
#######################################################
#                                                     #
#                        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   34 (  168),  selected   34 , name T0335TS245_1-D1
# Molecule2: number of CA atoms   36 (  584),  selected   36 , name T0335_D1.pdb
# PARAMETERS: T0335TS245_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      A       5           -
LGA    K       6      K       6           #
LGA    I       7      -       -           -
LGA    A       8      -       -           -
LGA    R       9      -       -           -
LGA    I      10      I       7          1.498
LGA    N      11      -       -           -
LGA    E      12      A       8          3.542
LGA    L      13      R       9          2.768
LGA    A      14      I      10          2.574
LGA    A      15      N      11          2.415
LGA    K      16      E      12          0.775
LGA    A      17      L      13          0.598
LGA    K      18      A      14          2.130
LGA    A      19      A      15          3.715
LGA    -       -      K      16           -
LGA    -       -      A      17           -
LGA    -       -      K      18           -
LGA    -       -      A      19           -
LGA    -       -      G      20           -
LGA    G      20      V      21          4.875
LGA    V      21      I      22          4.650
LGA    I      22      T      23          1.685
LGA    E      24      E      24          2.252
LGA    E      25      E      25          2.918
LGA    E      26      E      26          2.729
LGA    K      27      K      27          2.512
LGA    A      28      A      28          2.628
LGA    E      29      E      29          1.906
LGA    Q      30      Q      30          0.732
LGA    Q      31      Q      31          1.728
LGA    K      32      K      32          1.554
LGA    L      33      L      33          1.907
LGA    R      34      R      34          1.954
LGA    Q      35      Q      35          1.668
LGA    E      36      E      36          2.125
LGA    L      38      Y      37          3.035
LGA    K      39      L      38          3.206
LGA    -       -      K      39           -
LGA    G      40      G      40          1.449

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   34   36    5.0     28    2.55    57.14     63.400     1.055

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.588071 * X  +   0.782431 * Y  +   0.204875 * Z  + -36.633575
  Y_new =   0.803919 * X  +   0.593265 * Y  +   0.041843 * Z  +   2.130997
  Z_new =  -0.088806 * X  +   0.189310 * Y  +  -0.977893 * Z  +  97.356644 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.950369   -0.191224  [ DEG:   169.0437    -10.9563 ]
  Theta =   0.088923    3.052669  [ DEG:     5.0949    174.9051 ]
  Phi   =   2.202356   -0.939237  [ DEG:   126.1857    -53.8143 ]
 
# 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: T0335TS245_1-D1                               
REMARK     2: T0335_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0335TS245_1-D1.T0335_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   34   36   5.0   28   2.55   57.14  63.400
REMARK  ---------------------------------------------------------- 
MOLECULE T0335TS245_1-D1
PFRMAT TS
TARGET T0335
MODEL 1
PARENT 1dg3A
ATOM      6  N   ALA     5      -3.526  -7.495 -16.398  1.00  0.00
ATOM      7  CA  ALA     5      -3.825  -8.433 -15.322  1.00  0.00
ATOM      8  C   ALA     5      -3.065  -8.045 -14.059  1.00  0.00
ATOM      9  O   ALA     5      -3.584  -8.184 -12.930  1.00  0.00
ATOM     10  CB  ALA     5      -3.420  -9.840 -15.767  1.00  0.00
ATOM     11  N   LYS     6      -1.842  -7.579 -14.236  1.00  0.00
ATOM     12  CA  LYS     6      -1.005  -7.191 -13.104  1.00  0.00
ATOM     13  C   LYS     6      -1.510  -5.921 -12.442  1.00  0.00
ATOM     14  O   LYS     6      -1.524  -5.860 -11.193  1.00  0.00
ATOM     15  CB  LYS     6       0.420  -6.985 -13.619  1.00  0.00
ATOM     16  N   ILE     7      -1.918  -4.953 -13.200  1.00  0.00
ATOM     17  CA  ILE     7      -2.433  -3.702 -12.655  1.00  0.00
ATOM     18  C   ILE     7      -3.719  -3.950 -11.879  1.00  0.00
ATOM     19  O   ILE     7      -3.898  -3.368 -10.787  1.00  0.00
ATOM     20  CB  ILE     7      -2.695  -2.735 -13.810  1.00  0.00
ATOM     21  N   ALA     8      -4.583  -4.789 -12.389  1.00  0.00
ATOM     22  CA  ALA     8      -5.836  -5.115 -11.717  1.00  0.00
ATOM     23  C   ALA     8      -5.565  -5.872 -10.425  1.00  0.00
ATOM     24  O   ALA     8      -6.170  -5.537  -9.384  1.00  0.00
ATOM     25  CB  ALA     8      -6.687  -5.970 -12.658  1.00  0.00
ATOM     26  N   ARG     9      -4.664  -6.820 -10.450  1.00  0.00
ATOM     27  CA  ARG     9      -4.297  -7.562  -9.250  1.00  0.00
ATOM     28  C   ARG     9      -3.692  -6.622  -8.214  1.00  0.00
ATOM     29  O   ARG     9      -3.927  -6.776  -6.996  1.00  0.00
ATOM     30  CB  ARG     9      -3.286  -8.646  -9.629  1.00  0.00
ATOM     31  N   ILE    10      -2.911  -5.672  -8.677  1.00  0.00
ATOM     32  CA  ILE    10      -2.258  -4.722  -7.779  1.00  0.00
ATOM     33  C   ILE    10      -3.290  -3.802  -7.141  1.00  0.00
ATOM     34  O   ILE    10      -3.227  -3.578  -5.913  1.00  0.00
ATOM     35  CB  ILE    10      -1.246  -3.902  -8.582  1.00  0.00
ATOM     36  N   ASN    11      -4.221  -3.296  -7.912  1.00  0.00
ATOM     37  CA  ASN    11      -5.265  -2.423  -7.388  1.00  0.00
ATOM     38  C   ASN    11      -6.116  -3.167  -6.368  1.00  0.00
ATOM     39  O   ASN    11      -6.501  -2.586  -5.330  1.00  0.00
ATOM     40  CB  ASN    11      -6.135  -1.947  -8.552  1.00  0.00
ATOM     41  N   GLU    12      -6.402  -4.434  -6.634  1.00  0.00
ATOM     42  CA  GLU    12      -7.193  -5.250  -5.721  1.00  0.00
ATOM     43  C   GLU    12      -6.470  -5.403  -4.388  1.00  0.00
ATOM     44  O   GLU    12      -7.125  -5.347  -3.324  1.00  0.00
ATOM     45  CB  GLU    12      -7.417  -6.624  -6.358  1.00  0.00
ATOM     46  N   LEU    13      -5.171  -5.595  -4.420  1.00  0.00
ATOM     47  CA  LEU    13      -4.384  -5.761  -3.199  1.00  0.00
ATOM     48  C   LEU    13      -4.342  -4.457  -2.415  1.00  0.00
ATOM     49  O   LEU    13      -4.494  -4.477  -1.174  1.00  0.00
ATOM     50  CB  LEU    13      -2.966  -6.190  -3.584  1.00  0.00
ATOM     51  N   ALA    14      -4.151  -3.340  -3.101  1.00  0.00
ATOM     52  CA  ALA    14      -4.107  -2.042  -2.437  1.00  0.00
ATOM     53  C   ALA    14      -5.416  -1.826  -1.688  1.00  0.00
ATOM     54  O   ALA    14      -5.452  -1.315  -0.548  1.00  0.00
ATOM     55  CB  ALA    14      -3.911  -0.942  -3.483  1.00  0.00
ATOM     56  N   ALA    15      -6.511  -2.262  -2.325  1.00  0.00
ATOM     57  CA  ALA    15      -7.825  -2.161  -1.702  1.00  0.00
ATOM     58  C   ALA    15      -7.888  -3.027  -0.451  1.00  0.00
ATOM     59  O   ALA    15      -8.416  -2.579   0.589  1.00  0.00
ATOM     60  CB  ALA    15      -8.882  -2.616  -2.709  1.00  0.00
ATOM     61  N   LYS    16      -7.325  -4.220  -0.516  1.00  0.00
ATOM     62  CA  LYS    16      -7.282  -5.110   0.639  1.00  0.00
ATOM     63  C   LYS    16      -6.460  -4.482   1.757  1.00  0.00
ATOM     64  O   LYS    16      -6.818  -4.626   2.946  1.00  0.00
ATOM     65  CB  LYS    16      -6.659  -6.441   0.212  1.00  0.00
ATOM     66  N   ALA    17      -5.369  -3.819   1.410  1.00  0.00
ATOM     67  CA  ALA    17      -4.491  -3.201   2.403  1.00  0.00
ATOM     68  C   ALA    17      -5.215  -2.066   3.114  1.00  0.00
ATOM     69  O   ALA    17      -5.559  -2.330   4.286  1.00  0.00
ATOM     70  CB  ALA    17      -3.246  -2.667   1.692  1.00  0.00
ATOM     71  N   LYS    18      -5.706  -1.070   2.440  1.00  0.00
ATOM     72  CA  LYS    18      -6.703  -0.150   2.954  1.00  0.00
ATOM     73  C   LYS    18      -8.020  -0.831   3.257  1.00  0.00
ATOM     74  O   LYS    18      -7.623  -0.522   4.401  1.00  0.00
ATOM     75  CB  LYS    18      -6.905   0.944   1.905  1.00  0.00
ATOM     76  N   ALA    19      -8.999  -1.857   3.018  1.00  0.00
ATOM     77  CA  ALA    19      -9.417  -2.439   4.300  1.00  0.00
ATOM     78  C   ALA    19      -8.960  -1.901   5.649  1.00  0.00
ATOM     79  O   ALA    19      -9.967  -1.350   5.156  1.00  0.00
ATOM     80  CB  ALA    19      -8.981  -3.896   4.140  1.00  0.00
ATOM     81  N   GLY    20      -6.607  -0.359  11.415  1.00  0.00
ATOM     82  CA  GLY    20      -6.345   0.220  12.720  1.00  0.00
ATOM     83  C   GLY    20      -4.867   0.296  13.036  1.00  0.00
ATOM     84  O   GLY    20      -4.120   0.990  13.759  1.00  0.00
ATOM     86  N   VAL    21      -4.390  -0.208  11.016  1.00  0.00
ATOM     87  CA  VAL    21      -3.156   0.347  10.657  1.00  0.00
ATOM     88  C   VAL    21      -2.874   1.751  10.971  1.00  0.00
ATOM     89  O   VAL    21      -4.084   1.814  11.281  1.00  0.00
ATOM     90  CB  VAL    21      -3.079   0.122   9.146  1.00  0.00
ATOM     91  N   ILE    22      -2.092   2.500  11.348  1.00  0.00
ATOM     92  CA  ILE    22      -2.198   3.666  12.221  1.00  0.00
ATOM     93  C   ILE    22      -1.799   4.810  11.325  1.00  0.00
ATOM     94  O   ILE    22      -2.268   4.850  10.167  1.00  0.00
ATOM     95  CB  ILE    22      -1.248   3.579  13.417  1.00  0.00
ATOM     96  N   GLU    24      -1.033   5.764  11.823  1.00  0.00
ATOM     97  CA  GLU    24      -0.670   6.949  11.056  1.00  0.00
ATOM     98  C   GLU    24       0.266   6.658   9.901  1.00  0.00
ATOM     99  O   GLU    24       0.201   7.424   8.915  1.00  0.00
ATOM    100  CB  GLU    24      -0.015   7.931  12.028  1.00  0.00
ATOM    101  N   GLU    25       1.103   5.648   9.966  1.00  0.00
ATOM    102  CA  GLU    25       2.040   5.318   8.897  1.00  0.00
ATOM    103  C   GLU    25       1.491   4.498   7.747  1.00  0.00
ATOM    104  O   GLU    25       2.336   3.921   7.030  1.00  0.00
ATOM    105  CB  GLU    25       3.188   4.568   9.576  1.00  0.00
ATOM    106  N   GLU    26       0.221   4.345   7.598  1.00  0.00
ATOM    107  CA  GLU    26      -0.378   3.489   6.581  1.00  0.00
ATOM    108  C   GLU    26      -0.060   3.983   5.177  1.00  0.00
ATOM    109  O   GLU    26       0.231   3.136   4.306  1.00  0.00
ATOM    110  CB  GLU    26      -1.892   3.474   6.802  1.00  0.00
ATOM    111  N   LYS    27      -0.134   5.257   4.930  1.00  0.00
ATOM    112  CA  LYS    27       0.116   5.825   3.608  1.00  0.00
ATOM    113  C   LYS    27       1.600   5.873   3.288  1.00  0.00
ATOM    114  O   LYS    27       1.964   5.481   2.158  1.00  0.00
ATOM    115  CB  LYS    27      -0.473   7.237   3.579  1.00  0.00
ATOM    116  N   ALA    28       2.416   6.295   4.171  1.00  0.00
ATOM    117  CA  ALA    28       3.852   6.357   3.937  1.00  0.00
ATOM    118  C   ALA    28       4.434   4.973   3.695  1.00  0.00
ATOM    119  O   ALA    28       5.345   4.849   2.847  1.00  0.00
ATOM    120  CB  ALA    28       4.508   6.997   5.161  1.00  0.00
ATOM    121  N   GLU    29       3.965   3.963   4.395  1.00  0.00
ATOM    122  CA  GLU    29       4.466   2.602   4.243  1.00  0.00
ATOM    123  C   GLU    29       4.094   2.020   2.889  1.00  0.00
ATOM    124  O   GLU    29       4.957   1.347   2.282  1.00  0.00
ATOM    125  CB  GLU    29       3.871   1.748   5.364  1.00  0.00
ATOM    126  N   GLN    30       2.883   2.215   2.421  1.00  0.00
ATOM    127  CA  GLN    30       2.419   1.671   1.149  1.00  0.00
ATOM    128  C   GLN    30       3.032   2.403  -0.033  1.00  0.00
ATOM    129  O   GLN    30       3.431   1.717  -0.999  1.00  0.00
ATOM    130  CB  GLN    30       0.895   1.793   1.109  1.00  0.00
ATOM    131  N   GLN    31       3.120   3.692  -0.002  1.00  0.00
ATOM    132  CA  GLN    31       3.694   4.474  -1.090  1.00  0.00
ATOM    133  C   GLN    31       5.177   4.165  -1.243  1.00  0.00
ATOM    134  O   GLN    31       5.657   3.948  -2.377  1.00  0.00
ATOM    135  CB  GLN    31       3.496   5.960  -0.784  1.00  0.00
ATOM    136  N   LYS    32       5.884   4.084  -0.141  1.00  0.00
ATOM    137  CA  LYS    32       7.298   3.728  -0.191  1.00  0.00
ATOM    138  C   LYS    32       7.474   2.364  -0.847  1.00  0.00
ATOM    139  O   LYS    32       8.440   2.121  -1.602  1.00  0.00
ATOM    140  CB  LYS    32       7.849   3.700   1.236  1.00  0.00
ATOM    141  N   LEU    33       6.534   1.465  -0.561  1.00  0.00
ATOM    142  CA  LEU    33       6.579   0.118  -1.127  1.00  0.00
ATOM    143  C   LEU    33       6.252   0.158  -2.613  1.00  0.00
ATOM    144  O   LEU    33       6.990  -0.454  -3.415  1.00  0.00
ATOM    145  CB  LEU    33       5.566  -0.759  -0.388  1.00  0.00
ATOM    146  N   ARG    34       5.231   0.866  -2.991  1.00  0.00
ATOM    147  CA  ARG    34       4.869   1.000  -4.396  1.00  0.00
ATOM    148  C   ARG    34       5.943   1.739  -5.177  1.00  0.00
ATOM    149  O   ARG    34       6.198   1.400  -6.352  1.00  0.00
ATOM    150  CB  ARG    34       3.544   1.761  -4.478  1.00  0.00
ATOM    151  N   GLN    35       6.589   2.709  -4.552  1.00  0.00
ATOM    152  CA  GLN    35       7.657   3.460  -5.201  1.00  0.00
ATOM    153  C   GLN    35       8.810   2.535  -5.567  1.00  0.00
ATOM    154  O   GLN    35       9.402   2.675  -6.659  1.00  0.00
ATOM    155  CB  GLN    35       8.141   4.551  -4.243  1.00  0.00
ATOM    156  N   GLU    36       9.121   1.587  -4.691  1.00  0.00
ATOM    157  CA  GLU    36      10.188   0.627  -4.943  1.00  0.00
ATOM    158  C   GLU    36       9.855  -0.274  -6.121  1.00  0.00
ATOM    159  O   GLU    36      10.774  -0.559  -6.919  1.00  0.00
ATOM    160  CB  GLU    36      10.385  -0.210  -3.679  1.00  0.00
ATOM    161  N   LEU    38       8.637  -0.705  -6.263  1.00  0.00
ATOM    162  CA  LEU    38       8.207  -1.564  -7.362  1.00  0.00
ATOM    163  C   LEU    38       7.826  -0.884  -8.664  1.00  0.00
ATOM    164  O   LEU    38       7.316  -1.541  -9.597  1.00  0.00
ATOM    165  CB  LEU    38       7.016  -2.351  -6.811  1.00  0.00
ATOM    166  N   LYS    39       8.049   0.433  -8.735  1.00  0.00
ATOM    167  CA  LYS    39       7.711   1.211  -9.921  1.00  0.00
ATOM    168  C   LYS    39       8.531   0.735 -11.115  1.00  0.00
ATOM    169  O   LYS    39       7.976   0.622 -12.230  1.00  0.00
ATOM    170  CB  LYS    39       7.999   2.687  -9.640  1.00  0.00
ATOM    171  N   GLY    40       9.789   0.472 -10.919  1.00  0.00
ATOM    172  CA  GLY    40      10.659   0.019 -12.004  1.00  0.00
ATOM    173  C   GLY    40      10.239  -1.366 -12.476  1.00  0.00
ATOM    174  O   GLY    40      10.154  -1.601 -13.700  1.00  0.00
TER
END
