
#######################################################
#                                                     #
#                        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   36 (  178),  selected   36 , name T0335TS437_3-D1
# Molecule2: number of CA atoms   36 (  584),  selected   36 , name T0335_D1.pdb
# PARAMETERS: T0335TS437_3-D1.T0335_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    A       5      -       -           -
LGA    K       6      -       -           -
LGA    I       7      -       -           -
LGA    A       8      -       -           -
LGA    R       9      -       -           -
LGA    I      10      -       -           -
LGA    N      11      -       -           -
LGA    E      12      -       -           -
LGA    L      13      -       -           -
LGA    A      14      -       -           -
LGA    A      15      A       5          4.370
LGA    K      16      K       6          0.929
LGA    A      17      I       7          2.673
LGA    K      18      -       -           -
LGA    A      19      A       8          1.092
LGA    G      20      R       9          3.368
LGA    V      21      I      10          3.600
LGA    I      22      N      11           -
LGA    -       -      E      12           -
LGA    T      23      L      13          2.720
LGA    E      24      A      14          3.888
LGA    -       -      A      15           -
LGA    -       -      K      16           -
LGA    E      25      A      17          1.886
LGA    -       -      K      18           -
LGA    -       -      A      19           -
LGA    -       -      G      20           -
LGA    -       -      V      21           -
LGA    E      26      I      22          0.859
LGA    K      27      T      23          0.840
LGA    A      28      E      24          1.047
LGA    E      29      E      25          0.971
LGA    Q      30      E      26          0.408
LGA    Q      31      K      27          0.915
LGA    K      32      A      28          1.163
LGA    L      33      E      29          0.308
LGA    R      34      Q      30          0.810
LGA    Q      35      Q      31          1.579
LGA    E      36      K      32          0.612
LGA    Y      37      L      33          1.335
LGA    L      38      R      34          1.956
LGA    K      39      Q      35          2.065
LGA    G      40      E      36          2.252
LGA    -       -      Y      37           -
LGA    -       -      L      38           -
LGA    -       -      K      39           -
LGA    -       -      G      40           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   36   36    5.0     24    2.07    20.83     59.737     1.105

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.845354 * X  +   0.373896 * Y  +  -0.381546 * Z  + 146.761108
  Y_new =  -0.208157 * X  +   0.427229 * Y  +   0.879856 * Z  +  46.443737
  Z_new =   0.491982 * X  +   0.823212 * Y  +  -0.283331 * Z  + -47.132870 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.902274   -1.239318  [ DEG:   108.9923    -71.0077 ]
  Theta =  -0.514365   -2.627228  [ DEG:   -29.4709   -150.5291 ]
  Phi   =  -2.900159    0.241434  [ DEG:  -166.1669     13.8331 ]
 
# 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: T0335TS437_3-D1                               
REMARK     2: T0335_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0335TS437_3-D1.T0335_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   36   36   5.0   24   2.07   20.83  59.737
REMARK  ---------------------------------------------------------- 
MOLECULE T0335TS437_3-D1
PFRMAT TS
TARGET T0335
MODEL     3 REFINED
PARENT N/A
ATOM     31  N   ALA     5      11.454 -15.942 -16.808  1.00   .00
ATOM     32  CA  ALA     5      11.918 -15.309 -15.484  1.00   .00
ATOM     33  C   ALA     5      11.398 -13.757 -15.556  1.00   .00
ATOM     34  O   ALA     5      10.584 -13.332 -14.736  1.00   .00
ATOM     35  CB  ALA     5      13.472 -15.455 -15.327  1.00   .00
ATOM     36  N   LYS     6      11.846 -12.957 -16.635  1.00   .00
ATOM     37  CA  LYS     6      11.307 -11.518 -16.875  1.00   .00
ATOM     38  C   LYS     6       9.665 -11.499 -17.112  1.00   .00
ATOM     39  O   LYS     6       8.958 -10.699 -16.494  1.00   .00
ATOM     40  CB  LYS     6      12.115 -10.920 -18.074  1.00   .00
ATOM     45  N   ILE     7       9.121 -12.464 -17.999  1.00   .00
ATOM     46  CA  ILE     7       7.577 -12.585 -18.223  1.00   .00
ATOM     47  C   ILE     7       6.767 -12.946 -16.813  1.00   .00
ATOM     48  O   ILE     7       5.745 -12.319 -16.502  1.00   .00
ATOM     49  CB  ILE     7       7.356 -13.654 -19.362  1.00   .00
ATOM     53  N   ALA     8       7.309 -13.933 -15.988  1.00   .00
ATOM     54  CA  ALA     8       6.691 -14.295 -14.607  1.00   .00
ATOM     55  C   ALA     8       6.874 -13.043 -13.511  1.00   .00
ATOM     56  O   ALA     8       5.900 -12.665 -12.866  1.00   .00
ATOM     57  CB  ALA     8       7.354 -15.612 -14.137  1.00   .00
ATOM     58  N   ARG     9       8.130 -12.422 -13.395  1.00   .00
ATOM     59  CA  ARG     9       8.369 -11.196 -12.461  1.00   .00
ATOM     60  C   ARG     9       7.414  -9.902 -12.866  1.00   .00
ATOM     61  O   ARG     9       6.792  -9.301 -11.976  1.00   .00
ATOM     62  CB  ARG     9       9.897 -10.883 -12.488  1.00   .00
ATOM     69  N   ILE    10       7.284  -9.574 -14.221  1.00   .00
ATOM     70  CA  ILE    10       6.313  -8.467 -14.709  1.00   .00
ATOM     71  C   ILE    10       4.729  -8.787 -14.276  1.00   .00
ATOM     72  O   ILE    10       4.022  -7.900 -13.756  1.00   .00
ATOM     73  CB  ILE    10       6.528  -8.335 -16.272  1.00   .00
ATOM     77  N   ASN    11       4.251 -10.095 -14.470  1.00   .00
ATOM     78  CA  ASN    11       2.835 -10.531 -14.024  1.00   .00
ATOM     79  C   ASN    11       2.669 -10.548 -12.366  1.00   .00
ATOM     80  O   ASN    11       1.700  -9.995 -11.818  1.00   .00
ATOM     81  CB  ASN    11       2.585 -11.928 -14.664  1.00   .00
ATOM     85  N   GLU    12       3.695 -11.153 -11.609  1.00   .00
ATOM     86  CA  GLU    12       3.676 -11.145 -10.035  1.00   .00
ATOM     87  C   GLU    12       3.714  -9.606  -9.430  1.00   .00
ATOM     88  O   GLU    12       2.903  -9.269  -8.544  1.00   .00
ATOM     89  CB  GLU    12       4.885 -12.029  -9.569  1.00   .00
ATOM     94  N   LEU    13       4.634  -8.692  -9.978  1.00   .00
ATOM     95  CA  LEU    13       4.663  -7.203  -9.535  1.00   .00
ATOM     96  C   LEU    13       3.237  -6.429  -9.887  1.00   .00
ATOM     97  O   LEU    13       2.676  -5.727  -9.024  1.00   .00
ATOM     98  CB  LEU    13       5.910  -6.580 -10.196  1.00   .00
ATOM    102  N   ALA    14       2.652  -6.652 -11.152  1.00   .00
ATOM    103  CA  ALA    14       1.252  -6.040 -11.521  1.00   .00
ATOM    104  C   ALA    14       0.058  -6.596 -10.502  1.00   .00
ATOM    105  O   ALA    14      -0.715  -5.789  -9.954  1.00   .00
ATOM    106  CB  ALA    14       1.001  -6.409 -13.013  1.00   .00
ATOM    107  N   ALA    15      -0.002  -7.972 -10.239  1.00   .00
ATOM    108  CA  ALA    15      -1.016  -8.571  -9.213  1.00   .00
ATOM    109  C   ALA    15      -0.823  -7.929  -7.696  1.00   .00
ATOM    110  O   ALA    15      -1.796  -7.489  -7.080  1.00   .00
ATOM    111  CB  ALA    15      -0.819 -10.128  -9.264  1.00   .00
ATOM    112  N   LYS    16       0.478  -7.860  -7.182  1.00   .00
ATOM    113  CA  LYS    16       0.786  -7.185  -5.813  1.00   .00
ATOM    114  C   LYS    16       0.387  -5.559  -5.783  1.00   .00
ATOM    115  O   LYS    16      -0.194  -5.058  -4.806  1.00   .00
ATOM    116  CB  LYS    16       2.304  -7.437  -5.540  1.00   .00
ATOM    121  N   ALA    17       0.702  -4.799  -6.912  1.00   .00
ATOM    122  CA  ALA    17       0.317  -3.305  -7.018  1.00   .00
ATOM    123  C   ALA    17      -1.327  -3.070  -7.115  1.00   .00
ATOM    124  O   ALA    17      -1.852  -2.182  -6.442  1.00   .00
ATOM    125  CB  ALA    17       1.114  -2.734  -8.250  1.00   .00
ATOM    126  N   LYS    18      -2.089  -3.918  -7.930  1.00   .00
ATOM    127  CA  LYS    18      -3.637  -3.803  -7.997  1.00   .00
ATOM    128  C   LYS    18      -4.385  -4.338  -6.636  1.00   .00
ATOM    129  O   LYS    18      -5.300  -3.679  -6.128  1.00   .00
ATOM    130  CB  LYS    18      -4.114  -4.587  -9.253  1.00   .00
ATOM    135  N   ALA    19      -3.952  -5.539  -6.062  1.00   .00
ATOM    136  CA  ALA    19      -4.600  -6.083  -4.739  1.00   .00
ATOM    137  C   ALA    19      -4.241  -5.212  -3.390  1.00   .00
ATOM    138  O   ALA    19      -5.004  -5.249  -2.424  1.00   .00
ATOM    139  CB  ALA    19      -4.083  -7.555  -4.621  1.00   .00
ATOM    140  N   GLY    20      -3.058  -4.478  -3.386  1.00   .00
ATOM    141  CA  GLY    20      -2.607  -3.663  -2.146  1.00   .00
ATOM    142  C   GLY    20      -1.679  -4.540  -1.239  1.00   .00
ATOM    143  O   GLY    20      -2.132  -5.175  -0.284  1.00   .00
ATOM    144  N   VAL    21      -0.331  -4.584  -1.543  1.00   .00
ATOM    145  CA  VAL    21       0.691  -5.463  -0.704  1.00   .00
ATOM    146  C   VAL    21       0.975  -4.978   0.894  1.00   .00
ATOM    147  O   VAL    21       2.104  -4.935   1.389  1.00   .00
ATOM    148  CB  VAL    21       1.987  -5.461  -1.578  1.00   .00
ATOM    151  N   ILE    22      -0.137  -4.653   1.598  1.00   .00
ATOM    152  CA  ILE    22      -0.180  -4.197   3.063  1.00   .00
ATOM    153  C   ILE    22      -1.767  -4.136   3.503  1.00   .00
ATOM    154  O   ILE    22      -2.619  -3.668   2.725  1.00   .00
ATOM    155  CB  ILE    22       0.517  -2.794   3.234  1.00   .00
ATOM    159  N   THR    23      -2.129  -4.604   4.746  1.00   .00
ATOM    160  CA  THR    23      -3.636  -4.586   5.210  1.00   .00
ATOM    161  C   THR    23      -4.291  -3.059   5.346  1.00   .00
ATOM    162  O   THR    23      -3.628  -2.097   5.775  1.00   .00
ATOM    163  CB  THR    23      -3.689  -5.398   6.536  1.00   .00
ATOM    166  N   GLU    24      -5.596  -2.915   4.923  1.00   .00
ATOM    167  CA  GLU    24      -6.314  -1.531   4.916  1.00   .00
ATOM    168  C   GLU    24      -6.700  -0.815   6.360  1.00   .00
ATOM    169  O   GLU    24      -7.886  -0.595   6.681  1.00   .00
ATOM    170  CB  GLU    24      -7.559  -1.729   3.988  1.00   .00
ATOM    175  N   GLU    25      -5.661  -0.421   7.152  1.00   .00
ATOM    176  CA  GLU    25      -5.881   0.339   8.504  1.00   .00
ATOM    177  C   GLU    25      -5.247   1.860   8.350  1.00   .00
ATOM    178  O   GLU    25      -4.038   2.042   8.181  1.00   .00
ATOM    179  CB  GLU    25      -5.191  -0.499   9.634  1.00   .00
ATOM    184  N   GLU    26      -6.095   2.933   8.378  1.00   .00
ATOM    185  CA  GLU    26      -5.561   4.400   8.182  1.00   .00
ATOM    186  C   GLU    26      -4.778   5.090   9.464  1.00   .00
ATOM    187  O   GLU    26      -5.310   5.963  10.172  1.00   .00
ATOM    188  CB  GLU    26      -6.780   5.226   7.697  1.00   .00
ATOM    193  N   LYS    27      -3.493   4.681   9.663  1.00   .00
ATOM    194  CA  LYS    27      -2.583   5.270  10.779  1.00   .00
ATOM    195  C   LYS    27      -1.155   5.779  10.142  1.00   .00
ATOM    196  O   LYS    27      -0.691   5.273   9.086  1.00   .00
ATOM    197  CB  LYS    27      -2.390   4.147  11.851  1.00   .00
ATOM    202  N   ALA    28      -0.471   6.784  10.814  1.00   .00
ATOM    203  CA  ALA    28       0.944   7.332  10.276  1.00   .00
ATOM    204  C   ALA    28       2.226   6.259  10.453  1.00   .00
ATOM    205  O   ALA    28       3.303   6.541  10.983  1.00   .00
ATOM    206  CB  ALA    28       1.174   8.684  10.981  1.00   .00
ATOM    207  N   GLU    29       1.968   5.047   9.933  1.00   .00
ATOM    208  CA  GLU    29       2.936   3.827   9.918  1.00   .00
ATOM    209  C   GLU    29       2.350   2.854   8.720  1.00   .00
ATOM    210  O   GLU    29       3.018   2.616   7.714  1.00   .00
ATOM    211  CB  GLU    29       3.006   3.149  11.335  1.00   .00
ATOM    216  N   GLN    30       1.031   2.389   8.866  1.00   .00
ATOM    217  CA  GLN    30       0.302   1.572   7.765  1.00   .00
ATOM    218  C   GLN    30       0.167   2.420   6.353  1.00   .00
ATOM    219  O   GLN    30       0.465   1.886   5.284  1.00   .00
ATOM    220  CB  GLN    30      -1.056   1.171   8.392  1.00   .00
ATOM    225  N   GLN    31      -0.225   3.774   6.413  1.00   .00
ATOM    226  CA  GLN    31      -0.255   4.682   5.121  1.00   .00
ATOM    227  C   GLN    31       1.239   4.802   4.409  1.00   .00
ATOM    228  O   GLN    31       1.379   4.652   3.187  1.00   .00
ATOM    229  CB  GLN    31      -0.842   6.066   5.558  1.00   .00
ATOM    234  N   LYS    32       2.329   5.012   5.267  1.00   .00
ATOM    235  CA  LYS    32       3.798   5.034   4.751  1.00   .00
ATOM    236  C   LYS    32       4.229   3.556   4.156  1.00   .00
ATOM    237  O   LYS    32       4.760   3.468   3.038  1.00   .00
ATOM    238  CB  LYS    32       4.679   5.509   5.952  1.00   .00
ATOM    243  N   LEU    33       3.941   2.427   4.935  1.00   .00
ATOM    244  CA  LEU    33       4.235   0.988   4.418  1.00   .00
ATOM    245  C   LEU    33       3.413   0.658   3.006  1.00   .00
ATOM    246  O   LEU    33       4.011   0.162   2.049  1.00   .00
ATOM    247  CB  LEU    33       3.856   0.013   5.585  1.00   .00
ATOM    251  N   ARG    34       2.052   1.011   2.930  1.00   .00
ATOM    252  CA  ARG    34       1.232   0.826   1.602  1.00   .00
ATOM    253  C   ARG    34       1.879   1.714   0.357  1.00   .00
ATOM    254  O   ARG    34       2.090   1.188  -0.744  1.00   .00
ATOM    255  CB  ARG    34      -0.245   1.217   1.936  1.00   .00
ATOM    262  N   GLN    35       2.222   3.053   0.628  1.00   .00
ATOM    263  CA  GLN    35       2.920   3.963  -0.435  1.00   .00
ATOM    264  C   GLN    35       4.404   3.365  -0.882  1.00   .00
ATOM    265  O   GLN    35       4.691   3.236  -2.076  1.00   .00
ATOM    266  CB  GLN    35       2.977   5.398   0.194  1.00   .00
ATOM    271  N   GLU    36       5.284   2.966   0.136  1.00   .00
ATOM    272  CA  GLU    36       6.648   2.310  -0.160  1.00   .00
ATOM    273  C   GLU    36       6.485   0.850  -0.950  1.00   .00
ATOM    274  O   GLU    36       7.163   0.602  -1.959  1.00   .00
ATOM    275  CB  GLU    36       7.387   2.199   1.204  1.00   .00
ATOM    280  N   TYR    37       5.535  -0.064  -0.462  1.00   .00
ATOM    281  CA  TYR    37       5.253  -1.426  -1.170  1.00   .00
ATOM    282  C   TYR    37       4.673  -1.227  -2.715  1.00   .00
ATOM    283  O   TYR    37       5.172  -1.870  -3.655  1.00   .00
ATOM    284  CB  TYR    37       4.288  -2.220  -0.234  1.00   .00
ATOM    292  N   LEU    38       3.657  -0.277  -2.924  1.00   .00
ATOM    293  CA  LEU    38       3.125   0.046  -4.344  1.00   .00
ATOM    294  C   LEU    38       4.313   0.713  -5.284  1.00   .00
ATOM    295  O   LEU    38       4.498   0.293  -6.437  1.00   .00
ATOM    296  CB  LEU    38       1.887   0.976  -4.155  1.00   .00
ATOM    300  N   LYS    39       5.137   1.717  -4.715  1.00   .00
ATOM    301  CA  LYS    39       6.335   2.323  -5.500  1.00   .00
ATOM    302  C   LYS    39       7.467   1.185  -5.883  1.00   .00
ATOM    303  O   LYS    39       7.869   1.095  -7.044  1.00   .00
ATOM    304  CB  LYS    39       6.920   3.476  -4.604  1.00   .00
ATOM    309  N   GLY    40       7.901   0.300  -4.871  1.00   .00
ATOM    310  CA  GLY    40       8.914  -0.891  -5.186  1.00   .00
ATOM    311  C   GLY    40       8.369  -1.888  -6.305  1.00   .00
ATOM    312  O   GLY    40       9.095  -2.190  -7.253  1.00   .00
TER   
END
