
#######################################################
#                                                     #
#                        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_4-D1
# Molecule2: number of CA atoms   36 (  584),  selected   36 , name T0335_D1.pdb
# PARAMETERS: T0335TS437_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      A       5          1.152
LGA    K       6      K       6          1.152
LGA    I       7      I       7          1.887
LGA    A       8      A       8          1.675
LGA    R       9      R       9          0.864
LGA    I      10      I      10          1.270
LGA    N      11      N      11          1.818
LGA    E      12      E      12          1.401
LGA    L      13      L      13          0.468
LGA    A      14      A      14          1.633
LGA    A      15      A      15          2.134
LGA    K      16      K      16          1.602
LGA    A      17      A      17          1.484
LGA    K      18      K      18          5.871
LGA    -       -      A      19           -
LGA    -       -      G      20           -
LGA    -       -      V      21           -
LGA    -       -      I      22           -
LGA    A      19      T      23          2.082
LGA    G      20      E      24          3.365
LGA    -       -      E      25           -
LGA    -       -      E      26           -
LGA    -       -      K      27           -
LGA    V      21      A      28          2.803
LGA    -       -      E      29           -
LGA    -       -      Q      30           -
LGA    I      22      Q      31          0.560
LGA    T      23      K      32          1.686
LGA    -       -      L      33           -
LGA    -       -      R      34           -
LGA    E      24      Q      35          1.308
LGA    E      25      E      36          3.068
LGA    -       -      Y      37           -
LGA    -       -      L      38           -
LGA    E      26      K      39          2.110
LGA    K      27      G      40          5.026
LGA    A      28      -       -           -
LGA    E      29      -       -           -
LGA    Q      30      -       -           -
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     23    2.39    65.22     54.041     0.926

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.672997 * X  +   0.356421 * Y  +   0.648104 * Z  + 119.054825
  Y_new =   0.051339 * X  +  -0.851613 * Y  +   0.521651 * Z  + -46.918617
  Z_new =   0.737861 * X  +   0.384343 * Y  +   0.554835 * Z  + -96.281487 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.605820   -2.535772  [ DEG:    34.7109   -145.2891 ]
  Theta =  -0.829896   -2.311697  [ DEG:   -47.5495   -132.4505 ]
  Phi   =   3.065456   -0.076137  [ DEG:   175.6377     -4.3623 ]
 
# 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_4-D1                               
REMARK     2: T0335_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0335TS437_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   23   2.39   65.22  54.041
REMARK  ---------------------------------------------------------- 
MOLECULE T0335TS437_4-D1
PFRMAT TS
TARGET T0335
MODEL     4 REFINED
PARENT N/A
ATOM     31  N   ALA     5      -2.155 -11.008  -7.155  1.00   .00
ATOM     32  CA  ALA     5      -1.807 -11.285  -5.676  1.00   .00
ATOM     33  C   ALA     5      -1.436  -9.799  -5.063  1.00   .00
ATOM     34  O   ALA     5      -2.096  -9.311  -4.145  1.00   .00
ATOM     35  CB  ALA     5      -0.651 -12.340  -5.557  1.00   .00
ATOM     36  N   LYS     6      -0.399  -9.084  -5.696  1.00   .00
ATOM     37  CA  LYS     6      -0.024  -7.637  -5.328  1.00   .00
ATOM     38  C   LYS     6      -1.280  -6.574  -5.506  1.00   .00
ATOM     39  O   LYS     6      -1.570  -5.775  -4.609  1.00   .00
ATOM     40  CB  LYS     6       1.204  -7.294  -6.245  1.00   .00
ATOM     45  N   ILE     7      -2.037  -6.645  -6.695  1.00   .00
ATOM     46  CA  ILE     7      -3.305  -5.744  -6.912  1.00   .00
ATOM     47  C   ILE     7      -4.508  -6.084  -5.801  1.00   .00
ATOM     48  O   ILE     7      -5.124  -5.167  -5.250  1.00   .00
ATOM     49  CB  ILE     7      -3.765  -5.933  -8.396  1.00   .00
ATOM     53  N   ALA     8      -4.735  -7.436  -5.492  1.00   .00
ATOM     54  CA  ALA     8      -5.758  -7.893  -4.411  1.00   .00
ATOM     55  C   ALA     8      -5.262  -7.452  -2.887  1.00   .00
ATOM     56  O   ALA     8      -6.046  -6.859  -2.138  1.00   .00
ATOM     57  CB  ALA     8      -5.949  -9.428  -4.587  1.00   .00
ATOM     58  N   ARG     9      -3.933  -7.718  -2.510  1.00   .00
ATOM     59  CA  ARG     9      -3.363  -7.251  -1.138  1.00   .00
ATOM     60  C   ARG     9      -3.396  -5.600  -0.994  1.00   .00
ATOM     61  O   ARG     9      -3.802  -5.092   0.061  1.00   .00
ATOM     62  CB  ARG     9      -1.934  -7.862  -0.991  1.00   .00
ATOM     69  N   ILE    10      -3.031  -4.819  -2.096  1.00   .00
ATOM     70  CA  ILE    10      -3.160  -3.274  -2.055  1.00   .00
ATOM     71  C   ILE    10      -4.726  -2.764  -1.864  1.00   .00
ATOM     72  O   ILE    10      -4.999  -1.852  -1.062  1.00   .00
ATOM     73  CB  ILE    10      -2.477  -2.706  -3.361  1.00   .00
ATOM     77  N   ASN    11      -5.734  -3.440  -2.573  1.00   .00
ATOM     78  CA  ASN    11      -7.236  -3.117  -2.360  1.00   .00
ATOM     79  C   ASN    11      -7.727  -3.545  -0.829  1.00   .00
ATOM     80  O   ASN    11      -8.358  -2.749  -0.124  1.00   .00
ATOM     81  CB  ASN    11      -8.016  -3.848  -3.491  1.00   .00
ATOM     85  N   GLU    12      -7.349  -4.808  -0.348  1.00   .00
ATOM     86  CA  GLU    12      -7.692  -5.272   1.100  1.00   .00
ATOM     87  C   GLU    12      -6.963  -4.307   2.254  1.00   .00
ATOM     88  O   GLU    12      -7.634  -3.855   3.191  1.00   .00
ATOM     89  CB  GLU    12      -7.291  -6.789   1.202  1.00   .00
ATOM     94  N   LEU    13      -5.605  -3.986   2.108  1.00   .00
ATOM     95  CA  LEU    13      -4.882  -3.013   3.115  1.00   .00
ATOM     96  C   LEU    13      -5.553  -1.481   3.109  1.00   .00
ATOM     97  O   LEU    13      -5.771  -0.876   4.178  1.00   .00
ATOM     98  CB  LEU    13      -3.372  -3.022   2.757  1.00   .00
ATOM    102  N   ALA    14      -5.920  -0.938   1.864  1.00   .00
ATOM    103  CA  ALA    14      -6.645   0.446   1.752  1.00   .00
ATOM    104  C   ALA    14      -8.176   0.372   2.392  1.00   .00
ATOM    105  O   ALA    14      -8.555   1.254   3.175  1.00   .00
ATOM    106  CB  ALA    14      -6.598   0.852   0.237  1.00   .00
ATOM    107  N   ALA    15      -8.977  -0.734   2.066  1.00   .00
ATOM    108  CA  ALA    15     -10.371  -0.930   2.700  1.00   .00
ATOM    109  C   ALA    15     -10.295  -1.172   4.342  1.00   .00
ATOM    110  O   ALA    15     -11.070  -0.575   5.084  1.00   .00
ATOM    111  CB  ALA    15     -11.039  -2.116   1.933  1.00   .00
ATOM    112  N   LYS    16      -9.328  -2.016   4.864  1.00   .00
ATOM    113  CA  LYS    16      -9.175  -2.224   6.417  1.00   .00
ATOM    114  C   LYS    16      -8.303  -1.019   7.197  1.00   .00
ATOM    115  O   LYS    16      -7.608  -1.267   8.186  1.00   .00
ATOM    116  CB  LYS    16      -8.537  -3.631   6.567  1.00   .00
ATOM    121  N   ALA    17      -8.428   0.258   6.688  1.00   .00
ATOM    122  CA  ALA    17      -7.731   1.523   7.286  1.00   .00
ATOM    123  C   ALA    17      -6.158   1.438   7.804  1.00   .00
ATOM    124  O   ALA    17      -5.836   1.736   8.963  1.00   .00
ATOM    125  CB  ALA    17      -8.706   2.107   8.343  1.00   .00
ATOM    126  N   LYS    18      -5.199   1.062   6.886  1.00   .00
ATOM    127  CA  LYS    18      -3.696   0.989   7.276  1.00   .00
ATOM    128  C   LYS    18      -2.984   2.500   7.354  1.00   .00
ATOM    129  O   LYS    18      -2.639   3.117   6.340  1.00   .00
ATOM    130  CB  LYS    18      -3.027   0.059   6.226  1.00   .00
ATOM    135  N   ALA    19      -2.816   3.042   8.593  1.00   .00
ATOM    136  CA  ALA    19      -2.187   4.473   8.784  1.00   .00
ATOM    137  C   ALA    19      -0.548   4.561   8.635  1.00   .00
ATOM    138  O   ALA    19       0.211   4.521   9.620  1.00   .00
ATOM    139  CB  ALA    19      -2.688   4.992  10.161  1.00   .00
ATOM    140  N   GLY    20      -0.059   4.701   7.363  1.00   .00
ATOM    141  CA  GLY    20       1.478   4.821   7.078  1.00   .00
ATOM    142  C   GLY    20       1.804   5.396   5.624  1.00   .00
ATOM    143  O   GLY    20       0.983   5.315   4.681  1.00   .00
ATOM    144  N   VAL    21       3.027   5.990   5.463  1.00   .00
ATOM    145  CA  VAL    21       3.462   6.584   4.099  1.00   .00
ATOM    146  C   VAL    21       3.933   5.427   3.050  1.00   .00
ATOM    147  O   VAL    21       4.870   4.653   3.318  1.00   .00
ATOM    148  CB  VAL    21       4.612   7.611   4.394  1.00   .00
ATOM    151  N   ILE    22       3.249   5.325   1.857  1.00   .00
ATOM    152  CA  ILE    22       3.618   4.244   0.814  1.00   .00
ATOM    153  C   ILE    22       5.062   4.561   0.044  1.00   .00
ATOM    154  O   ILE    22       5.232   5.610  -0.609  1.00   .00
ATOM    155  CB  ILE    22       2.400   4.134  -0.150  1.00   .00
ATOM    159  N   THR    23       6.071   3.636   0.163  1.00   .00
ATOM    160  CA  THR    23       7.453   3.854  -0.498  1.00   .00
ATOM    161  C   THR    23       7.510   3.521  -2.105  1.00   .00
ATOM    162  O   THR    23       7.576   2.351  -2.520  1.00   .00
ATOM    163  CB  THR    23       8.467   2.980   0.331  1.00   .00
ATOM    166  N   GLU    24       7.487   4.595  -2.972  1.00   .00
ATOM    167  CA  GLU    24       7.542   4.419  -4.502  1.00   .00
ATOM    168  C   GLU    24       9.075   4.307  -5.050  1.00   .00
ATOM    169  O   GLU    24       9.839   5.283  -5.052  1.00   .00
ATOM    170  CB  GLU    24       6.762   5.641  -5.102  1.00   .00
ATOM    175  N   GLU    25       9.479   3.080  -5.477  1.00   .00
ATOM    176  CA  GLU    25      10.902   2.825  -6.026  1.00   .00
ATOM    177  C   GLU    25      10.919   2.807  -7.665  1.00   .00
ATOM    178  O   GLU    25      10.556   1.801  -8.294  1.00   .00
ATOM    179  CB  GLU    25      11.375   1.474  -5.397  1.00   .00
ATOM    184  N   GLU    26      11.343   3.940  -8.320  1.00   .00
ATOM    185  CA  GLU    26      11.391   4.014  -9.877  1.00   .00
ATOM    186  C   GLU    26      12.838   3.570 -10.483  1.00   .00
ATOM    187  O   GLU    26      13.884   4.192 -10.204  1.00   .00
ATOM    188  CB  GLU    26      10.982   5.458 -10.263  1.00   .00
ATOM    193  N   LYS    27      12.845   2.491 -11.308  1.00   .00
ATOM    194  CA  LYS    27      14.130   1.954 -11.958  1.00   .00
ATOM    195  C   LYS    27      14.245   2.432 -13.518  1.00   .00
ATOM    196  O   LYS    27      13.603   1.852 -14.422  1.00   .00
ATOM    197  CB  LYS    27      14.086   0.388 -11.802  1.00   .00
ATOM    202  N   ALA    28      15.081   3.503 -13.794  1.00   .00
ATOM    203  CA  ALA    28      15.301   4.031 -15.290  1.00   .00
ATOM    204  C   ALA    28      16.147   2.982 -16.258  1.00   .00
ATOM    205  O   ALA    28      15.777   2.676 -17.385  1.00   .00
ATOM    206  CB  ALA    28      15.979   5.433 -15.154  1.00   .00
ATOM    207  N   GLU    29      17.239   2.466 -15.681  1.00   .00
ATOM    208  CA  GLU    29      18.144   1.409 -16.305  1.00   .00
ATOM    209  C   GLU    29      18.512   0.400 -15.050  1.00   .00
ATOM    210  O   GLU    29      18.371   0.790 -13.852  1.00   .00
ATOM    211  CB  GLU    29      19.411   2.126 -16.920  1.00   .00
ATOM    216  N   GLN    30      18.992  -0.872 -15.299  1.00   .00
ATOM    217  CA  GLN    30      19.379  -1.834 -14.077  1.00   .00
ATOM    218  C   GLN    30      20.787  -1.360 -13.270  1.00   .00
ATOM    219  O   GLN    30      21.768  -2.090 -13.117  1.00   .00
ATOM    220  CB  GLN    30      19.435  -3.267 -14.666  1.00   .00
ATOM    225  N   GLN    31      20.741  -0.090 -12.820  1.00   .00
ATOM    226  CA  GLN    31      21.854   0.664 -12.070  1.00   .00
ATOM    227  C   GLN    31      21.218   2.017 -11.325  1.00   .00
ATOM    228  O   GLN    31      21.560   2.317 -10.179  1.00   .00
ATOM    229  CB  GLN    31      22.967   1.042 -13.112  1.00   .00
ATOM    234  N   LYS    32      20.305   2.804 -12.044  1.00   .00
ATOM    235  CA  LYS    32      19.671   4.086 -11.464  1.00   .00
ATOM    236  C   LYS    32      18.199   3.829 -10.755  1.00   .00
ATOM    237  O   LYS    32      17.135   3.845 -11.424  1.00   .00
ATOM    238  CB  LYS    32      19.581   5.075 -12.672  1.00   .00
ATOM    243  N   LEU    33      18.196   3.619  -9.389  1.00   .00
ATOM    244  CA  LEU    33      16.881   3.377  -8.588  1.00   .00
ATOM    245  C   LEU    33      16.440   4.671  -7.663  1.00   .00
ATOM    246  O   LEU    33      17.106   5.029  -6.670  1.00   .00
ATOM    247  CB  LEU    33      17.132   2.098  -7.723  1.00   .00
ATOM    251  N   ARG    34      15.305   5.352  -8.031  1.00   .00
ATOM    252  CA  ARG    34      14.792   6.589  -7.245  1.00   .00
ATOM    253  C   ARG    34      13.619   6.217  -6.160  1.00   .00
ATOM    254  O   ARG    34      12.471   5.888  -6.526  1.00   .00
ATOM    255  CB  ARG    34      14.290   7.593  -8.327  1.00   .00
ATOM    262  N   GLN    35      13.968   6.296  -4.829  1.00   .00
ATOM    263  CA  GLN    35      12.961   5.976  -3.691  1.00   .00
ATOM    264  C   GLN    35      12.135   7.299  -3.125  1.00   .00
ATOM    265  O   GLN    35      12.664   8.116  -2.342  1.00   .00
ATOM    266  CB  GLN    35      13.805   5.301  -2.565  1.00   .00
ATOM    271  N   GLU    36      10.839   7.438  -3.543  1.00   .00
ATOM    272  CA  GLU    36       9.951   8.608  -3.069  1.00   .00
ATOM    273  C   GLU    36       8.800   8.098  -1.985  1.00   .00
ATOM    274  O   GLU    36       7.890   7.327  -2.320  1.00   .00
ATOM    275  CB  GLU    36       9.348   9.254  -4.357  1.00   .00
ATOM    280  N   TYR    37       8.891   8.568  -0.694  1.00   .00
ATOM    281  CA  TYR    37       7.847   8.165   0.394  1.00   .00
ATOM    282  C   TYR    37       6.459   9.044   0.277  1.00   .00
ATOM    283  O   TYR    37       6.428  10.268   0.530  1.00   .00
ATOM    284  CB  TYR    37       8.564   8.327   1.765  1.00   .00
ATOM    292  N   LEU    38       5.335   8.378  -0.121  1.00   .00
ATOM    293  CA  LEU    38       3.989   9.091  -0.294  1.00   .00
ATOM    294  C   LEU    38       3.106   9.322   1.075  1.00   .00
ATOM    295  O   LEU    38       2.188   8.532   1.416  1.00   .00
ATOM    296  CB  LEU    38       3.206   8.258  -1.369  1.00   .00
ATOM    300  N   LYS    39       3.390  10.454   1.811  1.00   .00
ATOM    301  CA  LYS    39       2.528  10.833   3.096  1.00   .00
ATOM    302  C   LYS    39       1.108  11.581   2.611  1.00   .00
ATOM    303  O   LYS    39       0.853  12.773   2.827  1.00   .00
ATOM    304  CB  LYS    39       3.425  11.713   3.993  1.00   .00
ATOM    309  N   GLY    40       0.277  10.779   1.906  1.00   .00
ATOM    310  CA  GLY    40      -1.059  11.254   1.259  1.00   .00
ATOM    311  C   GLY    40      -1.153  10.494  -0.113  1.00   .00
ATOM    312  O   GLY    40      -1.655   9.376  -0.167  1.00   .00
TER   
END
