
#######################################################
#                                                     #
#                        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 T0335TS383_3-D1
# Molecule2: number of CA atoms   36 (  584),  selected   36 , name T0335_D1.pdb
# PARAMETERS: T0335TS383_3-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           #
LGA    K       6      R       9           -
LGA    I       7      I      10           -
LGA    A       8      N      11           -
LGA    R       9      -       -           -
LGA    I      10      -       -           -
LGA    N      11      -       -           -
LGA    E      12      -       -           -
LGA    L      13      -       -           -
LGA    A      14      E      12           #
LGA    A      15      L      13           -
LGA    K      16      A      14           -
LGA    A      17      A      15          5.304
LGA    K      18      K      16          2.548
LGA    A      19      A      17          1.807
LGA    G      20      K      18          1.128
LGA    -       -      A      19           -
LGA    -       -      G      20           -
LGA    V      21      V      21          1.378
LGA    I      22      I      22          1.819
LGA    T      23      T      23          0.423
LGA    E      24      E      24          1.547
LGA    E      25      E      25          1.644
LGA    E      26      E      26          1.211
LGA    K      27      K      27          1.569
LGA    -       -      A      28           -
LGA    -       -      E      29           -
LGA    -       -      Q      30           -
LGA    -       -      Q      31           -
LGA    A      28      K      32          0.250
LGA    E      29      L      33          1.055
LGA    Q      30      R      34          1.227
LGA    Q      31      Q      35          0.787
LGA    K      32      E      36          1.463
LGA    L      33      Y      37          1.972
LGA    R      34      L      38          1.524
LGA    Q      35      K      39          1.816
LGA    E      36      G      40          2.811
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     20    1.95    55.00     51.066     0.973

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.723193 * X  +  -0.354417 * Y  +   0.592774 * Z  +   5.456182
  Y_new =   0.525047 * X  +  -0.275460 * Y  +  -0.805262 * Z  +  -2.878931
  Z_new =   0.448684 * X  +   0.893594 * Y  +  -0.013125 * Z  + -12.442093 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.585483   -1.556110  [ DEG:    90.8415    -89.1585 ]
  Theta =  -0.465293   -2.676300  [ DEG:   -26.6593   -153.3407 ]
  Phi   =   0.627972   -2.513621  [ DEG:    35.9801   -144.0199 ]
 
# 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: T0335TS383_3-D1                               
REMARK     2: T0335_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0335TS383_3-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   20   1.95   55.00  51.066
REMARK  ---------------------------------------------------------- 
MOLECULE T0335TS383_3-D1
PFRMAT TS
TARGET T0335
MODEL 3
PARENT 2cs1A
ATOM      5  N   ALA     5      -8.220 -12.152  -1.471  1.00  0.00
ATOM      6  CA  ALA     5      -8.379 -13.608  -1.529  1.00  0.00
ATOM      7  C   ALA     5      -8.362 -14.248  -0.145  1.00  0.00
ATOM      8  O   ALA     5      -9.185 -15.111   0.159  1.00  0.00
ATOM      9  N   LYS     6      -7.420 -13.818   0.689  1.00  0.00
ATOM     10  CA  LYS     6      -7.298 -14.351   2.041  1.00  0.00
ATOM     11  C   LYS     6      -8.619 -14.235   2.793  1.00  0.00
ATOM     12  O   LYS     6      -8.934 -15.064   3.648  1.00  0.00
ATOM     13  N   ILE     7      -9.391 -13.203   2.470  1.00  0.00
ATOM     14  CA  ILE     7     -10.678 -12.978   3.116  1.00  0.00
ATOM     15  C   ILE     7     -11.723 -13.966   2.605  1.00  0.00
ATOM     16  O   ILE     7     -12.645 -14.343   3.330  1.00  0.00
ATOM     17  N   ALA     8     -11.573 -14.380   1.352  1.00  0.00
ATOM     18  CA  ALA     8     -12.504 -15.323   0.742  1.00  0.00
ATOM     19  C   ALA     8     -12.208 -16.750   1.194  1.00  0.00
ATOM     20  O   ALA     8     -13.058 -17.412   1.790  1.00  0.00
ATOM     21  N   ARG     9     -10.996 -17.217   0.908  1.00  0.00
ATOM     22  CA  ARG     9     -10.588 -18.563   1.288  1.00  0.00
ATOM     23  C   ARG     9     -11.097 -18.920   2.681  1.00  0.00
ATOM     24  O   ARG     9     -11.776 -19.930   2.863  1.00  0.00
ATOM     25  N   ILE    10     -10.768 -18.081   3.658  1.00  0.00
ATOM     26  CA  ILE    10     -11.194 -18.307   5.035  1.00  0.00
ATOM     27  C   ILE    10     -12.675 -17.985   5.205  1.00  0.00
ATOM     28  O   ILE    10     -13.371 -18.617   6.000  1.00  0.00
ATOM     29  N   ASN    11     -13.150 -16.998   4.454  1.00  0.00
ATOM     30  CA  ASN    11     -14.549 -16.589   4.523  1.00  0.00
ATOM     31  C   ASN    11     -15.167 -16.529   3.129  1.00  0.00
ATOM     32  O   ASN    11     -15.291 -15.464   2.524  1.00  0.00
ATOM     33  N   GLU    12     -18.633  -7.447  -0.870  1.00  0.00
ATOM     34  CA  GLU    12     -18.646  -7.420   0.588  1.00  0.00
ATOM     35  C   GLU    12     -17.239  -7.606   1.147  1.00  0.00
ATOM     36  O   GLU    12     -16.811  -6.868   2.036  1.00  0.00
ATOM     37  N   LEU    13     -16.524  -8.595   0.622  1.00  0.00
ATOM     38  CA  LEU    13     -15.164  -8.877   1.068  1.00  0.00
ATOM     39  C   LEU    13     -14.282  -7.638   0.954  1.00  0.00
ATOM     40  O   LEU    13     -13.574  -7.278   1.895  1.00  0.00
ATOM     41  N   ALA    14     -14.328  -6.988  -0.205  1.00  0.00
ATOM     42  CA  ALA    14     -13.532  -5.791  -0.442  1.00  0.00
ATOM     43  C   ALA    14     -14.077  -4.603   0.343  1.00  0.00
ATOM     44  O   ALA    14     -13.354  -3.973   1.115  1.00  0.00
ATOM     45  N   ALA    15     -15.355  -4.304   0.140  1.00  0.00
ATOM     46  CA  ALA    15     -15.997  -3.190   0.830  1.00  0.00
ATOM     47  C   ALA    15     -15.498  -3.079   2.267  1.00  0.00
ATOM     48  O   ALA    15     -15.377  -1.979   2.808  1.00  0.00
ATOM     49  N   LYS    16     -15.206  -4.223   2.877  1.00  0.00
ATOM     50  CA  LYS    16     -14.717  -4.253   4.250  1.00  0.00
ATOM     51  C   LYS    16     -13.216  -3.988   4.300  1.00  0.00
ATOM     52  O   LYS    16     -12.728  -3.291   5.190  1.00  0.00
ATOM     53  N   ALA    17     -12.547  -0.031   3.813  1.00  0.00
ATOM     54  CA  ALA    17     -12.776   0.765   5.013  1.00  0.00
ATOM     55  C   ALA    17     -11.780   0.398   6.109  1.00  0.00
ATOM     56  O   ALA    17     -11.553   1.169   7.042  1.00  0.00
ATOM     57  N   LYS    18     -11.187  -0.786   5.989  1.00  0.00
ATOM     58  CA  LYS    18     -10.215  -1.258   6.969  1.00  0.00
ATOM     59  C   LYS    18      -8.844  -0.640   6.716  1.00  0.00
ATOM     60  O   LYS    18      -7.974  -0.658   7.587  1.00  0.00
ATOM     61  N   ALA    19      -8.659  -0.095   5.519  1.00  0.00
ATOM     62  CA  ALA    19      -7.394   0.531   5.152  1.00  0.00
ATOM     63  C   ALA    19      -7.424   2.029   5.435  1.00  0.00
ATOM     64  O   ALA    19      -6.380   2.664   5.585  1.00  0.00
ATOM     65  N   GLY    20      -8.626   2.589   5.507  1.00  0.00
ATOM     66  CA  GLY    20      -8.794   4.012   5.774  1.00  0.00
ATOM     67  C   GLY    20      -8.696   4.302   7.268  1.00  0.00
ATOM     68  O   GLY    20      -8.426   5.432   7.676  1.00  0.00
ATOM     69  N   VAL    21      -8.915   3.273   8.081  1.00  0.00
ATOM     70  CA  VAL    21      -8.852   3.416   9.530  1.00  0.00
ATOM     71  C   VAL    21      -7.440   3.167  10.046  1.00  0.00
ATOM     72  O   VAL    21      -7.141   3.415  11.214  1.00  0.00
ATOM     73  N   ILE    22      -6.572   2.675   9.167  1.00  0.00
ATOM     74  CA  ILE    22      -5.189   2.392   9.533  1.00  0.00
ATOM     75  C   ILE    22      -4.450   3.675   9.900  1.00  0.00
ATOM     76  O   ILE    22      -4.943   4.777   9.662  1.00  0.00
ATOM     77  N   THR    23      -3.263   3.523  10.479  1.00  0.00
ATOM     78  CA  THR    23      -2.456   4.670  10.880  1.00  0.00
ATOM     79  C   THR    23      -1.516   5.093   9.755  1.00  0.00
ATOM     80  O   THR    23      -1.481   4.469   8.695  1.00  0.00
ATOM     81  N   GLU    24      -0.758   6.158   9.994  1.00  0.00
ATOM     82  CA  GLU    24       0.181   6.666   9.001  1.00  0.00
ATOM     83  C   GLU    24       1.285   5.649   8.726  1.00  0.00
ATOM     84  O   GLU    24       1.406   5.135   7.615  1.00  0.00
ATOM     85  N   GLU    25       2.087   5.364   9.748  1.00  0.00
ATOM     86  CA  GLU    25       3.182   4.410   9.616  1.00  0.00
ATOM     87  C   GLU    25       2.710   3.132   8.926  1.00  0.00
ATOM     88  O   GLU    25       3.246   2.741   7.890  1.00  0.00
ATOM     89  N   GLU    26       1.705   2.488   9.511  1.00  0.00
ATOM     90  CA  GLU    26       1.162   1.255   8.953  1.00  0.00
ATOM     91  C   GLU    26       1.029   1.356   7.437  1.00  0.00
ATOM     92  O   GLU    26       1.315   0.403   6.712  1.00  0.00
ATOM     93  N   LYS    27       0.592   2.518   6.963  1.00  0.00
ATOM     94  CA  LYS    27       0.421   2.746   5.532  1.00  0.00
ATOM     95  C   LYS    27       1.772   2.891   4.839  1.00  0.00
ATOM     96  O   LYS    27       2.005   2.305   3.782  1.00  0.00
ATOM     97  N   ALA    28       5.811   2.327   0.390  1.00  0.00
ATOM     98  CA  ALA    28       7.133   2.080  -0.174  1.00  0.00
ATOM     99  C   ALA    28       7.072   1.003  -1.253  1.00  0.00
ATOM    100  O   ALA    28       7.899   0.971  -2.164  1.00  0.00
ATOM    101  N   GLU    29       6.086   0.119  -1.143  1.00  0.00
ATOM    102  CA  GLU    29       5.914  -0.962  -2.107  1.00  0.00
ATOM    103  C   GLU    29       5.381  -0.428  -3.432  1.00  0.00
ATOM    104  O   GLU    29       5.521  -1.070  -4.473  1.00  0.00
ATOM    105  N   GLN    30       4.768   0.752  -3.386  1.00  0.00
ATOM    106  CA  GLN    30       4.217   1.373  -4.584  1.00  0.00
ATOM    107  C   GLN    30       5.239   2.290  -5.248  1.00  0.00
ATOM    108  O   GLN    30       5.373   2.305  -6.471  1.00  0.00
ATOM    109  N   GLN    31       5.959   3.054  -4.431  1.00  0.00
ATOM    110  CA  GLN    31       6.967   3.975  -4.939  1.00  0.00
ATOM    111  C   GLN    31       8.150   3.221  -5.537  1.00  0.00
ATOM    112  O   GLN    31       8.664   3.588  -6.595  1.00  0.00
ATOM    113  N   LYS    32       8.577   2.163  -4.856  1.00  0.00
ATOM    114  CA  LYS    32       9.698   1.355  -5.321  1.00  0.00
ATOM    115  C   LYS    32       9.433   0.811  -6.721  1.00  0.00
ATOM    116  O   LYS    32      10.365   0.545  -7.480  1.00  0.00
ATOM    117  N   LEU    33       8.158   0.649  -7.056  1.00  0.00
ATOM    118  CA  LEU    33       7.770   0.139  -8.366  1.00  0.00
ATOM    119  C   LEU    33       7.383   1.281  -9.300  1.00  0.00
ATOM    120  O   LEU    33       7.090   1.063 -10.477  1.00  0.00
ATOM    121  N   ARG    34       7.379   2.498  -8.769  1.00  0.00
ATOM    122  CA  ARG    34       7.025   3.676  -9.554  1.00  0.00
ATOM    123  C   ARG    34       8.020   3.890 -10.692  1.00  0.00
ATOM    124  O   ARG    34       7.705   4.540 -11.688  1.00  0.00
ATOM    125  N   GLN    35       9.218   3.336 -10.536  1.00  0.00
ATOM    126  CA  GLN    35      10.256   3.465 -11.552  1.00  0.00
ATOM    127  C   GLN    35       9.719   3.091 -12.930  1.00  0.00
ATOM    128  O   GLN    35      10.309   3.439 -13.953  1.00  0.00
ATOM    129  N   GLU    36       8.598   2.378 -12.948  1.00  0.00
ATOM    130  CA  GLU    36       7.983   1.954 -14.199  1.00  0.00
ATOM    131  C   GLU    36       7.237   3.111 -14.858  1.00  0.00
ATOM    132  O   GLU    36       7.470   3.429 -16.024  1.00  0.00
ATOM    133  N   TYR    37       6.339   3.736 -14.104  1.00  0.00
ATOM    134  CA  TYR    37       5.558   4.855 -14.615  1.00  0.00
ATOM    135  C   TYR    37       6.467   5.990 -15.074  1.00  0.00
ATOM    136  O   TYR    37       6.192   6.657 -16.071  1.00  0.00
ATOM    137  N   LEU    38       7.554   6.203 -14.339  1.00  0.00
ATOM    138  CA  LEU    38       8.506   7.258 -14.669  1.00  0.00
ATOM    139  C   LEU    38       9.137   7.011 -16.035  1.00  0.00
ATOM    140  O   LEU    38       9.539   7.950 -16.724  1.00  0.00
ATOM    141  N   LYS    39       9.221   5.743 -16.424  1.00  0.00
ATOM    142  CA  LYS    39       9.806   5.372 -17.707  1.00  0.00
ATOM    143  C   LYS    39       8.792   5.536 -18.834  1.00  0.00
ATOM    144  O   LYS    39       9.153   5.853 -19.967  1.00  0.00
ATOM    145  N   GLY    40       7.520   5.317 -18.514  1.00  0.00
ATOM    146  CA  GLY    40       6.452   5.440 -19.499  1.00  0.00
ATOM    147  C   GLY    40       6.108   6.905 -19.749  1.00  0.00
ATOM    148  O   GLY    40       5.216   7.217 -20.537  1.00  0.00
TER
END
