
#######################################################
#                                                     #
#                        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_2-D1
# Molecule2: number of CA atoms   36 (  584),  selected   36 , name T0335_D1.pdb
# PARAMETERS: T0335TS437_2-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      A       5          1.528
LGA    R       9      K       6          1.093
LGA    I      10      I       7          1.320
LGA    N      11      A       8          1.093
LGA    E      12      R       9          0.743
LGA    L      13      I      10          0.757
LGA    A      14      N      11          1.131
LGA    A      15      E      12          0.998
LGA    K      16      L      13          0.659
LGA    A      17      A      14          0.789
LGA    K      18      A      15          1.228
LGA    A      19      K      16          1.094
LGA    G      20      A      17          1.890
LGA    -       -      K      18           -
LGA    -       -      A      19           -
LGA    -       -      G      20           -
LGA    V      21      V      21          5.685
LGA    I      22      I      22          1.746
LGA    T      23      T      23          2.855
LGA    E      24      E      24          3.004
LGA    E      25      -       -           -
LGA    E      26      E      25          2.261
LGA    K      27      E      26          2.043
LGA    A      28      K      27          2.943
LGA    E      29      A      28          1.402
LGA    Q      30      E      29          1.076
LGA    Q      31      Q      30          2.610
LGA    K      32      Q      31          1.062
LGA    L      33      K      32          1.787
LGA    R      34      L      33          2.975
LGA    Q      35      R      34          2.341
LGA    E      36      Q      35          1.994
LGA    Y      37      E      36          4.188
LGA    L      38      -       -           -
LGA    K      39      -       -           -
LGA    G      40      Y      37          2.220
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     30    2.18    30.00     68.902     1.315

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.064204 * X  +   0.949690 * Y  +  -0.306539 * Z  +  34.461220
  Y_new =  -0.990788 * X  +   0.023961 * Y  +  -0.133285 * Z  + 141.233276
  Z_new =  -0.119234 * X  +   0.312273 * Y  +   0.942480 * Z  +  21.306726 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.319947   -2.821645  [ DEG:    18.3316   -161.6684 ]
  Theta =   0.119519    3.022074  [ DEG:     6.8479    173.1521 ]
  Phi   =  -1.506086    1.635507  [ DEG:   -86.2924     93.7076 ]
 
# 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_2-D1                               
REMARK     2: T0335_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0335TS437_2-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   30   2.18   30.00  68.902
REMARK  ---------------------------------------------------------- 
MOLECULE T0335TS437_2-D1
PFRMAT TS
TARGET T0335
MODEL     2 REFINED
PARENT N/A
ATOM     31  N   ALA     5       4.596 -13.024  -9.130  1.00   .00
ATOM     32  CA  ALA     5       5.184 -12.276  -7.920  1.00   .00
ATOM     33  C   ALA     5       4.673 -10.717  -8.084  1.00   .00
ATOM     34  O   ALA     5       4.006 -10.183  -7.198  1.00   .00
ATOM     35  CB  ALA     5       6.746 -12.476  -7.883  1.00   .00
ATOM     36  N   LYS     6       4.943 -10.051  -9.295  1.00   .00
ATOM     37  CA  LYS     6       4.400  -8.626  -9.603  1.00   .00
ATOM     38  C   LYS     6       2.742  -8.591  -9.574  1.00   .00
ATOM     39  O   LYS     6       2.144  -7.745  -8.901  1.00   .00
ATOM     40  CB  LYS     6       5.030  -8.192 -10.975  1.00   .00
ATOM     45  N   ILE     7       2.037  -9.584 -10.290  1.00   .00
ATOM     46  CA  ILE     7       0.465  -9.690 -10.229  1.00   .00
ATOM     47  C   ILE     7      -0.083  -9.919  -8.677  1.00   .00
ATOM     48  O   ILE     7      -1.034  -9.264  -8.247  1.00   .00
ATOM     49  CB  ILE     7       0.044 -10.835 -11.229  1.00   .00
ATOM     53  N   ALA     8       0.619 -10.831  -7.883  1.00   .00
ATOM     54  CA  ALA     8       0.268 -11.059  -6.373  1.00   .00
ATOM     55  C   ALA     8       0.548  -9.689  -5.474  1.00   .00
ATOM     56  O   ALA     8      -0.344  -9.256  -4.722  1.00   .00
ATOM     57  CB  ALA     8       1.094 -12.286  -5.913  1.00   .00
ATOM     58  N   ARG     9       1.779  -9.040  -5.638  1.00   .00
ATOM     59  CA  ARG     9       2.105  -7.699  -4.906  1.00   .00
ATOM     60  C   ARG     9       1.049  -6.486  -5.319  1.00   .00
ATOM     61  O   ARG     9       0.560  -5.770  -4.429  1.00   .00
ATOM     62  CB  ARG     9       3.585  -7.372  -5.258  1.00   .00
ATOM     69  N   ILE    10       0.678  -6.345  -6.678  1.00   .00
ATOM     70  CA  ILE    10      -0.394  -5.300  -7.121  1.00   .00
ATOM     71  C   ILE    10      -1.864  -5.588  -6.412  1.00   .00
ATOM     72  O   ILE    10      -2.497  -4.666  -5.879  1.00   .00
ATOM     73  CB  ILE    10      -0.462  -5.322  -8.691  1.00   .00
ATOM     77  N   ASN    11      -2.337  -6.912  -6.397  1.00   .00
ATOM     78  CA  ASN    11      -3.656  -7.297  -5.686  1.00   .00
ATOM     79  C   ASN    11      -3.561  -7.122  -4.040  1.00   .00
ATOM     80  O   ASN    11      -4.448  -6.517  -3.428  1.00   .00
ATOM     81  CB  ASN    11      -3.994  -8.745  -6.145  1.00   .00
ATOM     85  N   GLU    12      -2.430  -7.634  -3.379  1.00   .00
ATOM     86  CA  GLU    12      -2.221  -7.447  -1.844  1.00   .00
ATOM     87  C   GLU    12      -2.136  -5.849  -1.408  1.00   .00
ATOM     88  O   GLU    12      -2.805  -5.430  -0.455  1.00   .00
ATOM     89  CB  GLU    12      -0.938  -8.237  -1.477  1.00   .00
ATOM     94  N   LEU    13      -1.329  -5.002  -2.177  1.00   .00
ATOM     95  CA  LEU    13      -1.247  -3.481  -1.903  1.00   .00
ATOM     96  C   LEU    13      -2.706  -2.728  -2.094  1.00   .00
ATOM     97  O   LEU    13      -3.124  -1.963  -1.212  1.00   .00
ATOM     98  CB  LEU    13      -0.136  -2.956  -2.856  1.00   .00
ATOM    102  N   ALA    14      -3.469  -3.027  -3.240  1.00   .00
ATOM    103  CA  ALA    14      -4.906  -2.438  -3.444  1.00   .00
ATOM    104  C   ALA    14      -5.951  -2.958  -2.274  1.00   .00
ATOM    105  O   ALA    14      -6.671  -2.136  -1.678  1.00   .00
ATOM    106  CB  ALA    14      -5.336  -2.799  -4.889  1.00   .00
ATOM    107  N   ALA    15      -5.954  -4.319  -1.938  1.00   .00
ATOM    108  CA  ALA    15      -6.834  -4.874  -0.775  1.00   .00
ATOM    109  C   ALA    15      -6.444  -4.171   0.678  1.00   .00
ATOM    110  O   ALA    15      -7.333  -3.680   1.387  1.00   .00
ATOM    111  CB  ALA    15      -6.659  -6.427  -0.771  1.00   .00
ATOM    112  N   LYS    16      -5.078  -4.098   1.028  1.00   .00
ATOM    113  CA  LYS    16      -4.617  -3.355   2.329  1.00   .00
ATOM    114  C   LYS    16      -5.060  -1.750   2.328  1.00   .00
ATOM    115  O   LYS    16      -5.557  -1.226   3.342  1.00   .00
ATOM    116  CB  LYS    16      -3.080  -3.572   2.418  1.00   .00
ATOM    121  N   ALA    17      -4.901  -1.025   1.142  1.00   .00
ATOM    122  CA  ALA    17      -5.369   0.436   1.016  1.00   .00
ATOM    123  C   ALA    17      -7.024   0.575   1.122  1.00   .00
ATOM    124  O   ALA    17      -7.534   1.428   1.863  1.00   .00
ATOM    125  CB  ALA    17      -4.814   0.967  -0.338  1.00   .00
ATOM    126  N   LYS    18      -7.822  -0.312   0.396  1.00   .00
ATOM    127  CA  LYS    18      -9.381  -0.287   0.501  1.00   .00
ATOM    128  C   LYS    18      -9.966  -0.728   1.991  1.00   .00
ATOM    129  O   LYS    18     -11.014  -0.235   2.417  1.00   .00
ATOM    130  CB  LYS    18      -9.904  -1.215  -0.625  1.00   .00
ATOM    135  N   ALA    19      -9.226  -1.638   2.747  1.00   .00
ATOM    136  CA  ALA    19      -9.670  -2.072   4.173  1.00   .00
ATOM    137  C   ALA    19      -9.597  -0.872   5.312  1.00   .00
ATOM    138  O   ALA    19     -10.490  -0.788   6.161  1.00   .00
ATOM    139  CB  ALA    19      -8.735  -3.263   4.549  1.00   .00
ATOM    140  N   GLY    20      -8.522   0.023   5.280  1.00   .00
ATOM    141  CA  GLY    20      -8.402   1.202   6.319  1.00   .00
ATOM    142  C   GLY    20      -7.079   1.259   7.166  1.00   .00
ATOM    143  O   GLY    20      -7.062   0.881   8.339  1.00   .00
ATOM    144  N   VAL    21      -5.970   1.787   6.567  1.00   .00
ATOM    145  CA  VAL    21      -4.621   1.924   7.325  1.00   .00
ATOM    146  C   VAL    21      -4.527   3.354   8.170  1.00   .00
ATOM    147  O   VAL    21      -4.368   4.438   7.584  1.00   .00
ATOM    148  CB  VAL    21      -3.503   1.779   6.246  1.00   .00
ATOM    151  N   ILE    22      -4.611   3.294   9.548  1.00   .00
ATOM    152  CA  ILE    22      -4.522   4.587  10.439  1.00   .00
ATOM    153  C   ILE    22      -3.003   5.250  10.482  1.00   .00
ATOM    154  O   ILE    22      -2.039   4.610  10.893  1.00   .00
ATOM    155  CB  ILE    22      -5.023   4.168  11.846  1.00   .00
ATOM    159  N   THR    23      -2.864   6.538  10.027  1.00   .00
ATOM    160  CA  THR    23      -1.465   7.280   9.934  1.00   .00
ATOM    161  C   THR    23      -0.397   7.431  11.221  1.00   .00
ATOM    162  O   THR    23       0.168   8.516  11.452  1.00   .00
ATOM    163  CB  THR    23      -1.848   8.679   9.340  1.00   .00
ATOM    166  N   GLU    24      -0.080   6.309  11.934  1.00   .00
ATOM    167  CA  GLU    24       1.015   6.346  13.056  1.00   .00
ATOM    168  C   GLU    24       2.528   6.216  12.356  1.00   .00
ATOM    169  O   GLU    24       2.657   5.767  11.192  1.00   .00
ATOM    170  CB  GLU    24       0.702   5.165  14.047  1.00   .00
ATOM    175  N   GLU    25       3.644   6.587  13.076  1.00   .00
ATOM    176  CA  GLU    25       5.129   6.457  12.445  1.00   .00
ATOM    177  C   GLU    25       5.696   4.879  12.216  1.00   .00
ATOM    178  O   GLU    25       6.774   4.471  12.622  1.00   .00
ATOM    179  CB  GLU    25       6.054   7.303  13.367  1.00   .00
ATOM    184  N   GLU    26       4.846   4.119  11.523  1.00   .00
ATOM    185  CA  GLU    26       5.056   2.644  11.118  1.00   .00
ATOM    186  C   GLU    26       3.909   2.375   9.974  1.00   .00
ATOM    187  O   GLU    26       4.220   2.076   8.811  1.00   .00
ATOM    188  CB  GLU    26       4.949   1.688  12.379  1.00   .00
ATOM    193  N   LYS    27       2.570   2.580  10.351  1.00   .00
ATOM    194  CA  LYS    27       1.402   2.471   9.346  1.00   .00
ATOM    195  C   LYS    27       1.508   3.595   8.123  1.00   .00
ATOM    196  O   LYS    27       1.275   3.251   6.955  1.00   .00
ATOM    197  CB  LYS    27       0.117   2.600  10.181  1.00   .00
ATOM    202  N   ALA    28       1.913   4.921   8.438  1.00   .00
ATOM    203  CA  ALA    28       2.136   5.992   7.310  1.00   .00
ATOM    204  C   ALA    28       3.324   5.485   6.250  1.00   .00
ATOM    205  O   ALA    28       3.132   5.543   5.034  1.00   .00
ATOM    206  CB  ALA    28       2.465   7.344   8.017  1.00   .00
ATOM    207  N   GLU    29       4.491   4.940   6.796  1.00   .00
ATOM    208  CA  GLU    29       5.607   4.324   5.913  1.00   .00
ATOM    209  C   GLU    29       5.041   2.983   5.110  1.00   .00
ATOM    210  O   GLU    29       5.239   2.864   3.898  1.00   .00
ATOM    211  CB  GLU    29       6.820   4.036   6.850  1.00   .00
ATOM    216  N   GLN    30       4.273   2.042   5.829  1.00   .00
ATOM    217  CA  GLN    30       3.602   0.810   5.132  1.00   .00
ATOM    218  C   GLN    30       2.566   1.261   3.939  1.00   .00
ATOM    219  O   GLN    30       2.661   0.752   2.821  1.00   .00
ATOM    220  CB  GLN    30       2.923  -0.033   6.264  1.00   .00
ATOM    225  N   GLN    31       1.638   2.274   4.214  1.00   .00
ATOM    226  CA  GLN    31       0.686   2.837   3.107  1.00   .00
ATOM    227  C   GLN    31       1.529   3.487   1.842  1.00   .00
ATOM    228  O   GLN    31       1.247   3.191   0.670  1.00   .00
ATOM    229  CB  GLN    31      -0.244   3.866   3.830  1.00   .00
ATOM    234  N   LYS    32       2.608   4.346   2.146  1.00   .00
ATOM    235  CA  LYS    32       3.522   4.948   1.044  1.00   .00
ATOM    236  C   LYS    32       4.337   3.759   0.218  1.00   .00
ATOM    237  O   LYS    32       4.346   3.753  -1.021  1.00   .00
ATOM    238  CB  LYS    32       4.469   5.949   1.777  1.00   .00
ATOM    243  N   LEU    33       4.972   2.752   0.974  1.00   .00
ATOM    244  CA  LEU    33       5.681   1.550   0.296  1.00   .00
ATOM    245  C   LEU    33       4.624   0.623  -0.586  1.00   .00
ATOM    246  O   LEU    33       4.922   0.281  -1.737  1.00   .00
ATOM    247  CB  LEU    33       6.373   0.756   1.448  1.00   .00
ATOM    251  N   ARG    34       3.388   0.303  -0.018  1.00   .00
ATOM    252  CA  ARG    34       2.288  -0.473  -0.811  1.00   .00
ATOM    253  C   ARG    34       1.841   0.365  -2.162  1.00   .00
ATOM    254  O   ARG    34       1.826  -0.209  -3.264  1.00   .00
ATOM    255  CB  ARG    34       1.117  -0.725   0.181  1.00   .00
ATOM    262  N   GLN    35       1.534   1.734  -2.039  1.00   .00
ATOM    263  CA  GLN    35       1.191   2.618  -3.290  1.00   .00
ATOM    264  C   GLN    35       2.417   2.621  -4.407  1.00   .00
ATOM    265  O   GLN    35       2.181   2.407  -5.596  1.00   .00
ATOM    266  CB  GLN    35       0.865   4.041  -2.728  1.00   .00
ATOM    271  N   GLU    36       3.731   2.806  -3.928  1.00   .00
ATOM    272  CA  GLU    36       4.970   2.713  -4.869  1.00   .00
ATOM    273  C   GLU    36       5.125   1.210  -5.541  1.00   .00
ATOM    274  O   GLU    36       5.316   1.091  -6.767  1.00   .00
ATOM    275  CB  GLU    36       6.205   3.138  -4.015  1.00   .00
ATOM    280  N   TYR    37       5.001   0.085  -4.703  1.00   .00
ATOM    281  CA  TYR    37       5.048  -1.374  -5.255  1.00   .00
ATOM    282  C   TYR    37       3.808  -1.666  -6.318  1.00   .00
ATOM    283  O   TYR    37       4.042  -2.225  -7.397  1.00   .00
ATOM    284  CB  TYR    37       5.042  -2.315  -4.020  1.00   .00
ATOM    292  N   LEU    38       2.526  -1.199  -5.980  1.00   .00
ATOM    293  CA  LEU    38       1.330  -1.327  -6.947  1.00   .00
ATOM    294  C   LEU    38       1.576  -0.504  -8.337  1.00   .00
ATOM    295  O   LEU    38       1.403  -1.063  -9.427  1.00   .00
ATOM    296  CB  LEU    38       0.076  -0.827  -6.171  1.00   .00
ATOM    300  N   LYS    39       2.038   0.823  -8.253  1.00   .00
ATOM    301  CA  LYS    39       2.389   1.643  -9.514  1.00   .00
ATOM    302  C   LYS    39       3.568   0.908 -10.420  1.00   .00
ATOM    303  O   LYS    39       3.398   0.723 -11.625  1.00   .00
ATOM    304  CB  LYS    39       2.790   3.075  -9.015  1.00   .00
ATOM    309  N   GLY    40       4.733   0.463  -9.761  1.00   .00
ATOM    310  CA  GLY    40       5.878  -0.327 -10.552  1.00   .00
ATOM    311  C   GLY    40       5.360  -1.708 -11.180  1.00   .00
ATOM    312  O   GLY    40       5.582  -1.977 -12.369  1.00   .00
TER   
END
