    209  O   TYR    25      18.606  11.024   7.913  1.00   .00
ATOM    210  CB  TYR    25      15.804  11.505   9.122  1.00   .00
ATOM    218  N   TYR    26      17.606  10.963   5.872  1.00   .00
ATOM    219  CA  TYR    26      18.902  11.214   5.089  1.00   .00
ATOM    220  C   TYR    26      19.120  12.766   4.673  1.00   .00
ATOM    221  O   TYR    26      18.321  13.348   3.914  1.00   .00
ATOM    222  CB  TYR    26      18.816  10.292   3.824  1.00   .00
ATOM    230  N   LEU    27      20.249  13.414   5.147  1.00   .00
ATOM    231  CA  LEU    27      20.560  14.892   4.709  1.00   .00
ATOM    232  C   LEU    27      20.770  15.043   3.046  1.00   .00
ATOM    233  O   LEU    27      20.389  16.040   2.437  1.00   .00
ATOM    234  CB  LEU    27      21.786  15.347   5.513  1.00   .00
ATOM    238  N   LYS    28      21.353  13.967   2.403  1.00   .00
ATOM    239  CA  LYS    28      21.547  13.896   0.878  1.00   .00
ATOM    240  C   LYS    28      21.188  12.348   0.412  1.00   .00
ATOM    241  O   LYS    28      20.026  12.041   0.123  1.00   .00
ATOM    242  CB  LYS    28      22.992  14.433   0.542  1.00   .00
ATOM    247  N   SER    29      22.198  11.400   0.390  1.00   .00
ATOM    248  CA  SER    29      21.915   9.897   0.001  1.00   .00
ATOM    249  C   SER    29      23.016   8.912   0.711  1.00   .00
ATOM    250  O   SER    29      24.054   8.553   0.141  1.00   .00
ATOM    251  CB  SER    29      21.900   9.778  -1.563  1.00   .00
ATOM    253  N   PHE    30      22.716   8.497   1.982  1.00   .00
ATOM    254  CA  PHE    30      23.648   7.537   2.798  1.00   .00
ATOM    255  C   PHE    30      22.711   6.539   3.721  1.00   .00
ATOM    256  O   PHE    30      21.594   6.901   4.147  1.00   .00
ATOM    257  CB  PHE    30      24.645   8.415   3.634  1.00   .00
ATOM    264  N   GLN    31      23.189   5.276   3.999  1.00   .00
ATOM    265  CA  GLN    31      22.362   4.260   4.846  1.00   .00
ATOM    266  C   GLN    31      22.976   4.063   6.350  1.00   .00
ATOM    267  O   GLN    31      24.149   3.687   6.530  1.00   .00
ATOM    268  CB  GLN    31      22.367   2.941   4.024  1.00   .00
ATOM    273  N   VAL    32      22.138   4.336   7.417  1.00   .00
ATOM    274  CA  VAL    32      22.619   4.194   8.899  1.00   .00
ATOM    275  C   VAL    32      21.947   2.966   9.736  1.00   .00
ATOM    276  O   VAL    32      21.108   3.164  10.614  1.00   .00
ATOM    277  CB  VAL    32      22.306   5.572   9.563  1.00   .00
ATOM    280  N   ASP    33      22.361   1.679   9.481  1.00   .00
ATOM    281  CA  ASP    33      21.753   0.459  10.304  1.00   .00
ATOM    282  C   ASP    33      22.322   0.350  11.887  1.00   .00
ATOM    283  O   ASP    33      22.761  -0.711  12.358  1.00   .00
ATOM    284  CB  ASP    33      22.074  -0.792   9.451  1.00   .00
ATOM    288  N   GLU    34      22.281   1.513  12.648  1.00   .00
ATOM    289  CA  GLU    34      22.783   1.595  14.143  1.00   .00
ATOM    290  C   GLU    34      22.417   3.024  14.888  1.00   .00
ATOM    291  O   GLU    34      21.942   3.032  16.030  1.00   .00
ATOM    292  CB  GLU    34      24.333   1.336  14.236  1.00   .00
ATOM    297  N   GLY    35      22.668   4.204  14.221  1.00   .00
ATOM    298  CA  GLY    35      22.359   5.598  14.870  1.00   .00
ATOM    299  C   GLY    35      22.501   6.795  13.864  1.00   .00
ATOM    300  O   GLY    35      21.572   7.074  13.102  1.00   .00
ATOM    301  N   ILE    36      23.673   7.500  13.863  1.00   .00
ATOM    302  CA  ILE    36      23.916   8.708  12.882  1.00   .00
ATOM    303  C   ILE    36      25.175   8.420  11.880  1.00   .00
ATOM    304  O   ILE    36      26.323   8.480  12.307  1.00   .00
ATOM    305  CB  ILE    36      24.116   9.997  13.757  1.00   .00
ATOM    309  N   THR    37      24.919   8.092  10.568  1.00   .00
ATOM    310  CA  THR    37      26.091   7.798   9.561  1.00   .00
ATOM    311  C   THR    37      26.514   9.121   8.694  1.00   .00
ATOM    312  O   THR    37      25.749   9.600   7.851  1.00   .00
ATOM    313  CB  THR    37      25.684   6.594   8.668  1.00   .00
ATOM    316  N   VAL    38      27.743   9.675   8.954  1.00   .00
ATOM    317  CA  VAL    38      28.263  10.937   8.212  1.00   .00
ATOM    318  C   VAL    38      29.386  10.581   7.095  1.00   .00
ATOM    319  O   VAL    38      30.562  10.321   7.423  1.00   .00
ATOM    320  CB  VAL    38      28.816  11.894   9.320  1.00   .00
ATOM    323  N   GLN    39      28.995  10.589   5.764  1.00   .00
ATOM    324  CA  GLN    39      30.014  10.281   4.616  1.00   .00
ATOM    325  C   GLN    39      30.718  11.650   4.078  1.00   .00
ATOM    326  O   GLN    39      30.056  12.520   3.471  1.00   .00
ATOM    327  CB  GLN    39      29.229   9.501   3.519  1.00   .00
ATOM    332  N   THR    40      32.062  11.818   4.355  1.00   .00
ATOM    333  CA  THR    40      32.821  13.094   3.948  1.00   .00
ATOM    334  C   THR    40      33.437  13.156   2.438  1.00   .00
ATOM    335  O   THR    40      34.489  12.565   2.141  1.00   .00
ATOM    336  CB  THR    40      33.962  13.240   4.997  1.00   .00
ATOM    339  N   ALA    41      32.792  13.959   1.537  1.00   .00
ATOM    340  CA  ALA    41      33.346  14.195   0.098  1.00   .00
ATOM    341  C   ALA    41      34.237  15.641   0.031  1.00   .00
ATOM    342  O   ALA    41      34.116  16.445  -0.893  1.00   .00
ATOM    343  CB  ALA    41      32.100  14.188  -0.836  1.00   .00
ATOM    344  N   ILE    42      35.098  15.869   1.098  1.00   .00
ATOM    345  CA  ILE    42      35.969  17.126   1.223  1.00   .00
ATOM    346  C   ILE    42      37.535  16.755   0.929  1.00   .00
ATOM    347  O   ILE    42      38.123  15.867   1.581  1.00   .00
ATOM    348  CB  ILE    42      35.766  17.663   2.688  1.00   .00
ATOM    352  N   THR    43      38.176  17.462  -0.067  1.00   .00
ATOM    353  CA  THR    43      39.666  17.160  -0.433  1.00   .00
ATOM    354  C   THR    43      40.835  17.672   0.626  1.00   .00
ATOM    355  O   THR    43      41.793  18.373   0.249  1.00   .00
ATOM    356  CB  THR    43      39.830  17.732  -1.874  1.00   .00
ATOM    359  N   GLN    44      40.743  17.261   1.918  1.00   .00
ATOM    360  CA  GLN    44      41.805  17.619   2.997  1.00   .00
ATOM    361  C   GLN    44      41.858  16.413   4.110  1.00   .00
ATOM    362  O   GLN    44      40.835  15.954   4.622  1.00   .00
ATOM    363  CB  GLN    44      41.488  19.026   3.598  1.00   .00
ATOM    368  N   SER    45      43.093  15.904   4.434  1.00   .00
ATOM    369  CA  SER    45      43.264  14.729   5.439  1.00   .00
ATOM    370  C   SER    45      43.117  15.095   7.041  1.00   .00
ATOM    371  O   SER    45      44.102  15.416   7.732  1.00   .00
ATOM    372  CB  SER    45      44.667  14.113   5.103  1.00   .00
ATOM    374  N   GLY    46      41.867  14.994   7.599  1.00   .00
ATOM    375  CA  GLY    46      41.636  15.267   9.147  1.00   .00
ATOM    376  C   GLY    46      40.174  15.654   9.577  1.00   .00
ATOM    377  O   GLY    46      39.402  14.815  10.061  1.00   .00
ATOM    378  N   ILE    47      39.813  16.974   9.429  1.00   .00
ATOM    379  CA  ILE    47      38.388  17.538   9.873  1.00   .00
ATOM    380  C   ILE    47      38.144  17.629  11.502  1.00   .00
ATOM    381  O   ILE    47      37.958  18.729  12.036  1.00   .00
ATOM    382  CB  ILE    47      37.211  16.886   9.063  1.00   .00
ATOM    386  N   LEU    48      38.146  16.454  12.242  1.00   .00
ATOM    387  CA  LEU    48      37.916  16.450  13.806  1.00   .00
ATOM    388  C   LEU    48      38.986  15.477  14.584  1.00   .00
ATOM    389  O   LEU    48      39.006  14.245  14.388  1.00   .00
ATOM    390  CB  LEU    48      36.441  16.001  14.051  1.00   .00
ATOM    394  N   SER    49      39.845  16.077  15.483  1.00   .00
ATOM    395  CA  SER    49      40.889  15.265  16.310  1.00   .00
ATOM    396  C   SER    49      40.441  15.251  17.880  1.00   .00
ATOM    397  O   SER    49      40.185  16.295  18.475  1.00   .00
ATOM    398  CB  SER    49      42.276  15.948  16.092  1.00   .00
ATOM    400  N   GLN    50      40.348  13.999  18.506  1.00   .00
ATOM    401  CA  GLN    50      39.865  13.827  20.023  1.00   .00
ATOM    402  C   GLN    50      38.248  14.129  20.160  1.00   .00
ATOM    403  O   GLN    50      37.743  15.113  19.620  1.00   .00
ATOM    404  CB  GLN    50      40.762  14.638  21.024  1.00   .00
ATOM    409  N   PHE    51      37.452  13.254  20.873  1.00   .00
ATOM    410  CA  PHE    51      35.887  13.499  20.973  1.00   .00
ATOM    411  C   PHE    51      35.189  14.091  22.344  1.00   .00
ATOM    412  O   PHE    51      33.991  13.779  22.563  1.00   .00
ATOM    413  CB  PHE    51      35.220  12.170  20.492  1.00   .00
ATOM    420  N   PRO    52      35.826  14.970  23.287  1.00   .00
ATOM    421  CA  PRO    52      35.050  15.553  24.527  1.00   .00
ATOM    422  C   PRO    52      34.055  16.809  24.036  1.00   .00
ATOM    423  O   PRO    52      34.168  17.941  24.491  1.00   .00
ATOM    424  CB  PRO    52      36.266  15.977  25.406  1.00   .00
ATOM    425  CG  PRO    52      37.363  16.428  24.386  1.00   .00
ATOM    426  CD  PRO    52      37.241  15.464  23.182  1.00   .00
ATOM    427  N   GLU    53      33.137  16.457  23.052  1.00   .00
ATOM    428  CA  GLU    53      32.138  17.400  22.305  1.00   .00
ATOM    429  C   GLU    53      32.642  17.429  20.720  1.00   .00
ATOM    430  O   GLU    53      33.460  18.268  20.302  1.00   .00
ATOM    431  CB  GLU    53      31.910  18.826  22.914  1.00   .00
ATOM    436  N   ILE    54      32.128  16.448  19.872  1.00   .00
ATOM    437  CA  ILE    54      32.570  16.338  18.379  1.00   .00
ATOM    438  C   ILE    54      32.190  17.588  17.357  1.00   .00
ATOM    439  O   ILE    54      31.163  17.586  16.650  1.00   .00
ATOM    440  CB  ILE    54      32.000  14.963  17.862  1.00   .00
ATOM    444  N   ASP    55      33.080  18.622  17.315  1.00   .00
ATOM    445  CA  ASP    55      32.877  19.850  16.412  1.00   .00
ATOM    446  C   ASP    55      33.301  19.580  14.852  1.00   .00
ATOM    447  O   ASP    55      34.486  19.339  14.529  1.00   .00
ATOM    448  CB  ASP    55      33.739  20.993  17.042  1.00   .00
ATOM    452  N   LEU    56      32.301  19.668  13.922  1.00   .00
ATOM    453  CA  LEU    56      32.581  19.478  12.410  1.00   .00
ATOM    454  C   LEU    56      32.910  20.917  11.663  1.00   .00
ATOM    455  O   LEU    56      32.881  21.986  12.290  1.00   .00
ATOM    456  CB  LEU    56      31.261  18.801  11.867  1.00   .00
TER   
END
