
#######################################################
#                                                     #
#                        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 T0335AL381_2-D1
# Molecule2: number of CA atoms   36 (  584),  selected   36 , name T0335_D1.pdb
# PARAMETERS: T0335AL381_2-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           -
LGA    A       5      N      11          1.574
LGA    K       6      E      12          3.209
LGA    -       -      L      13           -
LGA    I       7      A      14          1.774
LGA    A       8      A      15          3.155
LGA    R       9      K      16          2.389
LGA    I      10      A      17          0.895
LGA    -       -      K      18           -
LGA    -       -      A      19           -
LGA    -       -      G      20           -
LGA    N      11      V      21          2.655
LGA    E      12      I      22          3.113
LGA    L      13      T      23          0.739
LGA    -       -      E      24           -
LGA    A      14      E      25          1.573
LGA    A      15      E      26          1.133
LGA    K      16      K      27          2.562
LGA    A      17      A      28          2.140
LGA    K      18      E      29          0.886
LGA    A      19      Q      30          1.510
LGA    G      20      Q      31          2.450
LGA    V      21      K      32          2.489
LGA    I      22      L      33          1.606
LGA    T      23      R      34          1.127
LGA    E      24      Q      35          1.308
LGA    E      25      E      36          1.482
LGA    E      26      Y      37          1.521
LGA    K      27      L      38          1.296
LGA    A      28      K      39          2.274
LGA    E      29      G      40          1.549
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     25    1.99    16.00     62.695     1.195

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.731971 * X  +  -0.551089 * Y  +   0.400649 * Z  +  20.232632
  Y_new =  -0.652286 * X  +  -0.736677 * Y  +   0.178409 * Z  +  41.530815
  Z_new =   0.196829 * X  +  -0.391928 * Y  +  -0.898694 * Z  +   6.111078 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.730351    0.411242  [ DEG:  -156.4376     23.5624 ]
  Theta =  -0.198123   -2.943470  [ DEG:   -11.3516   -168.6484 ]
  Phi   =  -0.727896    2.413696  [ DEG:   -41.7054    138.2946 ]
 
# 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: T0335AL381_2-D1                               
REMARK     2: T0335_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0335AL381_2-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   25   1.99   16.00  62.695
REMARK  ---------------------------------------------------------- 
MOLECULE T0335AL381_2-D1
REMARK Aligment from pdb entry: 2fzfA
ATOM     13  N   ALA     5      -5.039  -0.657  -3.148  1.00  0.00              
ATOM     14  CA  ALA     5      -6.283  -1.008  -2.474  1.00  0.00              
ATOM     15  C   ALA     5      -6.039  -1.428  -1.049  1.00  0.00              
ATOM     16  O   ALA     5      -6.893  -1.255  -0.181  1.00  0.00              
ATOM     17  N   LYS     6      -4.878  -2.021  -0.825  1.00  0.00              
ATOM     18  CA  LYS     6      -4.511  -2.475   0.498  1.00  0.00              
ATOM     19  C   LYS     6      -4.411  -1.239   1.378  1.00  0.00              
ATOM     20  O   LYS     6      -5.097  -1.134   2.386  1.00  0.00              
ATOM     21  N   ILE     7      -3.563  -0.291   0.985  1.00  0.00              
ATOM     22  CA  ILE     7      -3.394   0.915   1.788  1.00  0.00              
ATOM     23  C   ILE     7      -4.743   1.577   2.000  1.00  0.00              
ATOM     24  O   ILE     7      -5.093   1.941   3.118  1.00  0.00              
ATOM     25  N   ALA     8      -5.482   1.717   0.904  1.00  0.00              
ATOM     26  CA  ALA     8      -6.803   2.324   0.887  1.00  0.00              
ATOM     27  C   ALA     8      -7.661   1.818   2.040  1.00  0.00              
ATOM     28  O   ALA     8      -8.429   2.559   2.658  1.00  0.00              
ATOM     29  N   ARG     9      -7.524   0.535   2.318  1.00  0.00              
ATOM     30  CA  ARG     9      -8.287  -0.105   3.368  1.00  0.00              
ATOM     31  C   ARG     9      -7.314  -0.551   4.445  1.00  0.00              
ATOM     32  O   ARG     9      -6.670  -1.583   4.301  1.00  0.00              
ATOM     33  N   ILE    10      -7.175   0.224   5.512  1.00  0.00              
ATOM     34  CA  ILE    10      -6.253  -0.166   6.572  1.00  0.00              
ATOM     35  C   ILE    10      -6.623   0.474   7.903  1.00  0.00              
ATOM     36  O   ILE    10      -6.693  -0.209   8.929  1.00  0.00              
ATOM     37  N   ASN    11      -6.867   1.778   7.897  1.00  0.00              
ATOM     38  CA  ASN    11      -7.238   2.467   9.128  1.00  0.00              
ATOM     39  C   ASN    11      -6.139   2.338  10.174  1.00  0.00              
ATOM     40  O   ASN    11      -6.398   2.454  11.370  1.00  0.00              
ATOM     41  N   GLU    12      -4.914   2.093   9.719  1.00  0.00              
ATOM     42  CA  GLU    12      -3.782   1.960  10.621  1.00  0.00              
ATOM     43  C   GLU    12      -2.695   2.937  10.213  1.00  0.00              
ATOM     44  O   GLU    12      -1.794   2.601   9.448  1.00  0.00              
ATOM     45  N   LEU    13      -2.808   4.157  10.728  1.00  0.00              
ATOM     46  CA  LEU    13      -1.860   5.228  10.446  1.00  0.00              
ATOM     47  C   LEU    13      -0.418   4.809  10.735  1.00  0.00              
ATOM     48  O   LEU    13       0.228   5.349  11.638  1.00  0.00              
ATOM     49  N   ALA    14       0.085   3.850   9.966  1.00  0.00              
ATOM     50  CA  ALA    14       1.448   3.368  10.143  1.00  0.00              
ATOM     51  C   ALA    14       1.746   2.339   9.070  1.00  0.00              
ATOM     52  O   ALA    14       2.714   2.457   8.320  1.00  0.00              
ATOM     53  N   ALA    15       0.892   1.328   9.009  1.00  0.00              
ATOM     54  CA  ALA    15       1.036   0.272   8.042  1.00  0.00              
ATOM     55  C   ALA    15       0.603   0.791   6.675  1.00  0.00              
ATOM     56  O   ALA    15       1.232   0.486   5.661  1.00  0.00              
ATOM     57  N   LYS    16      -0.468   1.584   6.662  1.00  0.00              
ATOM     58  CA  LYS    16      -0.985   2.191   5.434  1.00  0.00              
ATOM     59  C   LYS    16       0.128   3.048   4.865  1.00  0.00              
ATOM     60  O   LYS    16       0.212   3.255   3.656  1.00  0.00              
ATOM     61  N   ALA    17       0.973   3.553   5.765  1.00  0.00              
ATOM     62  CA  ALA    17       2.120   4.394   5.412  1.00  0.00              
ATOM     63  C   ALA    17       3.137   3.513   4.685  1.00  0.00              
ATOM     64  O   ALA    17       3.550   3.824   3.565  1.00  0.00              
ATOM     65  N   LYS    18       3.541   2.421   5.339  1.00  0.00              
ATOM     66  CA  LYS    18       4.487   1.473   4.762  1.00  0.00              
ATOM     67  C   LYS    18       3.899   0.951   3.465  1.00  0.00              
ATOM     68  O   LYS    18       4.553   0.972   2.433  1.00  0.00              
ATOM     69  N   ALA    19       2.655   0.497   3.495  1.00  0.00              
ATOM     70  CA  ALA    19       2.089  -0.024   2.265  1.00  0.00              
ATOM     71  C   ALA    19       1.994   1.002   1.153  1.00  0.00              
ATOM     72  O   ALA    19       2.007   0.640  -0.016  1.00  0.00              
ATOM     73  N   GLY    20       1.907   2.279   1.513  1.00  0.00              
ATOM     74  CA  GLY    20       1.828   3.342   0.521  1.00  0.00              
ATOM     75  C   GLY    20       3.195   3.668  -0.099  1.00  0.00              
ATOM     76  O   GLY    20       3.297   3.891  -1.307  1.00  0.00              
ATOM     77  N   VAL    21       4.245   3.691   0.718  1.00  0.00              
ATOM     78  CA  VAL    21       5.581   3.981   0.210  1.00  0.00              
ATOM     79  C   VAL    21       6.014   2.853  -0.707  1.00  0.00              
ATOM     80  O   VAL    21       6.694   3.059  -1.712  1.00  0.00              
ATOM     81  N   ILE    22       5.609   1.647  -0.339  1.00  0.00              
ATOM     82  CA  ILE    22       5.938   0.458  -1.093  1.00  0.00              
ATOM     83  C   ILE    22       5.220   0.484  -2.442  1.00  0.00              
ATOM     84  O   ILE    22       5.774   0.061  -3.454  1.00  0.00              
ATOM     85  N   THR    23       3.993   0.990  -2.462  1.00  0.00              
ATOM     86  CA  THR    23       3.225   1.066  -3.706  1.00  0.00              
ATOM     87  C   THR    23       3.861   2.040  -4.699  1.00  0.00              
ATOM     88  O   THR    23       3.901   1.780  -5.905  1.00  0.00              
ATOM     89  N   GLU    24       4.349   3.161  -4.171  1.00  0.00              
ATOM     90  CA  GLU    24       4.986   4.203  -4.970  1.00  0.00              
ATOM     91  C   GLU    24       6.274   3.690  -5.574  1.00  0.00              
ATOM     92  O   GLU    24       6.515   3.818  -6.777  1.00  0.00              
ATOM     93  N   GLU    25       7.102   3.107  -4.718  1.00  0.00              
ATOM     94  CA  GLU    25       8.376   2.543  -5.135  1.00  0.00              
ATOM     95  C   GLU    25       8.214   1.639  -6.356  1.00  0.00              
ATOM     96  O   GLU    25       8.979   1.744  -7.310  1.00  0.00              
ATOM     97  N   GLU    26       7.218   0.761  -6.331  1.00  0.00              
ATOM     98  CA  GLU    26       7.003  -0.156  -7.436  1.00  0.00              
ATOM     99  C   GLU    26       6.209   0.401  -8.599  1.00  0.00              
ATOM    100  O   GLU    26       5.845  -0.351  -9.503  1.00  0.00              
ATOM    101  N   LYS    27       5.922   1.700  -8.588  1.00  0.00              
ATOM    102  CA  LYS    27       5.151   2.299  -9.686  1.00  0.00              
ATOM    103  C   LYS    27       6.007   2.418 -10.933  1.00  0.00              
ATOM    104  O   LYS    27       5.523   2.249 -12.053  1.00  0.00              
ATOM    105  N   ALA    28       7.287   2.703 -10.727  1.00  0.00              
ATOM    106  CA  ALA    28       8.215   2.857 -11.828  1.00  0.00              
ATOM    107  C   ALA    28       8.656   1.534 -12.445  1.00  0.00              
ATOM    108  O   ALA    28       9.282   1.534 -13.501  1.00  0.00              
ATOM    109  N   GLU    29       8.341   0.415 -11.798  1.00  0.00              
ATOM    110  CA  GLU    29       8.741  -0.898 -12.312  1.00  0.00              
ATOM    111  C   GLU    29       8.124  -1.200 -13.680  1.00  0.00              
ATOM    112  O   GLU    29       8.790  -1.707 -14.583  1.00  0.00              
ATOM    113  N   GLN    30       6.841  -0.895 -13.824  1.00  0.00              
ATOM    114  CA  GLN    30       6.145  -1.159 -15.067  1.00  0.00              
ATOM    115  C   GLN    30       6.771  -0.412 -16.220  1.00  0.00              
ATOM    116  O   GLN    30       7.178  -1.010 -17.212  1.00  0.00              
ATOM    117  N   GLN    31       6.838   0.908 -16.089  1.00  0.00              
ATOM    118  CA  GLN    31       7.417   1.741 -17.132  1.00  0.00              
ATOM    119  C   GLN    31       8.852   1.306 -17.428  1.00  0.00              
ATOM    120  O   GLN    31       9.293   1.387 -18.570  1.00  0.00              
ATOM    121  N   LYS    32       9.577   0.842 -16.409  1.00  0.00              
ATOM    122  CA  LYS    32      10.954   0.397 -16.613  1.00  0.00              
ATOM    123  C   LYS    32      11.016  -0.860 -17.474  1.00  0.00              
ATOM    124  O   LYS    32      11.873  -0.991 -18.351  1.00  0.00              
ATOM    125  N   LEU    33      10.101  -1.784 -17.223  1.00  0.00              
ATOM    126  CA  LEU    33      10.063  -3.028 -17.970  1.00  0.00              
ATOM    127  C   LEU    33       9.602  -2.795 -19.395  1.00  0.00              
ATOM    128  O   LEU    33      10.135  -3.395 -20.321  1.00  0.00              
ATOM    129  N   ARG    34       8.611  -1.920 -19.561  1.00  0.00              
ATOM    130  CA  ARG    34       8.050  -1.623 -20.876  1.00  0.00              
ATOM    131  C   ARG    34       9.134  -1.020 -21.752  1.00  0.00              
ATOM    132  O   ARG    34       9.134  -1.188 -22.976  1.00  0.00              
ATOM    133  N   GLN    35      10.064  -0.323 -21.113  1.00  0.00              
ATOM    134  CA  GLN    35      11.155   0.290 -21.834  1.00  0.00              
ATOM    135  C   GLN    35      12.098  -0.785 -22.324  1.00  0.00              
ATOM    136  O   GLN    35      12.519  -0.772 -23.484  1.00  0.00              
ATOM    137  N   GLU    36      12.436  -1.717 -21.439  1.00  0.00              
ATOM    138  CA  GLU    36      13.337  -2.797 -21.807  1.00  0.00              
ATOM    139  C   GLU    36      12.701  -3.601 -22.947  1.00  0.00              
ATOM    140  O   GLU    36      13.322  -3.795 -23.985  1.00  0.00              
ATOM    141  N   TYR    37      11.461  -4.043 -22.759  1.00  0.00              
ATOM    142  CA  TYR    37      10.779  -4.820 -23.778  1.00  0.00              
ATOM    143  C   TYR    37      10.814  -4.102 -25.121  1.00  0.00              
ATOM    144  O   TYR    37      10.826  -4.723 -26.177  1.00  0.00              
ATOM    145  N   LEU    38      10.839  -2.780 -25.066  1.00  0.00              
ATOM    146  CA  LEU    38      10.878  -1.943 -26.262  1.00  0.00              
ATOM    147  C   LEU    38      12.317  -1.933 -26.787  1.00  0.00              
ATOM    148  O   LEU    38      12.547  -1.872 -27.992  1.00  0.00              
ATOM    149  N   LYS    39      13.279  -2.011 -25.870  1.00  0.00              
ATOM    150  CA  LYS    39      14.696  -2.027 -26.228  1.00  0.00              
ATOM    151  C   LYS    39      15.147  -3.350 -26.853  1.00  0.00              
ATOM    152  O   LYS    39      16.040  -3.355 -27.697  1.00  0.00              
ATOM    153  N   GLY    40      14.543  -4.470 -26.458  1.00  0.00              
ATOM    154  CA  GLY    40      14.947  -5.762 -27.024  1.00  0.00              
ATOM    155  C   GLY    40      13.949  -6.228 -28.097  1.00  0.00              
ATOM    156  O   GLY    40      14.228  -7.168 -28.844  1.00  0.00              
END
