
#######################################################
#                                                     #
#                        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 T0335TS239_1-D1
# Molecule2: number of CA atoms   36 (  584),  selected   36 , name T0335_D1.pdb
# PARAMETERS: T0335TS239_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       5      A       8          2.055
LGA    K       6      R       9          1.675
LGA    I       7      I      10          0.798
LGA    A       8      N      11          0.679
LGA    R       9      E      12          0.952
LGA    I      10      L      13          1.309
LGA    N      11      A      14          1.278
LGA    E      12      A      15          1.290
LGA    L      13      K      16          1.427
LGA    A      14      A      17          1.348
LGA    A      15      K      18          0.811
LGA    -       -      A      19           -
LGA    -       -      G      20           -
LGA    K      16      V      21          1.377
LGA    A      17      I      22          1.112
LGA    K      18      T      23          1.716
LGA    A      19      E      24          2.261
LGA    G      20      E      25          4.458
LGA    V      21      E      26           -
LGA    I      22      K      27           -
LGA    T      23      A      28           -
LGA    E      24      E      29           -
LGA    E      25      Q      30           -
LGA    E      26      Q      31           -
LGA    K      27      -       -           -
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      K      32           #
LGA    L      38      L      33           -
LGA    K      39      R      34           -
LGA    G      40      Q      35          5.835
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     17    2.22    17.65     42.320     0.733

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.259580 * X  +  -0.904159 * Y  +  -0.339284 * Z  +  39.458912
  Y_new =  -0.897866 * X  +  -0.096588 * Y  +  -0.429544 * Z  +   2.546071
  Z_new =   0.355605 * X  +   0.416133 * Y  +  -0.836886 * Z  +  10.900370 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.680156   -0.461437  [ DEG:   153.5616    -26.4384 ]
  Theta =  -0.363562   -2.778031  [ DEG:   -20.8305   -159.1694 ]
  Phi   =  -1.289362    1.852231  [ DEG:   -73.8750    106.1250 ]
 
# 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: T0335TS239_1-D1                               
REMARK     2: T0335_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0335TS239_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   17   2.22   17.65  42.320
REMARK  ---------------------------------------------------------- 
MOLECULE T0335TS239_1-D1
PFRMAT TS
TARGET T0335
MODEL 1
PARENT 2axp_A
ATOM     21  N   ALA     5      -3.677  -5.147  -6.382  1.00  9.99
ATOM     22  CA  ALA     5      -5.007  -5.513  -5.902  1.00  9.99
ATOM     23  C   ALA     5      -4.909  -5.910  -4.428  1.00  9.99
ATOM     24  O   ALA     5      -5.733  -5.506  -3.610  1.00  9.99
ATOM     25  CB  ALA     5      -5.558  -6.678  -6.734  1.00  9.99
ATOM     26  N   LYS     6      -3.889  -6.686  -4.088  1.00  9.99
ATOM     27  CA  LYS     6      -3.701  -7.118  -2.704  1.00  9.99
ATOM     28  C   LYS     6      -3.413  -5.955  -1.769  1.00  9.99
ATOM     29  O   LYS     6      -3.740  -5.997  -0.584  1.00  9.99
ATOM     30  CB  LYS     6      -2.553  -8.110  -2.604  1.00  9.99
ATOM     31  N   ILE     7      -2.779  -4.923  -2.302  1.00  9.99
ATOM     32  CA  ILE     7      -2.458  -3.777  -1.489  1.00  9.99
ATOM     33  C   ILE     7      -3.744  -3.016  -1.186  1.00  9.99
ATOM     34  O   ILE     7      -4.091  -2.789  -0.016  1.00  9.99
ATOM     35  CB  ILE     7      -1.483  -2.866  -2.226  1.00  9.99
ATOM     36  N   ALA     8      -4.449  -2.632  -2.248  1.00  9.99
ATOM     37  CA  ALA     8      -5.700  -1.882  -2.123  1.00  9.99
ATOM     38  C   ALA     8      -6.697  -2.635  -1.245  1.00  9.99
ATOM     39  O   ALA     8      -7.543  -2.038  -0.572  1.00  9.99
ATOM     40  CB  ALA     8      -6.280  -1.608  -3.515  1.00  9.99
ATOM     41  N   ARG     9      -6.573  -3.955  -1.240  1.00  9.99
ATOM     42  CA  ARG     9      -7.435  -4.779  -0.423  1.00  9.99
ATOM     43  C   ARG     9      -7.131  -4.507   1.042  1.00  9.99
ATOM     44  O   ARG     9      -8.036  -4.263   1.842  1.00  9.99
ATOM     45  CB  ARG     9      -7.192  -6.247  -0.749  1.00  9.99
ATOM     46  N   ILE    10      -5.845  -4.548   1.382  1.00  9.99
ATOM     47  CA  ILE    10      -5.397  -4.301   2.749  1.00  9.99
ATOM     48  C   ILE    10      -5.632  -2.845   3.155  1.00  9.99
ATOM     49  O   ILE    10      -6.093  -2.572   4.268  1.00  9.99
ATOM     50  CB  ILE    10      -3.901  -4.704   2.913  1.00  9.99
ATOM     51  N   ASN    11      -5.354  -1.911   2.255  1.00  9.99
ATOM     52  CA  ASN    11      -5.577  -0.509   2.584  1.00  9.99
ATOM     53  C   ASN    11      -7.061  -0.260   2.867  1.00  9.99
ATOM     54  O   ASN    11      -7.400   0.578   3.696  1.00  9.99
ATOM     55  CB  ASN    11      -5.123   0.398   1.447  1.00  9.99
ATOM     56  N   GLU    12      -7.932  -0.988   2.169  1.00  9.99
ATOM     57  CA  GLU    12      -9.378  -0.864   2.344  1.00  9.99
ATOM     58  C   GLU    12      -9.785  -1.312   3.728  1.00  9.99
ATOM     59  O   GLU    12     -10.617  -0.679   4.376  1.00  9.99
ATOM     60  CB  GLU    12     -10.134  -1.732   1.337  1.00  9.99
ATOM     61  N   LEU    13      -9.210  -2.422   4.175  1.00  9.99
ATOM     62  CA  LEU    13      -9.537  -2.961   5.493  1.00  9.99
ATOM     63  C   LEU    13      -9.024  -2.097   6.647  1.00  9.99
ATOM     64  O   LEU    13      -9.460  -2.256   7.792  1.00  9.99
ATOM     65  CB  LEU    13      -8.969  -4.375   5.661  1.00  9.99
ATOM     66  N   ALA    14      -8.097  -1.188   6.349  1.00  9.99
ATOM     67  CA  ALA    14      -7.511  -0.334   7.373  1.00  9.99
ATOM     68  C   ALA    14      -7.748   1.159   7.142  1.00  9.99
ATOM     69  O   ALA    14      -7.457   1.970   8.008  1.00  9.99
ATOM     70  CB  ALA    14      -5.980  -0.601   7.486  1.00  9.99
ATOM     71  N   ALA    15      -8.304   1.510   5.988  1.00  9.99
ATOM     72  CA  ALA    15      -8.556   2.910   5.641  1.00  9.99
ATOM     73  C   ALA    15      -9.157   3.761   6.756  1.00  9.99
ATOM     74  O   ALA    15      -8.882   4.959   6.852  1.00  9.99
ATOM     75  CB  ALA    15      -9.480   3.001   4.418  1.00  9.99
ATOM     76  N   LYS    16      -9.001   2.995  10.194  1.00  9.99
ATOM     77  CA  LYS    16      -8.260   2.911  11.436  1.00  9.99
ATOM     78  C   LYS    16      -6.754   3.003  11.225  1.00  9.99
ATOM     79  O   LYS    16      -5.978   2.510  12.050  1.00  9.99
ATOM     80  CB  LYS    16      -8.560   1.576  12.108  1.00  9.99
ATOM     81  N   ALA    17      -6.322   3.626  10.140  1.00  9.99
ATOM     82  CA  ALA    17      -4.893   3.665   9.884  1.00  9.99
ATOM     83  C   ALA    17      -4.228   5.022   9.829  1.00  9.99
ATOM     84  O   ALA    17      -4.764   5.978   9.263  1.00  9.99
ATOM     85  CB  ALA    17      -4.596   2.911   8.599  1.00  9.99
ATOM     86  N   LYS    18      -3.053   5.090  10.443  1.00  9.99
ATOM     87  CA  LYS    18      -2.209   6.294  10.440  1.00  9.99
ATOM     88  C   LYS    18      -0.878   5.787   9.898  1.00  9.99
ATOM     89  O   LYS    18      -0.130   5.080  10.579  1.00  9.99
ATOM     90  CB  LYS    18      -2.027   6.856  11.859  1.00  9.99
ATOM     91  N   ALA    19      -0.613   6.115   8.648  1.00  9.99
ATOM     92  CA  ALA    19       0.612   5.683   8.006  1.00  9.99
ATOM     93  C   ALA    19       1.682   6.726   8.258  1.00  9.99
ATOM     94  O   ALA    19       1.569   7.878   7.824  1.00  9.99
ATOM     95  CB  ALA    19       0.409   5.521   6.496  1.00  9.99
ATOM     96  N   GLY    20       2.718   6.311   8.968  1.00  9.99
ATOM     97  CA  GLY    20       3.801   7.207   9.303  1.00  9.99
ATOM     98  C   GLY    20       5.089   6.864   8.563  1.00  9.99
ATOM     99  O   GLY    20       5.540   5.713   8.534  1.00  9.99
ATOM    100  N   VAL    21       5.672   7.889   7.961  1.00  9.99
ATOM    101  CA  VAL    21       6.908   7.737   7.236  1.00  9.99
ATOM    102  C   VAL    21       8.021   8.602   7.832  1.00  9.99
ATOM    103  O   VAL    21       8.025   9.823   7.698  1.00  9.99
ATOM    104  CB  VAL    21       6.685   8.106   5.779  1.00  9.99
ATOM    105  N   ILE    22       8.955   7.943   8.498  1.00  9.99
ATOM    106  CA  ILE    22      10.099   8.597   9.108  1.00  9.99
ATOM    107  C   ILE    22      11.295   8.424   8.174  1.00  9.99
ATOM    108  O   ILE    22      11.678   7.293   7.858  1.00  9.99
ATOM    109  CB  ILE    22      10.412   7.954  10.456  1.00  9.99
ATOM    110  N   THR    23      11.887   9.540   7.751  1.00  9.99
ATOM    111  CA  THR    23      13.027   9.516   6.846  1.00  9.99
ATOM    112  C   THR    23      14.085  10.558   7.249  1.00  9.99
ATOM    113  O   THR    23      14.045  11.094   8.357  1.00  9.99
ATOM    114  CB  THR    23      12.542   9.800   5.432  1.00  9.99
ATOM    115  N   GLU    24      15.033  10.816   6.347  1.00  9.99
ATOM    116  CA  GLU    24      16.112  11.798   6.532  1.00  9.99
ATOM    117  C   GLU    24      16.854  11.917   5.213  1.00  9.99
ATOM    118  O   GLU    24      16.693  11.072   4.333  1.00  9.99
ATOM    119  CB  GLU    24      17.085  11.355   7.631  1.00  9.99
ATOM    120  N   GLU    25      17.657  12.969   5.070  1.00  9.99
ATOM    121  CA  GLU    25      18.435  13.164   3.846  1.00  9.99
ATOM    122  C   GLU    25      19.472  12.046   3.705  1.00  9.99
ATOM    123  O   GLU    25      19.979  11.527   4.708  1.00  9.99
ATOM    124  CB  GLU    25      19.153  14.515   3.861  1.00  9.99
ATOM    125  N   GLU    26      19.805  11.679   2.454  1.00  9.99
ATOM    126  CA  GLU    26      20.776  10.625   2.125  1.00  9.99
ATOM    127  C   GLU    26      22.100  10.851   2.845  1.00  9.99
ATOM    128  O   GLU    26      22.698   9.927   3.412  1.00  9.99
ATOM    129  CB  GLU    26      20.926  10.754   0.611  1.00  9.99
ATOM    130  N   LYS    27      22.554  12.095   2.802  1.00  9.99
ATOM    131  CA  LYS    27      23.800  12.478   3.440  1.00  9.99
ATOM    132  C   LYS    27      23.710  12.187   4.928  1.00  9.99
ATOM    133  O   LYS    27      24.607  11.566   5.501  1.00  9.99
ATOM    134  CB  LYS    27      24.060  13.957   3.192  1.00  9.99
ATOM    135  N   ALA    28      22.619  12.611   5.557  1.00  9.99
ATOM    136  CA  ALA    28      22.459  12.358   6.982  1.00  9.99
ATOM    137  C   ALA    28      22.422  10.865   7.297  1.00  9.99
ATOM    138  O   ALA    28      23.047  10.417   8.263  1.00  9.99
ATOM    139  CB  ALA    28      21.170  13.001   7.544  1.00  9.99
ATOM    140  N   GLU    29      21.702  10.087   6.494  1.00  9.99
ATOM    141  CA  GLU    29      21.619   8.655   6.775  1.00  9.99
ATOM    142  C   GLU    29      22.964   7.945   6.666  1.00  9.99
ATOM    143  O   GLU    29      23.292   7.099   7.506  1.00  9.99
ATOM    144  CB  GLU    29      20.565   7.934   5.866  1.00  9.99
ATOM    145  N   GLN    30      23.739   8.271   5.635  1.00  9.99
ATOM    146  CA  GLN    30      25.057   7.644   5.481  1.00  9.99
ATOM    147  C   GLN    30      25.918   8.037   6.687  1.00  9.99
ATOM    148  O   GLN    30      26.647   7.203   7.250  1.00  9.99
ATOM    149  CB  GLN    30      25.718   8.084   4.165  1.00  9.99
ATOM    150  N   GLN    31      25.810   9.298   7.100  1.00  9.99
ATOM    151  CA  GLN    31      26.563   9.766   8.250  1.00  9.99
ATOM    152  C   GLN    31      26.197   8.914   9.481  1.00  9.99
ATOM    153  O   GLN    31      27.085   8.427  10.199  1.00  9.99
ATOM    154  CB  GLN    31      26.294  11.270   8.469  1.00  9.99
ATOM    155  N   LYS    32      24.902   8.684   9.709  1.00  9.99
ATOM    156  CA  LYS    32      24.477   7.876  10.876  1.00  9.99
ATOM    157  C   LYS    32      24.928   6.429  10.731  1.00  9.99
ATOM    158  O   LYS    32      25.235   5.758  11.716  1.00  9.99
ATOM    159  CB  LYS    32      22.951   7.924  11.057  1.00  9.99
ATOM    160  N   LEU    33      24.952   5.962   9.487  1.00  9.99
ATOM    161  CA  LEU    33      25.382   4.605   9.184  1.00  9.99
ATOM    162  C   LEU    33      26.866   4.502   9.508  1.00  9.99
ATOM    163  O   LEU    33      27.309   3.554  10.165  1.00  9.99
ATOM    164  CB  LEU    33      25.127   4.291   7.704  1.00  9.99
ATOM    165  N   ARG    34      27.638   5.483   9.049  1.00  9.99
ATOM    166  CA  ARG    34      29.070   5.481   9.333  1.00  9.99
ATOM    167  C   ARG    34      29.293   5.516  10.833  1.00  9.99
ATOM    168  O   ARG    34      30.130   4.785  11.372  1.00  9.99
ATOM    169  CB  ARG    34      29.759   6.668   8.663  1.00  9.99
ATOM    170  N   GLN    35      20.357   6.168  -1.523  1.00  9.99
ATOM    171  CA  GLN    35      19.662   7.106  -2.390  1.00  9.99
ATOM    172  C   GLN    35      18.504   6.410  -3.066  1.00  9.99
ATOM    173  O   GLN    35      17.397   6.944  -3.129  1.00  9.99
ATOM    174  CB  GLN    35      20.621   7.654  -3.447  1.00  9.99
ATOM    175  N   GLU    36      18.768   5.211  -3.569  1.00  9.99
ATOM    176  CA  GLU    36      17.742   4.426  -4.238  1.00  9.99
ATOM    177  C   GLU    36      16.629   4.037  -3.258  1.00  9.99
ATOM    178  O   GLU    36      15.443   4.182  -3.559  1.00  9.99
ATOM    179  CB  GLU    36      18.358   3.167  -4.848  1.00  9.99
ATOM    180  N   TYR    37      17.019   3.539  -2.087  1.00  9.99
ATOM    181  CA  TYR    37      16.047   3.146  -1.079  1.00  9.99
ATOM    182  C   TYR    37      15.136   4.326  -0.787  1.00  9.99
ATOM    183  O   TYR    37      13.917   4.185  -0.787  1.00  9.99
ATOM    184  CB  TYR    37      16.738   2.678   0.234  1.00  9.99
ATOM    185  N   LEU    38      15.726   5.492  -0.553  1.00  9.99
ATOM    186  CA  LEU    38      14.935   6.680  -0.270  1.00  9.99
ATOM    187  C   LEU    38      14.098   7.079  -1.463  1.00  9.99
ATOM    188  O   LEU    38      12.934   7.443  -1.317  1.00  9.99
ATOM    189  CB  LEU    38      15.829   7.853   0.124  1.00  9.99
ATOM    190  N   LYS    39      14.685   7.015  -2.649  1.00  9.99
ATOM    191  CA  LYS    39      13.955   7.394  -3.845  1.00  9.99
ATOM    192  C   LYS    39      12.800   6.423  -4.060  1.00  9.99
ATOM    193  O   LYS    39      11.727   6.798  -4.538  1.00  9.99
ATOM    194  CB  LYS    39      14.904   7.404  -5.046  1.00  9.99
ATOM    195  N   GLY    40      13.024   5.176  -3.665  1.00  9.99
ATOM    196  CA  GLY    40      12.028   4.114  -3.794  1.00  9.99
ATOM    197  C   GLY    40      10.871   4.286  -2.801  1.00  9.99
ATOM    198  O   GLY    40       9.705   4.122  -3.165  1.00  9.99
TER
END
