
#######################################################
#                                                     #
#                        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_5-D1
# Molecule2: number of CA atoms   36 (  584),  selected   36 , name T0335_D1.pdb
# PARAMETERS: T0335TS437_5-D1.T0335_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    A       5      -       -           -
LGA    K       6      -       -           -
LGA    I       7      -       -           -
LGA    A       8      A       5          2.514
LGA    R       9      K       6          1.821
LGA    I      10      I       7          1.481
LGA    N      11      A       8          1.519
LGA    E      12      R       9          2.116
LGA    L      13      I      10          1.828
LGA    A      14      N      11          1.490
LGA    A      15      E      12          1.673
LGA    K      16      L      13          2.052
LGA    A      17      A      14          1.622
LGA    K      18      A      15          2.093
LGA    A      19      K      16           -
LGA    G      20      A      17           -
LGA    V      21      -       -           -
LGA    I      22      -       -           -
LGA    T      23      -       -           -
LGA    E      24      -       -           -
LGA    E      25      -       -           -
LGA    E      26      -       -           -
LGA    K      27      -       -           -
LGA    A      28      -       -           -
LGA    E      29      K      18          5.407
LGA    -       -      A      19           -
LGA    -       -      G      20           -
LGA    -       -      V      21           -
LGA    Q      30      I      22          5.323
LGA    Q      31      T      23          2.386
LGA    K      32      E      24          2.511
LGA    L      33      E      25          1.266
LGA    R      34      E      26          2.457
LGA    Q      35      K      27          1.868
LGA    E      36      A      28          0.749
LGA    Y      37      E      29          2.935
LGA    L      38      Q      30          3.397
LGA    K      39      Q      31          1.772
LGA    G      40      K      32          2.975
LGA    -       -      L      33           -
LGA    -       -      R      34           -
LGA    -       -      Q      35           -
LGA    -       -      E      36           -
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     23    2.57    13.04     47.527     0.862

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.957481 * X  +   0.055591 * Y  +  -0.283091 * Z  + 141.494308
  Y_new =   0.263191 * X  +   0.570206 * Y  +  -0.778201 * Z  + -12.246324
  Z_new =   0.118160 * X  +  -0.819619 * Y  +  -0.560592 * Z  + -64.138863 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.170680    0.970912  [ DEG:  -124.3708     55.6292 ]
  Theta =  -0.118436   -3.023156  [ DEG:    -6.7859   -173.2141 ]
  Phi   =   2.873340   -0.268253  [ DEG:   164.6302    -15.3698 ]
 
# 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_5-D1                               
REMARK     2: T0335_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0335TS437_5-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   23   2.57   13.04  47.527
REMARK  ---------------------------------------------------------- 
MOLECULE T0335TS437_5-D1
PFRMAT TS
TARGET T0335
MODEL     5 REFINED
PARENT N/A
ATOM     31  N   ALA     5       3.413 -13.334 -11.056  1.00   .00
ATOM     32  CA  ALA     5       4.241 -12.777  -9.887  1.00   .00
ATOM     33  C   ALA     5       3.796 -11.205  -9.771  1.00   .00
ATOM     34  O   ALA     5       3.262 -10.780  -8.745  1.00   .00
ATOM     35  CB  ALA     5       5.764 -13.012 -10.149  1.00   .00
ATOM     36  N   LYS     6       3.973 -10.386 -10.919  1.00   .00
ATOM     37  CA  LYS     6       3.475  -8.919 -10.978  1.00   .00
ATOM     38  C   LYS     6       1.823  -8.837 -10.812  1.00   .00
ATOM     39  O   LYS     6       1.329  -8.002 -10.029  1.00   .00
ATOM     40  CB  LYS     6       3.991  -8.353 -12.339  1.00   .00
ATOM     45  N   ILE     7       1.018  -9.746 -11.518  1.00   .00
ATOM     46  CA  ILE     7      -0.541  -9.785 -11.326  1.00   .00
ATOM     47  C   ILE     7      -0.948 -10.217  -9.762  1.00   .00
ATOM     48  O   ILE     7      -1.825  -9.609  -9.154  1.00   .00
ATOM     49  CB  ILE     7      -1.111 -10.752 -12.428  1.00   .00
ATOM     53  N   ALA     8      -0.221 -11.244  -9.159  1.00   .00
ATOM     54  CA  ALA     8      -0.451 -11.661  -7.687  1.00   .00
ATOM     55  C   ALA     8       0.065 -10.491  -6.633  1.00   .00
ATOM     56  O   ALA     8      -0.676 -10.136  -5.717  1.00   .00
ATOM     57  CB  ALA     8       0.281 -13.024  -7.486  1.00   .00
ATOM     58  N   ARG     9       1.323  -9.908  -6.824  1.00   .00
ATOM     59  CA  ARG     9       1.852  -8.751  -5.918  1.00   .00
ATOM     60  C   ARG     9       0.899  -7.419  -5.974  1.00   .00
ATOM     61  O   ARG     9       0.546  -6.865  -4.924  1.00   .00
ATOM     62  CB  ARG     9       3.326  -8.501  -6.365  1.00   .00
ATOM     69  N   ILE    10       0.460  -6.969  -7.239  1.00   .00
ATOM     70  CA  ILE    10      -0.529  -5.767  -7.381  1.00   .00
ATOM     71  C   ILE    10      -1.993  -6.098  -6.636  1.00   .00
ATOM     72  O   ILE    10      -2.522  -5.260  -5.879  1.00   .00
ATOM     73  CB  ILE    10      -0.671  -5.450  -8.907  1.00   .00
ATOM     77  N   ASN    11      -2.572  -7.360  -6.845  1.00   .00
ATOM     78  CA  ASN    11      -3.872  -7.798  -6.128  1.00   .00
ATOM     79  C   ASN    11      -3.661  -7.956  -4.489  1.00   .00
ATOM     80  O   ASN    11      -4.467  -7.425  -3.725  1.00   .00
ATOM     81  CB  ASN    11      -4.324  -9.128  -6.808  1.00   .00
ATOM     85  N   GLU    12      -2.523  -8.645  -4.018  1.00   .00
ATOM     86  CA  GLU    12      -2.198  -8.747  -2.493  1.00   .00
ATOM     87  C   GLU    12      -2.042  -7.249  -1.781  1.00   .00
ATOM     88  O   GLU    12      -2.648  -6.980  -0.734  1.00   .00
ATOM     89  CB  GLU    12      -0.905  -9.614  -2.384  1.00   .00
ATOM     94  N   LEU    13      -1.270  -6.296  -2.450  1.00   .00
ATOM     95  CA  LEU    13      -1.142  -4.853  -1.953  1.00   .00
ATOM     96  C   LEU    13      -2.604  -4.074  -1.926  1.00   .00
ATOM     97  O   LEU    13      -2.955  -3.455  -0.905  1.00   .00
ATOM     98  CB  LEU    13      -0.089  -4.194  -2.902  1.00   .00
ATOM    102  N   ALA    14      -3.431  -4.197  -3.057  1.00   .00
ATOM    103  CA  ALA    14      -4.869  -3.587  -3.115  1.00   .00
ATOM    104  C   ALA    14      -5.915  -4.238  -1.999  1.00   .00
ATOM    105  O   ALA    14      -6.764  -3.543  -1.457  1.00   .00
ATOM    106  CB  ALA    14      -5.356  -3.832  -4.574  1.00   .00
ATOM    107  N   ALA    15      -5.783  -5.580  -1.676  1.00   .00
ATOM    108  CA  ALA    15      -6.666  -6.252  -0.577  1.00   .00
ATOM    109  C   ALA    15      -6.160  -5.859   0.956  1.00   .00
ATOM    110  O   ALA    15      -6.993  -5.633   1.846  1.00   .00
ATOM    111  CB  ALA    15      -6.639  -7.779  -0.872  1.00   .00
ATOM    112  N   LYS    16      -4.783  -5.749   1.199  1.00   .00
ATOM    113  CA  LYS    16      -4.215  -5.307   2.581  1.00   .00
ATOM    114  C   LYS    16      -4.456  -3.685   2.902  1.00   .00
ATOM    115  O   LYS    16      -4.804  -3.327   4.028  1.00   .00
ATOM    116  CB  LYS    16      -2.699  -5.710   2.559  1.00   .00
ATOM    121  N   ALA    17      -4.255  -2.790   1.865  1.00   .00
ATOM    122  CA  ALA    17      -4.488  -1.270   2.008  1.00   .00
ATOM    123  C   ALA    17      -5.532  -0.773   0.852  1.00   .00
ATOM    124  O   ALA    17      -5.513  -1.275  -0.278  1.00   .00
ATOM    125  CB  ALA    17      -3.098  -0.564   1.884  1.00   .00
ATOM    126  N   LYS    18      -6.430   0.225   1.179  1.00   .00
ATOM    127  CA  LYS    18      -7.493   0.777   0.144  1.00   .00
ATOM    128  C   LYS    18      -6.911   1.500  -1.254  1.00   .00
ATOM    129  O   LYS    18      -7.255   2.636  -1.606  1.00   .00
ATOM    130  CB  LYS    18      -8.408   1.732   0.960  1.00   .00
ATOM    135  N   ALA    19      -6.066   0.760  -1.997  1.00   .00
ATOM    136  CA  ALA    19      -5.432   1.238  -3.333  1.00   .00
ATOM    137  C   ALA    19      -5.997   0.385  -4.625  1.00   .00
ATOM    138  O   ALA    19      -6.514  -0.734  -4.473  1.00   .00
ATOM    139  CB  ALA    19      -3.891   1.071  -3.131  1.00   .00
ATOM    140  N   GLY    20      -5.879   0.943  -5.885  1.00   .00
ATOM    141  CA  GLY    20      -6.428   0.174  -7.156  1.00   .00
ATOM    142  C   GLY    20      -5.459   0.071  -8.421  1.00   .00
ATOM    143  O   GLY    20      -5.527   0.892  -9.345  1.00   .00
ATOM    144  N   VAL    21      -4.586  -0.992  -8.438  1.00   .00
ATOM    145  CA  VAL    21      -3.586  -1.296  -9.655  1.00   .00
ATOM    146  C   VAL    21      -2.565  -0.147 -10.291  1.00   .00
ATOM    147  O   VAL    21      -1.427  -0.489 -10.631  1.00   .00
ATOM    148  CB  VAL    21      -4.387  -2.039 -10.779  1.00   .00
ATOM    151  N   ILE    22      -2.974   1.144 -10.443  1.00   .00
ATOM    152  CA  ILE    22      -2.018   2.263 -11.050  1.00   .00
ATOM    153  C   ILE    22      -2.211   3.751 -10.386  1.00   .00
ATOM    154  O   ILE    22      -1.220   4.391  -9.994  1.00   .00
ATOM    155  CB  ILE    22      -2.172   2.281 -12.621  1.00   .00
ATOM    159  N   THR    23      -3.488   4.261 -10.272  1.00   .00
ATOM    160  CA  THR    23      -3.762   5.657  -9.655  1.00   .00
ATOM    161  C   THR    23      -3.864   5.661  -8.009  1.00   .00
ATOM    162  O   THR    23      -4.304   4.682  -7.370  1.00   .00
ATOM    163  CB  THR    23      -5.069   6.176 -10.348  1.00   .00
ATOM    166  N   GLU    24      -3.438   6.805  -7.368  1.00   .00
ATOM    167  CA  GLU    24      -3.481   6.948  -5.837  1.00   .00
ATOM    168  C   GLU    24      -4.967   7.289  -5.244  1.00   .00
ATOM    169  O   GLU    24      -5.707   8.129  -5.782  1.00   .00
ATOM    170  CB  GLU    24      -2.455   8.073  -5.481  1.00   .00
ATOM    175  N   GLU    25      -5.346   6.608  -4.101  1.00   .00
ATOM    176  CA  GLU    25      -6.705   6.869  -3.425  1.00   .00
ATOM    177  C   GLU    25      -6.697   8.281  -2.555  1.00   .00
ATOM    178  O   GLU    25      -5.727   8.616  -1.857  1.00   .00
ATOM    179  CB  GLU    25      -7.002   5.621  -2.555  1.00   .00
ATOM    184  N   GLU    26      -7.789   9.075  -2.676  1.00   .00
ATOM    185  CA  GLU    26      -7.886  10.480  -1.963  1.00   .00
ATOM    186  C   GLU    26      -7.840  10.606  -0.321  1.00   .00
ATOM    187  O   GLU    26      -7.459  11.670   0.189  1.00   .00
ATOM    188  CB  GLU    26      -9.190  11.123  -2.550  1.00   .00
ATOM    193  N   LYS    27      -8.239   9.560   0.479  1.00   .00
ATOM    194  CA  LYS    27      -8.223   9.661   2.042  1.00   .00
ATOM    195  C   LYS    27      -7.338   8.482   2.743  1.00   .00
ATOM    196  O   LYS    27      -7.635   7.293   2.591  1.00   .00
ATOM    197  CB  LYS    27      -9.718   9.616   2.508  1.00   .00
ATOM    202  N   ALA    28      -6.273   8.886   3.515  1.00   .00
ATOM    203  CA  ALA    28      -5.358   7.881   4.248  1.00   .00
ATOM    204  C   ALA    28      -5.626   7.949   5.877  1.00   .00
ATOM    205  O   ALA    28      -5.846   9.027   6.466  1.00   .00
ATOM    206  CB  ALA    28      -3.896   8.275   3.882  1.00   .00
ATOM    207  N   GLU    29      -5.601   6.755   6.579  1.00   .00
ATOM    208  CA  GLU    29      -5.858   6.723   8.132  1.00   .00
ATOM    209  C   GLU    29      -4.573   7.272   9.031  1.00   .00
ATOM    210  O   GLU    29      -3.401   6.940   8.788  1.00   .00
ATOM    211  CB  GLU    29      -6.288   5.256   8.475  1.00   .00
ATOM    216  N   GLN    30      -4.870   8.149  10.053  1.00   .00
ATOM    217  CA  GLN    30      -3.767   8.800  10.948  1.00   .00
ATOM    218  C   GLN    30      -2.980   7.858  12.059  1.00   .00
ATOM    219  O   GLN    30      -3.201   7.942  13.273  1.00   .00
ATOM    220  CB  GLN    30      -4.475  10.034  11.610  1.00   .00
ATOM    225  N   GLN    31      -2.033   7.025  11.567  1.00   .00
ATOM    226  CA  GLN    31      -1.153   6.133  12.491  1.00   .00
ATOM    227  C   GLN    31       0.262   5.852  11.743  1.00   .00
ATOM    228  O   GLN    31       0.299   5.572  10.514  1.00   .00
ATOM    229  CB  GLN    31      -1.931   4.812  12.847  1.00   .00
ATOM    234  N   LYS    32       1.437   5.897  12.500  1.00   .00
ATOM    235  CA  LYS    32       2.866   5.610  11.846  1.00   .00
ATOM    236  C   LYS    32       3.144   4.000  11.449  1.00   .00
ATOM    237  O   LYS    32       4.132   3.367  11.793  1.00   .00
ATOM    238  CB  LYS    32       3.906   6.189  12.824  1.00   .00
ATOM    243  N   LEU    33       2.166   3.477  10.713  1.00   .00
ATOM    244  CA  LEU    33       2.100   2.040  10.179  1.00   .00
ATOM    245  C   LEU    33       1.000   2.079   8.959  1.00   .00
ATOM    246  O   LEU    33       1.332   1.738   7.821  1.00   .00
ATOM    247  CB  LEU    33       1.750   1.024  11.338  1.00   .00
ATOM    251  N   ARG    34      -0.291   2.597   9.240  1.00   .00
ATOM    252  CA  ARG    34      -1.357   2.800   8.143  1.00   .00
ATOM    253  C   ARG    34      -0.848   3.841   6.961  1.00   .00
ATOM    254  O   ARG    34      -0.961   3.533   5.768  1.00   .00
ATOM    255  CB  ARG    34      -2.635   3.297   8.884  1.00   .00
ATOM    262  N   GLN    35      -0.241   5.044   7.353  1.00   .00
ATOM    263  CA  GLN    35       0.354   6.037   6.306  1.00   .00
ATOM    264  C   GLN    35       1.601   5.341   5.444  1.00   .00
ATOM    265  O   GLN    35       1.648   5.454   4.214  1.00   .00
ATOM    266  CB  GLN    35       0.797   7.299   7.109  1.00   .00
ATOM    271  N   GLU    36       2.551   4.593   6.162  1.00   .00
ATOM    272  CA  GLU    36       3.697   3.823   5.457  1.00   .00
ATOM    273  C   GLU    36       3.098   2.601   4.500  1.00   .00
ATOM    274  O   GLU    36       3.478   2.489   3.333  1.00   .00
ATOM    275  CB  GLU    36       4.650   3.313   6.580  1.00   .00
ATOM    280  N   TYR    37       2.110   1.775   5.044  1.00   .00
ATOM    281  CA  TYR    37       1.403   0.678   4.207  1.00   .00
ATOM    282  C   TYR    37       0.611   1.290   2.886  1.00   .00
ATOM    283  O   TYR    37       0.773   0.777   1.785  1.00   .00
ATOM    284  CB  TYR    37       0.448  -0.080   5.196  1.00   .00
ATOM    292  N   LEU    38      -0.185   2.448   3.055  1.00   .00
ATOM    293  CA  LEU    38      -0.866   3.146   1.853  1.00   .00
ATOM    294  C   LEU    38       0.251   3.711   0.753  1.00   .00
ATOM    295  O   LEU    38       0.119   3.464  -0.451  1.00   .00
ATOM    296  CB  LEU    38      -1.766   4.263   2.445  1.00   .00
ATOM    300  N   LYS    39       1.354   4.414   1.247  1.00   .00
ATOM    301  CA  LYS    39       2.504   4.905   0.329  1.00   .00
ATOM    302  C   LYS    39       3.315   3.648  -0.386  1.00   .00
ATOM    303  O   LYS    39       3.516   3.656  -1.614  1.00   .00
ATOM    304  CB  LYS    39       3.413   5.812   1.193  1.00   .00
ATOM    309  N   GLY    40       3.696   2.570   0.423  1.00   .00
ATOM    310  CA  GLY    40       4.377   1.283  -0.179  1.00   .00
ATOM    311  C   GLY    40       3.443   0.497  -1.223  1.00   .00
ATOM    312  O   GLY    40       3.894   0.137  -2.315  1.00   .00
TER   
END
