
#######################################################
#                                                     #
#                        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 (  144),  selected   36 , name T0335TS474_1-D1
# Molecule2: number of CA atoms   36 (  584),  selected   36 , name T0335_D1.pdb
# PARAMETERS: T0335TS474_1-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       5      A      15          4.097
LGA    K       6      K      16          2.780
LGA    I       7      A      17          0.815
LGA    A       8      K      18          3.083
LGA    R       9      A      19          3.288
LGA    I      10      G      20          4.599
LGA    N      11      -       -           -
LGA    E      12      -       -           -
LGA    L      13      V      21          4.520
LGA    A      14      I      22          3.348
LGA    A      15      T      23          3.403
LGA    K      16      E      24          1.717
LGA    A      17      E      25          3.267
LGA    K      18      E      26          3.310
LGA    A      19      K      27          1.605
LGA    G      20      A      28          1.092
LGA    V      21      E      29          2.482
LGA    I      22      Q      30          2.191
LGA    T      23      Q      31          0.877
LGA    E      24      K      32          1.382
LGA    E      25      L      33          0.870
LGA    E      26      R      34          1.831
LGA    K      27      Q      35          2.417
LGA    A      28      E      36          2.006
LGA    E      29      Y      37          1.453
LGA    -       -      L      38           -
LGA    -       -      K      39           -
LGA    Q      30      G      40          1.512
LGA    Q      31      -       -           -
LGA    K      32      -       -           -
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     24    2.66     8.33     52.822     0.869

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.855353 * X  +   0.117196 * Y  +  -0.504615 * Z  +  12.796179
  Y_new =   0.196335 * X  +   0.828072 * Y  +   0.525119 * Z  + -15.067503
  Z_new =   0.479399 * X  +  -0.548236 * Y  +   0.685284 * Z  +  12.039191 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.674748    2.466844  [ DEG:   -38.6602    141.3398 ]
  Theta =  -0.499969   -2.641623  [ DEG:   -28.6461   -151.3539 ]
  Phi   =   0.225629   -2.915964  [ DEG:    12.9276   -167.0724 ]
 
# 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: T0335TS474_1-D1                               
REMARK     2: T0335_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0335TS474_1-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   2.66    8.33  52.822
REMARK  ---------------------------------------------------------- 
MOLECULE T0335TS474_1-D1
PFRMAT TS
TARGET T0335
MODEL 1
PARENT N/A
ATOM     17  N   ALA     5      -8.338   4.225   2.766  1.00  0.00
ATOM     18  CA  ALA     5      -9.593   3.659   3.230  1.00  0.00
ATOM     19  C   ALA     5      -9.385   2.201   3.608  1.00  0.00
ATOM     20  O   ALA     5      -9.977   1.691   4.559  1.00  0.00
ATOM     21  N   LYS     6      -8.523   1.543   2.843  1.00  0.00
ATOM     22  CA  LYS     6      -8.203   0.141   3.070  1.00  0.00
ATOM     23  C   LYS     6      -7.525  -0.056   4.424  1.00  0.00
ATOM     24  O   LYS     6      -7.535  -1.154   4.977  1.00  0.00
ATOM     25  N   ILE     7      -6.935   1.013   4.952  1.00  0.00
ATOM     26  CA  ILE     7      -6.252   0.952   6.238  1.00  0.00
ATOM     27  C   ILE     7      -7.122   1.515   7.354  1.00  0.00
ATOM     28  O   ILE     7      -7.031   1.082   8.500  1.00  0.00
ATOM     29  N   ALA     8      -7.979   2.470   7.008  1.00  0.00
ATOM     30  CA  ALA     8      -8.871   3.072   7.988  1.00  0.00
ATOM     31  C   ALA     8      -9.926   2.061   8.404  1.00  0.00
ATOM     32  O   ALA     8     -10.596   2.218   9.426  1.00  0.00
ATOM     33  N   ARG     9     -10.057   1.022   7.591  1.00  0.00
ATOM     34  CA  ARG     9     -11.011  -0.035   7.832  1.00  0.00
ATOM     35  C   ARG     9     -10.324  -1.276   8.402  1.00  0.00
ATOM     36  O   ARG     9     -10.973  -2.149   8.975  1.00  0.00
ATOM     37  N   ILE    10      -9.003  -1.350   8.230  1.00  0.00
ATOM     38  CA  ILE    10      -8.231  -2.489   8.715  1.00  0.00
ATOM     39  C   ILE    10      -7.395  -2.129   9.946  1.00  0.00
ATOM     40  O   ILE    10      -6.721  -2.990  10.514  1.00  0.00
ATOM     41  N   ASN    11      -7.439  -0.866  10.364  1.00  0.00
ATOM     42  CA  ASN    11      -6.677  -0.426  11.532  1.00  0.00
ATOM     43  C   ASN    11      -7.607   0.021  12.662  1.00  0.00
ATOM     44  O   ASN    11      -7.552   1.168  13.107  1.00  0.00
ATOM     45  N   GLU    12      -8.476  -0.886  13.145  1.00  0.00
ATOM     46  CA  GLU    12      -7.714  -0.849  14.387  1.00  0.00
ATOM     47  C   GLU    12      -6.489   0.044  14.249  1.00  0.00
ATOM     48  O   GLU    12      -5.552  -0.035  15.044  1.00  0.00
ATOM     49  N   LEU    13      -6.508   0.901  13.238  1.00  0.00
ATOM     50  CA  LEU    13      -5.405   1.823  12.987  1.00  0.00
ATOM     51  C   LEU    13      -5.928   3.257  12.897  1.00  0.00
ATOM     52  O   LEU    13      -6.927   3.598  13.530  1.00  0.00
ATOM     53  N   ALA    14      -5.253   4.099  12.117  1.00  0.00
ATOM     54  CA  ALA    14      -5.663   5.489  11.968  1.00  0.00
ATOM     55  C   ALA    14      -5.536   5.949  10.520  1.00  0.00
ATOM     56  O   ALA    14      -6.504   6.397   9.907  1.00  0.00
ATOM     57  N   ALA    15      -4.323   5.845   9.992  1.00  0.00
ATOM     58  CA  ALA    15      -4.028   6.254   8.620  1.00  0.00
ATOM     59  C   ALA    15      -2.523   6.254   8.380  1.00  0.00
ATOM     60  O   ALA    15      -2.063   6.125   7.245  1.00  0.00
ATOM     61  N   LYS    16      -1.758   6.393   9.458  1.00  0.00
ATOM     62  CA  LYS    16      -0.306   6.398   9.368  1.00  0.00
ATOM     63  C   LYS    16       0.199   5.016   8.981  1.00  0.00
ATOM     64  O   LYS    16       1.150   4.883   8.213  1.00  0.00
ATOM     65  N   ALA    17      -0.460   3.989   9.508  1.00  0.00
ATOM     66  CA  ALA    17      -0.088   2.613   9.207  1.00  0.00
ATOM     67  C   ALA    17      -0.234   2.345   7.712  1.00  0.00
ATOM     68  O   ALA    17       0.707   1.913   7.050  1.00  0.00
ATOM     69  N   LYS    18      -1.427   2.612   7.191  1.00  0.00
ATOM     70  CA  LYS    18      -1.711   2.412   5.775  1.00  0.00
ATOM     71  C   LYS    18      -0.812   3.290   4.906  1.00  0.00
ATOM     72  O   LYS    18      -0.253   2.826   3.913  1.00  0.00
ATOM     73  N   ALA    19      -0.675   4.558   5.287  1.00  0.00
ATOM     74  CA  ALA    19       0.161   5.495   4.538  1.00  0.00
ATOM     75  C   ALA    19       1.551   4.912   4.295  1.00  0.00
ATOM     76  O   ALA    19       2.099   5.026   3.198  1.00  0.00
ATOM     77  N   GLY    20       2.113   4.282   5.321  1.00  0.00
ATOM     78  CA  GLY    20       3.433   3.674   5.218  1.00  0.00
ATOM     79  C   GLY    20       3.421   2.565   4.169  1.00  0.00
ATOM     80  O   GLY    20       4.392   2.374   3.435  1.00  0.00
ATOM     81  N   VAL    21       2.314   1.835   4.109  1.00  0.00
ATOM     82  CA  VAL    21       2.157   0.741   3.159  1.00  0.00
ATOM     83  C   VAL    21       2.232   1.243   1.719  1.00  0.00
ATOM     84  O   VAL    21       2.900   0.643   0.875  1.00  0.00
ATOM     85  N   ILE    22       1.532   2.337   1.443  1.00  0.00
ATOM     86  CA  ILE    22       1.504   2.914   0.104  1.00  0.00
ATOM     87  C   ILE    22       2.839   3.559  -0.264  1.00  0.00
ATOM     88  O   ILE    22       3.127   3.773  -1.441  1.00  0.00
ATOM     89  N   THR    23       3.651   3.868   0.741  1.00  0.00
ATOM     90  CA  THR    23       4.950   4.484   0.502  1.00  0.00
ATOM     91  C   THR    23       5.991   3.433   0.132  1.00  0.00
ATOM     92  O   THR    23       7.022   3.746  -0.462  1.00  0.00
ATOM     93  N   GLU    24       5.711   2.185   0.486  1.00  0.00
ATOM     94  CA  GLU    24       6.611   1.087   0.198  1.00  0.00
ATOM     95  C   GLU    24       6.313   0.478  -1.167  1.00  0.00
ATOM     96  O   GLU    24       7.227   0.110  -1.907  1.00  0.00
ATOM     97  N   GLU    25       5.030   0.376  -1.495  1.00  0.00
ATOM     98  CA  GLU    25       4.610  -0.188  -2.772  1.00  0.00
ATOM     99  C   GLU    25       4.909   0.776  -3.915  1.00  0.00
ATOM    100  O   GLU    25       5.551   0.408  -4.897  1.00  0.00
ATOM    101  N   GLU    26       4.432   2.010  -3.781  1.00  0.00
ATOM    102  CA  GLU    26       4.636   3.029  -4.795  1.00  0.00
ATOM    103  C   GLU    26       6.099   3.109  -5.227  1.00  0.00
ATOM    104  O   GLU    26       6.396   3.181  -6.415  1.00  0.00
ATOM    105  N   LYS    27       7.008   3.095  -4.259  1.00  0.00
ATOM    106  CA  LYS    27       8.434   3.166  -4.560  1.00  0.00
ATOM    107  C   LYS    27       8.912   1.878  -5.216  1.00  0.00
ATOM    108  O   LYS    27       9.543   1.902  -6.273  1.00  0.00
ATOM    109  N   ALA    28       8.609   0.756  -4.576  1.00  0.00
ATOM    110  CA  ALA    28       9.006  -0.555  -5.085  1.00  0.00
ATOM    111  C   ALA    28       8.681  -0.698  -6.572  1.00  0.00
ATOM    112  O   ALA    28       9.342  -1.450  -7.288  1.00  0.00
ATOM    113  N   GLU    29       7.662   0.025  -7.029  1.00  0.00
ATOM    114  CA  GLU    29       7.253  -0.025  -8.431  1.00  0.00
ATOM    115  C   GLU    29       8.448   0.171  -9.366  1.00  0.00
ATOM    116  O   GLU    29       9.221   1.115  -9.209  1.00  0.00
ATOM    117  N   GLN    30       8.612  -0.726 -10.357  1.00  0.00
ATOM    118  CA  GLN    30       9.715  -0.651 -11.322  1.00  0.00
ATOM    119  C   GLN    30       9.548   0.462 -12.348  1.00  0.00
ATOM    120  O   GLN    30      10.081   0.379 -13.454  1.00  0.00
ATOM    121  N   GLN    31       8.791   1.480 -11.992  1.00  0.00
ATOM    122  CA  GLN    31       8.531   2.597 -12.897  1.00  0.00
ATOM    123  C   GLN    31       7.866   2.109 -14.182  1.00  0.00
ATOM    124  O   GLN    31       7.705   2.878 -15.129  1.00  0.00
ATOM    125  N   LYS    32       7.476   0.835 -14.215  1.00  0.00
ATOM    126  CA  LYS    32       6.827   0.285 -15.395  1.00  0.00
ATOM    127  C   LYS    32       5.367   0.724 -15.449  1.00  0.00
ATOM    128  O   LYS    32       4.808   0.938 -16.525  1.00  0.00
ATOM    129  N   LEU    33       4.761   0.861 -14.273  1.00  0.00
ATOM    130  CA  LEU    33       3.365   1.280 -14.170  1.00  0.00
ATOM    131  C   LEU    33       3.270   2.775 -13.878  1.00  0.00
ATOM    132  O   LEU    33       2.283   3.423 -14.228  1.00  0.00
ATOM    133  N   ARG    34       4.304   3.318 -13.243  1.00  0.00
ATOM    134  CA  ARG    34       4.344   4.738 -12.913  1.00  0.00
ATOM    135  C   ARG    34       4.362   5.567 -14.184  1.00  0.00
ATOM    136  O   ARG    34       3.715   6.611 -14.267  1.00  0.00
ATOM    137  N   GLN    35       5.091   5.080 -15.187  1.00  0.00
ATOM    138  CA  GLN    35       5.175   5.762 -16.473  1.00  0.00
ATOM    139  C   GLN    35       3.783   6.176 -16.937  1.00  0.00
ATOM    140  O   GLN    35       3.616   7.167 -17.645  1.00  0.00
ATOM    141  N   GLU    36       2.784   5.410 -16.503  1.00  0.00
ATOM    142  CA  GLU    36       1.397   5.691 -16.842  1.00  0.00
ATOM    143  C   GLU    36       0.867   6.817 -15.960  1.00  0.00
ATOM    144  O   GLU    36       0.271   7.778 -16.445  1.00  0.00
ATOM    145  N   TYR    37       1.098   6.687 -14.655  1.00  0.00
ATOM    146  CA  TYR    37       0.657   7.689 -13.696  1.00  0.00
ATOM    147  C   TYR    37       1.346   9.022 -13.954  1.00  0.00
ATOM    148  O   TYR    37       0.690  10.057 -14.070  1.00  0.00
ATOM    149  N   LEU    38       2.674   8.993 -14.045  1.00  0.00
ATOM    150  CA  LEU    38       3.434  10.210 -14.293  1.00  0.00
ATOM    151  C   LEU    38       2.999  10.832 -15.616  1.00  0.00
ATOM    152  O   LEU    38       2.977  12.055 -15.763  1.00  0.00
ATOM    153  N   LYS    39       2.630   9.978 -16.565  1.00  0.00
ATOM    154  CA  LYS    39       2.170  10.440 -17.862  1.00  0.00
ATOM    155  C   LYS    39       0.801  11.084 -17.713  1.00  0.00
ATOM    156  O   LYS    39       0.373  11.868 -18.560  1.00  0.00
ATOM    157  N   GLY    40       0.127  10.759 -16.612  1.00  0.00
ATOM    158  CA  GLY    40      -1.183  11.317 -16.330  1.00  0.00
ATOM    159  C   GLY    40      -1.029  12.629 -15.569  1.00  0.00
ATOM    160  O   GLY    40      -1.858  13.532 -15.683  1.00  0.00
TER
END
