
#######################################################
#                                                     #
#                        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 T0335TS556_4-D1
# Molecule2: number of CA atoms   36 (  584),  selected   36 , name T0335_D1.pdb
# PARAMETERS: T0335TS556_4-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      A       5          3.759
LGA    N      11      K       6          0.944
LGA    E      12      I       7          1.833
LGA    L      13      A       8          2.086
LGA    A      14      R       9          1.027
LGA    A      15      I      10          1.121
LGA    K      16      N      11          1.353
LGA    A      17      E      12          0.447
LGA    K      18      L      13          1.545
LGA    A      19      A      14          2.337
LGA    G      20      A      15          2.624
LGA    V      21      K      16          2.737
LGA    I      22      A      17          3.111
LGA    -       -      K      18           -
LGA    -       -      A      19           -
LGA    -       -      G      20           -
LGA    T      23      V      21          4.069
LGA    E      24      I      22          1.383
LGA    E      25      T      23          1.633
LGA    -       -      E      24           -
LGA    E      26      E      25          3.603
LGA    K      27      E      26          4.153
LGA    A      28      K      27          2.151
LGA    E      29      A      28          1.304
LGA    Q      30      E      29          3.010
LGA    Q      31      Q      30          2.860
LGA    K      32      Q      31          0.777
LGA    L      33      K      32          1.802
LGA    R      34      L      33          2.043
LGA    Q      35      R      34          1.453
LGA    E      36      Q      35          2.542
LGA    Y      37      E      36          2.908
LGA    L      38      Y      37          1.100
LGA    K      39      L      38          2.275
LGA    -       -      K      39           -
LGA    G      40      G      40          3.010

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   36   36    5.0     31    2.37    12.90     63.426     1.254

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.571539 * X  +   0.620039 * Y  +   0.537490 * Z  +  -2.674011
  Y_new =  -0.757452 * X  +   0.650575 * Y  +   0.054943 * Z  +  -8.580571
  Z_new =  -0.315611 * X  +  -0.438525 * Y  +   0.841478 * Z  + -21.649393 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.480413    2.661179  [ DEG:   -27.5257    152.4743 ]
  Theta =   0.321100    2.820493  [ DEG:    18.3977    161.6023 ]
  Phi   =  -0.924386    2.217206  [ DEG:   -52.9634    127.0366 ]
 
# 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: T0335TS556_4-D1                               
REMARK     2: T0335_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0335TS556_4-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   31   2.37   12.90  63.426
REMARK  ---------------------------------------------------------- 
MOLECULE T0335TS556_4-D1
PFRMAT TS
TARGET T0335
MODEL 4
PARENT N/A
ATOM     21  N   ALA     5       3.327  -7.847 -16.292  1.00 10.00
ATOM     22  CA  ALA     5       2.428  -6.770 -15.894  1.00 10.00
ATOM     23  C   ALA     5       1.361  -7.269 -14.929  1.00 10.00
ATOM     24  O   ALA     5       0.938  -6.546 -14.028  1.00 10.00
ATOM     25  CB  ALA     5       1.785  -6.136 -17.118  1.00 10.00
ATOM     26  N   LYS     6       0.929  -8.511 -15.124  1.00 10.00
ATOM     27  CA  LYS     6      -0.086  -9.112 -14.268  1.00 10.00
ATOM     28  C   LYS     6       0.422  -9.278 -12.842  1.00 10.00
ATOM     29  O   LYS     6      -0.257  -8.909 -11.885  1.00 10.00
ATOM     30  CB  LYS     6      -0.531 -10.451 -14.834  1.00 10.00
ATOM     31  N   ILE     7       1.621  -9.835 -12.708  1.00 10.00
ATOM     32  CA  ILE     7       2.230 -10.036 -11.398  1.00 10.00
ATOM     33  C   ILE     7       2.333  -8.726 -10.631  1.00 10.00
ATOM     34  O   ILE     7       2.056  -8.673  -9.432  1.00 10.00
ATOM     35  CB  ILE     7       3.602 -10.677 -11.545  1.00 10.00
ATOM     36  N   ALA     8       2.732  -7.667 -11.328  1.00 10.00
ATOM     37  CA  ALA     8       2.825  -6.343 -10.725  1.00 10.00
ATOM     38  C   ALA     8       1.464  -5.863 -10.237  1.00 10.00
ATOM     39  O   ALA     8       1.348  -5.301  -9.148  1.00 10.00
ATOM     40  CB  ALA     8       3.416  -5.350 -11.714  1.00 10.00
ATOM     41  N   ARG     9       0.437  -6.089 -11.049  1.00 10.00
ATOM     42  CA  ARG     9      -0.909  -5.627 -10.728  1.00 10.00
ATOM     43  C   ARG     9      -1.480  -6.381  -9.535  1.00 10.00
ATOM     44  O   ARG     9      -2.177  -5.804  -8.699  1.00 10.00
ATOM     45  CB  ARG     9      -1.821  -5.773 -11.936  1.00 10.00
ATOM     46  N   ILE    10      -1.182  -7.674  -9.460  1.00 10.00
ATOM     47  CA  ILE    10      -1.633  -8.501  -8.348  1.00 10.00
ATOM     48  C   ILE    10      -1.055  -8.011  -7.027  1.00 10.00
ATOM     49  O   ILE    10      -1.752  -7.960  -6.014  1.00 10.00
ATOM     50  CB  ILE    10      -1.260  -9.957  -8.585  1.00 10.00
ATOM     51  N   ASN    11       0.225  -7.653  -7.043  1.00 10.00
ATOM     52  CA  ASN    11       0.898  -7.159  -5.848  1.00 10.00
ATOM     53  C   ASN    11       0.278  -5.855  -5.366  1.00 10.00
ATOM     54  O   ASN    11       0.067  -5.661  -4.168  1.00 10.00
ATOM     55  CB  ASN    11       2.384  -6.977  -6.112  1.00 10.00
ATOM     56  N   GLU    12      -0.011  -4.961  -6.305  1.00 10.00
ATOM     57  CA  GLU    12      -0.610  -3.671  -5.977  1.00 10.00
ATOM     58  C   GLU    12      -2.013  -3.844  -5.412  1.00 10.00
ATOM     59  O   GLU    12      -2.418  -3.122  -4.500  1.00 10.00
ATOM     60  CB  GLU    12      -0.637  -2.773  -7.204  1.00 10.00
ATOM     61  N   LEU    13      -2.752  -4.804  -5.956  1.00 10.00
ATOM     62  CA  LEU    13      -4.066  -5.152  -5.430  1.00 10.00
ATOM     63  C   LEU    13      -3.963  -5.722  -4.021  1.00 10.00
ATOM     64  O   LEU    13      -4.796  -5.435  -3.162  1.00 10.00
ATOM     65  CB  LEU    13      -4.764  -6.139  -6.354  1.00 10.00
ATOM     66  N   ALA    14      -2.934  -6.532  -3.791  1.00 10.00
ATOM     67  CA  ALA    14      -2.666  -7.070  -2.462  1.00 10.00
ATOM     68  C   ALA    14      -2.421  -5.953  -1.456  1.00 10.00
ATOM     69  O   ALA    14      -2.935  -5.988  -0.337  1.00 10.00
ATOM     70  CB  ALA    14      -1.477  -8.017  -2.504  1.00 10.00
ATOM     71  N   ALA    15      -1.633  -4.961  -1.858  1.00 10.00
ATOM     72  CA  ALA    15      -1.329  -3.825  -0.997  1.00 10.00
ATOM     73  C   ALA    15      -2.583  -3.016  -0.689  1.00 10.00
ATOM     74  O   ALA    15      -2.765  -2.537   0.430  1.00 10.00
ATOM     75  CB  ALA    15      -0.270  -2.942  -1.637  1.00 10.00
ATOM     76  N   LYS    16      -3.445  -2.868  -1.690  1.00 10.00
ATOM     77  CA  LYS    16      -4.711  -2.166  -1.513  1.00 10.00
ATOM     78  C   LYS    16      -5.522  -2.771  -0.373  1.00 10.00
ATOM     79  O   LYS    16      -5.967  -2.062   0.529  1.00 10.00
ATOM     80  CB  LYS    16      -5.513  -2.184  -2.805  1.00 10.00
ATOM     81  N   ALA    17      -5.710  -4.086  -0.422  1.00 10.00
ATOM     82  CA  ALA    17      -6.489  -4.785   0.592  1.00 10.00
ATOM     83  C   ALA    17      -5.853  -4.648   1.969  1.00 10.00
ATOM     84  O   ALA    17      -6.544  -4.436   2.965  1.00 10.00
ATOM     85  CB  ALA    17      -6.645  -6.253   0.222  1.00 10.00
ATOM     86  N   LYS    18      -4.530  -4.771   2.019  1.00 10.00
ATOM     87  CA  LYS    18      -3.795  -4.636   3.271  1.00 10.00
ATOM     88  C   LYS    18      -3.963  -3.243   3.861  1.00 10.00
ATOM     89  O   LYS    18      -4.202  -3.091   5.059  1.00 10.00
ATOM     90  CB  LYS    18      -2.321  -4.949   3.055  1.00 10.00
ATOM     91  N   ALA    19      -3.836  -2.227   3.015  1.00 10.00
ATOM     92  CA  ALA    19      -3.929  -0.842   3.461  1.00 10.00
ATOM     93  C   ALA    19      -5.310  -0.538   4.026  1.00 10.00
ATOM     94  O   ALA    19      -5.438   0.140   5.046  1.00 10.00
ATOM     95  CB  ALA    19      -3.601   0.107   2.317  1.00 10.00
ATOM     96  N   GLY    20      -6.342  -1.041   3.357  1.00 10.00
ATOM     97  CA  GLY    20      -7.717  -0.822   3.792  1.00 10.00
ATOM     98  C   GLY    20      -7.999  -1.539   5.105  1.00 10.00
ATOM     99  O   GLY    20      -8.930  -1.186   5.829  1.00 10.00
ATOM    100  N   VAL    21      -7.189  -2.549   5.409  1.00 10.00
ATOM    101  CA  VAL    21      -7.358  -3.326   6.631  1.00 10.00
ATOM    102  C   VAL    21      -6.608  -2.691   7.795  1.00 10.00
ATOM    103  O   VAL    21      -6.904  -2.964   8.959  1.00 10.00
ATOM    104  CB  VAL    21      -6.894  -4.758   6.417  1.00 10.00
ATOM    105  N   ILE    22      -5.637  -1.842   7.475  1.00 10.00
ATOM    106  CA  ILE    22      -4.789  -1.230   8.491  1.00 10.00
ATOM    107  C   ILE    22      -5.328   0.132   8.910  1.00 10.00
ATOM    108  O   ILE    22      -6.303   0.626   8.341  1.00 10.00
ATOM    109  CB  ILE    22      -3.361  -1.103   7.983  1.00 10.00
ATOM    110  N   THR    23      -4.691   0.733   9.908  1.00 10.00
ATOM    111  CA  THR    23      -5.120   2.029  10.421  1.00 10.00
ATOM    112  C   THR    23      -4.783   3.147   9.444  1.00 10.00
ATOM    113  O   THR    23      -4.013   2.953   8.504  1.00 10.00
ATOM    114  CB  THR    23      -4.485   2.298  11.777  1.00 10.00
ATOM    115  N   GLU    24      -5.365   4.320   9.672  1.00 10.00
ATOM    116  CA  GLU    24      -5.117   5.476   8.819  1.00 10.00
ATOM    117  C   GLU    24      -3.638   5.834   8.792  1.00 10.00
ATOM    118  O   GLU    24      -3.117   6.288   7.773  1.00 10.00
ATOM    119  CB  GLU    24      -5.943   6.665   9.285  1.00 10.00
ATOM    120  N   GLU    25      -2.963   5.628   9.919  1.00 10.00
ATOM    121  CA  GLU    25      -1.550   5.967  10.039  1.00 10.00
ATOM    122  C   GLU    25      -0.683   5.005   9.238  1.00 10.00
ATOM    123  O   GLU    25       0.230   5.423   8.526  1.00 10.00
ATOM    124  CB  GLU    25      -1.128   5.972  11.500  1.00 10.00
ATOM    125  N   GLU    26      -0.975   3.714   9.357  1.00 10.00
ATOM    126  CA  GLU    26      -0.213   2.688   8.654  1.00 10.00
ATOM    127  C   GLU    26      -0.597   2.631   7.180  1.00 10.00
ATOM    128  O   GLU    26       0.214   2.259   6.332  1.00 10.00
ATOM    129  CB  GLU    26      -0.419   1.332   9.309  1.00 10.00
ATOM    130  N   LYS    27      -1.837   3.002   6.883  1.00 10.00
ATOM    131  CA  LYS    27      -2.292   3.115   5.502  1.00 10.00
ATOM    132  C   LYS    27      -1.386   4.037   4.696  1.00 10.00
ATOM    133  O   LYS    27      -1.006   3.720   3.570  1.00 10.00
ATOM    134  CB  LYS    27      -3.730   3.610   5.456  1.00 10.00
ATOM    135  N   ALA    28      -1.042   5.180   5.282  1.00 10.00
ATOM    136  CA  ALA    28      -0.164   6.141   4.627  1.00 10.00
ATOM    137  C   ALA    28       1.210   5.540   4.362  1.00 10.00
ATOM    138  O   ALA    28       1.774   5.708   3.282  1.00 10.00
ATOM    139  CB  ALA    28      -0.040   7.404   5.467  1.00 10.00
ATOM    140  N   GLU    29       1.746   4.839   5.357  1.00 10.00
ATOM    141  CA  GLU    29       3.010   4.130   5.200  1.00 10.00
ATOM    142  C   GLU    29       2.909   3.056   4.126  1.00 10.00
ATOM    143  O   GLU    29       3.794   2.925   3.280  1.00 10.00
ATOM    144  CB  GLU    29       3.442   3.519   6.525  1.00 10.00
ATOM    145  N   GLN    30       1.825   2.287   4.164  1.00 10.00
ATOM    146  CA  GLN    30       1.605   1.224   3.191  1.00 10.00
ATOM    147  C   GLN    30       1.510   1.783   1.777  1.00 10.00
ATOM    148  O   GLN    30       2.107   1.245   0.845  1.00 10.00
ATOM    149  CB  GLN    30       0.349   0.440   3.538  1.00 10.00
ATOM    150  N   GLN    31       0.757   2.868   1.624  1.00 10.00
ATOM    151  CA  GLN    31       0.576   3.497   0.322  1.00 10.00
ATOM    152  C   GLN    31       1.908   3.952  -0.260  1.00 10.00
ATOM    153  O   GLN    31       2.130   3.872  -1.468  1.00 10.00
ATOM    154  CB  GLN    31      -0.387   4.670   0.428  1.00 10.00
ATOM    155  N   LYS    32       2.794   4.431   0.608  1.00 10.00
ATOM    156  CA  LYS    32       4.111   4.889   0.183  1.00 10.00
ATOM    157  C   LYS    32       4.991   3.719  -0.240  1.00 10.00
ATOM    158  O   LYS    32       5.707   3.798  -1.239  1.00 10.00
ATOM    159  CB  LYS    32       4.781   5.682   1.295  1.00 10.00
ATOM    160  N   LEU    33       4.933   2.635   0.526  1.00 10.00
ATOM    161  CA  LEU    33       5.680   1.426   0.199  1.00 10.00
ATOM    162  C   LEU    33       5.094   0.729  -1.022  1.00 10.00
ATOM    163  O   LEU    33       5.826   0.184  -1.849  1.00 10.00
ATOM    164  CB  LEU    33       5.705   0.481   1.390  1.00 10.00
ATOM    165  N   ARG    34       3.770   0.752  -1.131  1.00 10.00
ATOM    166  CA  ARG    34       3.089   0.229  -2.309  1.00 10.00
ATOM    167  C   ARG    34       3.523   0.967  -3.568  1.00 10.00
ATOM    168  O   ARG    34       3.720   0.359  -4.621  1.00 10.00
ATOM    169  CB  ARG    34       1.581   0.317  -2.133  1.00 10.00
ATOM    170  N   GLN    35       3.670   2.283  -3.456  1.00 10.00
ATOM    171  CA  GLN    35       4.105   3.105  -4.579  1.00 10.00
ATOM    172  C   GLN    35       5.542   2.784  -4.972  1.00 10.00
ATOM    173  O   GLN    35       5.861   2.673  -6.155  1.00 10.00
ATOM    174  CB  GLN    35       3.963   4.582  -4.243  1.00 10.00
ATOM    175  N   GLU    36       6.404   2.636  -3.972  1.00 10.00
ATOM    176  CA  GLU    36       7.788   2.244  -4.206  1.00 10.00
ATOM    177  C   GLU    36       7.867   0.932  -4.975  1.00 10.00
ATOM    178  O   GLU    36       8.563   0.834  -5.985  1.00 10.00
ATOM    179  CB  GLU    36       8.539   2.133  -2.888  1.00 10.00
ATOM    180  N   TYR    37       7.146  -0.075  -4.492  1.00 10.00
ATOM    181  CA  TYR    37       7.108  -1.375  -5.151  1.00 10.00
ATOM    182  C   TYR    37       6.605  -1.253  -6.583  1.00 10.00
ATOM    183  O   TYR    37       7.222  -1.769  -7.514  1.00 10.00
ATOM    184  CB  TYR    37       6.241  -2.344  -4.362  1.00 10.00
ATOM    185  N   LEU    38       5.478  -0.569  -6.752  1.00 10.00
ATOM    186  CA  LEU    38       4.844  -0.447  -8.060  1.00 10.00
ATOM    187  C   LEU    38       5.771   0.229  -9.061  1.00 10.00
ATOM    188  O   LEU    38       5.949  -0.254 -10.179  1.00 10.00
ATOM    189  CB  LEU    38       3.534   0.317  -7.944  1.00 10.00
ATOM    190  N   LYS    39       6.358   1.349  -8.652  1.00 10.00
ATOM    191  CA  LYS    39       7.264   2.098  -9.516  1.00 10.00
ATOM    192  C   LYS    39       8.404   1.219 -10.012  1.00 10.00
ATOM    193  O   LYS    39       8.674   1.154 -11.211  1.00 10.00
ATOM    194  CB  LYS    39       7.807   3.315  -8.785  1.00 10.00
ATOM    195  N   GLY    40       9.072   0.544  -9.082  1.00 10.00
ATOM    196  CA  GLY    40      10.185  -0.333  -9.423  1.00 10.00
ATOM    197  C   GLY    40       9.719  -1.508 -10.272  1.00 10.00
ATOM    198  O   GLY    40      10.418  -1.938 -11.190  1.00 10.00
TER
END
