
#######################################################
#                                                     #
#                        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   42 (  168),  selected   42 , name T0335AL381_2
# Molecule2: number of CA atoms   42 (  691),  selected   42 , name T0335.pdb
# PARAMETERS: T0335AL381_2.T0335.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      M       1           -
LGA    -       -      I       2           -
LGA    -       -      S       3           -
LGA    -       -      N       4           -
LGA    I       2      A       5          3.365
LGA    S       3      K       6          2.545
LGA    N       4      I       7          1.860
LGA    A       5      A       8          1.706
LGA    K       6      R       9          2.100
LGA    I       7      I      10          1.541
LGA    A       8      N      11          1.000
LGA    R       9      E      12          1.977
LGA    I      10      L      13          1.973
LGA    -       -      A      14           -
LGA    -       -      A      15           -
LGA    -       -      K      16           -
LGA    N      11      A      17          2.401
LGA    -       -      K      18           -
LGA    -       -      A      19           -
LGA    -       -      G      20           -
LGA    -       -      V      21           -
LGA    -       -      I      22           -
LGA    -       -      T      23           -
LGA    -       -      E      24           -
LGA    -       -      E      25           -
LGA    E      12      E      26          1.881
LGA    L      13      K      27          1.043
LGA    A      14      A      28          1.157
LGA    A      15      E      29          0.671
LGA    K      16      Q      30          1.002
LGA    A      17      Q      31          1.124
LGA    K      18      K      32          1.095
LGA    A      19      L      33          0.818
LGA    G      20      R      34          0.676
LGA    V      21      Q      35          0.783
LGA    I      22      E      36          1.328
LGA    T      23      Y      37          1.609
LGA    E      24      L      38          1.363
LGA    E      25      K      39          1.855
LGA    E      26      G      40          2.336
LGA    K      27      F      41          1.473
LGA    A      28      R      42          1.554
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      -       -           -
LGA    F      41      -       -           -
LGA    R      42      -       -           -
LGA    S      43      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   42   42    5.0     27    1.69    18.52     59.273     1.511

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.937334 * X  +  -0.265430 * Y  +   0.225727 * Z  +   5.861951
  Y_new =  -0.292534 * X  +  -0.951426 * Y  +   0.095981 * Z  +  44.138317
  Z_new =   0.189286 * X  +  -0.155999 * Y  +  -0.969451 * Z  +  -8.433558 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.982046    0.159547  [ DEG:  -170.8586      9.1414 ]
  Theta =  -0.190435   -2.951158  [ DEG:   -10.9111   -169.0889 ]
  Phi   =  -0.302513    2.839080  [ DEG:   -17.3327    162.6673 ]
 
# 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                                  
REMARK     2: T0335.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0335AL381_2.T0335.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   42   42   5.0   27   1.69   18.52  59.273
REMARK  ---------------------------------------------------------- 
MOLECULE T0335AL381_2
REMARK Aligment from pdb entry: 2fzfA
ATOM      1  N   ILE     2       0.532  -7.762  -8.559  1.00  0.00              
ATOM      2  CA  ILE     2       0.689  -8.339  -7.234  1.00  0.00              
ATOM      3  C   ILE     2       0.807  -7.208  -6.226  1.00  0.00              
ATOM      4  O   ILE     2       0.151  -7.215  -5.180  1.00  0.00              
ATOM      5  N   SER     3       1.645  -6.233  -6.537  1.00  0.00              
ATOM      6  CA  SER     3       1.822  -5.105  -5.641  1.00  0.00              
ATOM      7  C   SER     3       0.565  -4.247  -5.596  1.00  0.00              
ATOM      8  O   SER     3       0.186  -3.726  -4.541  1.00  0.00              
ATOM      9  N   ASN     4      -0.093  -4.111  -6.741  1.00  0.00              
ATOM     10  CA  ASN     4      -1.318  -3.320  -6.802  1.00  0.00              
ATOM     11  C   ASN     4      -2.348  -3.820  -5.803  1.00  0.00              
ATOM     12  O   ASN     4      -3.070  -3.026  -5.214  1.00  0.00              
ATOM     13  N   ALA     5      -2.407  -5.136  -5.612  1.00  0.00              
ATOM     14  CA  ALA     5      -3.365  -5.734  -4.691  1.00  0.00              
ATOM     15  C   ALA     5      -2.860  -5.704  -3.274  1.00  0.00              
ATOM     16  O   ALA     5      -3.639  -5.645  -2.323  1.00  0.00              
ATOM     17  N   LYS     6      -1.546  -5.786  -3.139  1.00  0.00              
ATOM     18  CA  LYS     6      -0.924  -5.768  -1.834  1.00  0.00              
ATOM     19  C   LYS     6      -1.220  -4.408  -1.221  1.00  0.00              
ATOM     20  O   LYS     6      -1.807  -4.321  -0.151  1.00  0.00              
ATOM     21  N   ILE     7      -0.828  -3.341  -1.913  1.00  0.00              
ATOM     22  CA  ILE     7      -1.056  -2.003  -1.381  1.00  0.00              
ATOM     23  C   ILE     7      -2.531  -1.822  -1.075  1.00  0.00              
ATOM     24  O   ILE     7      -2.895  -1.358   0.001  1.00  0.00              
ATOM     25  N   ALA     8      -3.360  -2.204  -2.042  1.00  0.00              
ATOM     26  CA  ALA     8      -4.809  -2.116  -1.952  1.00  0.00              
ATOM     27  C   ALA     8      -5.312  -2.611  -0.602  1.00  0.00              
ATOM     28  O   ALA     8      -6.245  -2.064  -0.011  1.00  0.00              
ATOM     29  N   ARG     9      -4.680  -3.666  -0.121  1.00  0.00              
ATOM     30  CA  ARG     9      -5.053  -4.273   1.138  1.00  0.00              
ATOM     31  C   ARG     9      -3.895  -4.093   2.104  1.00  0.00              
ATOM     32  O   ARG     9      -2.926  -4.839   2.046  1.00  0.00              
ATOM     33  N   ILE    10      -3.967  -3.096   2.975  1.00  0.00              
ATOM     34  CA  ILE    10      -2.879  -2.885   3.923  1.00  0.00              
ATOM     35  C   ILE    10      -3.346  -2.128   5.157  1.00  0.00              
ATOM     36  O   ILE    10      -3.067  -2.539   6.288  1.00  0.00              
ATOM     37  N   ASN    11      -4.061  -1.029   4.955  1.00  0.00              
ATOM     38  CA  ASN    11      -4.557  -0.251   6.084  1.00  0.00              
ATOM     39  C   ASN    11      -3.406   0.255   6.942  1.00  0.00              
ATOM     40  O   ASN    11      -3.585   0.543   8.123  1.00  0.00              
ATOM     41  N   GLU    12      -2.222   0.355   6.345  1.00  0.00              
ATOM     42  CA  GLU    12      -1.050   0.835   7.057  1.00  0.00              
ATOM     43  C   GLU    12      -0.449   2.009   6.307  1.00  0.00              
ATOM     44  O   GLU    12       0.443   1.842   5.478  1.00  0.00              
ATOM     45  N   LEU    13      -0.967   3.197   6.603  1.00  0.00              
ATOM     46  CA  LEU    13      -0.518   4.436   5.980  1.00  0.00              
ATOM     47  C   LEU    13       0.995   4.624   6.100  1.00  0.00              
ATOM     48  O   LEU    13       1.465   5.546   6.771  1.00  0.00              
ATOM     49  N   ALA    14       1.753   3.751   5.445  1.00  0.00              
ATOM     50  CA  ALA    14       3.207   3.828   5.481  1.00  0.00              
ATOM     51  C   ALA    14       3.776   2.752   4.579  1.00  0.00              
ATOM     52  O   ALA    14       4.561   3.024   3.671  1.00  0.00              
ATOM     53  N   ALA    15       3.363   1.521   4.844  1.00  0.00              
ATOM     54  CA  ALA    15       3.809   0.390   4.073  1.00  0.00              
ATOM     55  C   ALA    15       3.098   0.398   2.725  1.00  0.00              
ATOM     56  O   ALA    15       3.705   0.108   1.694  1.00  0.00              
ATOM     57  N   LYS    16       1.810   0.742   2.744  1.00  0.00              
ATOM     58  CA  LYS    16       1.000   0.832   1.528  1.00  0.00              
ATOM     59  C   LYS    16       1.657   1.869   0.638  1.00  0.00              
ATOM     60  O   LYS    16       1.553   1.810  -0.586  1.00  0.00              
ATOM     61  N   ALA    17       2.324   2.828   1.281  1.00  0.00              
ATOM     62  CA  ALA    17       3.036   3.912   0.597  1.00  0.00              
ATOM     63  C   ALA    17       4.243   3.300  -0.115  1.00  0.00              
ATOM     64  O   ALA    17       4.411   3.470  -1.324  1.00  0.00              
ATOM     65  N   LYS    18       5.082   2.597   0.652  1.00  0.00              
ATOM     66  CA  LYS    18       6.261   1.933   0.110  1.00  0.00              
ATOM     67  C   LYS    18       5.804   0.958  -0.957  1.00  0.00              
ATOM     68  O   LYS    18       6.312   0.968  -2.069  1.00  0.00              
ATOM     69  N   ALA    19       4.830   0.117  -0.642  1.00  0.00              
ATOM     70  CA  ALA    19       4.397  -0.835  -1.646  1.00  0.00              
ATOM     71  C   ALA    19       3.829  -0.190  -2.896  1.00  0.00              
ATOM     72  O   ALA    19       3.877  -0.782  -3.966  1.00  0.00              
ATOM     73  N   GLY    20       3.300   1.022  -2.764  1.00  0.00              
ATOM     74  CA  GLY    20       2.743   1.734  -3.906  1.00  0.00              
ATOM     75  C   GLY    20       3.829   2.365  -4.791  1.00  0.00              
ATOM     76  O   GLY    20       3.735   2.326  -6.019  1.00  0.00              
ATOM     77  N   VAL    21       4.859   2.939  -4.174  1.00  0.00              
ATOM     78  CA  VAL    21       5.939   3.552  -4.939  1.00  0.00              
ATOM     79  C   VAL    21       6.685   2.467  -5.694  1.00  0.00              
ATOM     80  O   VAL    21       7.149   2.662  -6.818  1.00  0.00              
ATOM     81  N   ILE    22       6.795   1.315  -5.052  1.00  0.00              
ATOM     82  CA  ILE    22       7.480   0.176  -5.621  1.00  0.00              
ATOM     83  C   ILE    22       6.693  -0.360  -6.817  1.00  0.00              
ATOM     84  O   ILE    22       7.276  -0.783  -7.812  1.00  0.00              
ATOM     85  N   THR    23       5.369  -0.332  -6.726  1.00  0.00              
ATOM     86  CA  THR    23       4.524  -0.816  -7.820  1.00  0.00              
ATOM     87  C   THR    23       4.661   0.064  -9.064  1.00  0.00              
ATOM     88  O   THR    23       4.692  -0.435 -10.194  1.00  0.00              
ATOM     89  N   GLU    24       4.735   1.374  -8.836  1.00  0.00              
ATOM     90  CA  GLU    24       4.863   2.359  -9.904  1.00  0.00              
ATOM     91  C   GLU    24       6.193   2.204 -10.608  1.00  0.00              
ATOM     92  O   GLU    24       6.264   2.129 -11.837  1.00  0.00              
ATOM     93  N   GLU    25       7.250   2.159  -9.807  1.00  0.00              
ATOM     94  CA  GLU    25       8.601   1.995 -10.319  1.00  0.00              
ATOM     95  C   GLU    25       8.687   0.837 -11.312  1.00  0.00              
ATOM     96  O   GLU    25       9.271   0.981 -12.381  1.00  0.00              
ATOM     97  N   GLU    26       8.099  -0.302 -10.965  1.00  0.00              
ATOM     98  CA  GLU    26       8.151  -1.464 -11.835  1.00  0.00              
ATOM     99  C   GLU    26       7.109  -1.501 -12.933  1.00  0.00              
ATOM    100  O   GLU    26       6.978  -2.518 -13.614  1.00  0.00              
ATOM    101  N   LYS    27       6.357  -0.418 -13.111  1.00  0.00              
ATOM    102  CA  LYS    27       5.327  -0.394 -14.158  1.00  0.00              
ATOM    103  C   LYS    27       5.965  -0.272 -15.530  1.00  0.00              
ATOM    104  O   LYS    27       5.486  -0.851 -16.505  1.00  0.00              
ATOM    105  N   ALA    28       7.057   0.480 -15.592  1.00  0.00              
ATOM    106  CA  ALA    28       7.761   0.691 -16.839  1.00  0.00              
ATOM    107  C   ALA    28       8.612  -0.498 -17.269  1.00  0.00              
ATOM    108  O   ALA    28       9.100  -0.522 -18.396  1.00  0.00              
ATOM    109  N   GLU    29       8.797  -1.478 -16.387  1.00  0.00              
ATOM    110  CA  GLU    29       9.615  -2.649 -16.713  1.00  0.00              
ATOM    111  C   GLU    29       9.042  -3.451 -17.883  1.00  0.00              
ATOM    112  O   GLU    29       9.770  -3.888 -18.776  1.00  0.00              
ATOM    113  N   GLN    30       7.732  -3.655 -17.868  1.00  0.00              
ATOM    114  CA  GLN    30       7.082  -4.422 -18.911  1.00  0.00              
ATOM    115  C   GLN    30       7.280  -3.789 -20.267  1.00  0.00              
ATOM    116  O   GLN    30       7.796  -4.418 -21.187  1.00  0.00              
ATOM    117  N   GLN    31       6.858  -2.536 -20.391  1.00  0.00              
ATOM    118  CA  GLN    31       6.990  -1.816 -21.648  1.00  0.00              
ATOM    119  C   GLN    31       8.452  -1.779 -22.091  1.00  0.00              
ATOM    120  O   GLN    31       8.731  -1.813 -23.286  1.00  0.00              
ATOM    121  N   LYS    32       9.383  -1.715 -21.138  1.00  0.00              
ATOM    122  CA  LYS    32      10.803  -1.686 -21.481  1.00  0.00              
ATOM    123  C   LYS    32      11.258  -3.003 -22.098  1.00  0.00              
ATOM    124  O   LYS    32      12.024  -3.025 -23.064  1.00  0.00              
ATOM    125  N   LEU    33      10.783  -4.105 -21.537  1.00  0.00              
ATOM    126  CA  LEU    33      11.150  -5.420 -22.029  1.00  0.00              
ATOM    127  C   LEU    33      10.516  -5.695 -23.378  1.00  0.00              
ATOM    128  O   LEU    33      11.154  -6.267 -24.254  1.00  0.00              
ATOM    129  N   ARG    34       9.259  -5.283 -23.535  1.00  0.00              
ATOM    130  CA  ARG    34       8.517  -5.510 -24.772  1.00  0.00              
ATOM    131  C   ARG    34       9.215  -4.785 -25.908  1.00  0.00              
ATOM    132  O   ARG    34       9.174  -5.218 -27.064  1.00  0.00              
ATOM    133  N   GLN    35       9.867  -3.680 -25.568  1.00  0.00              
ATOM    134  CA  GLN    35      10.582  -2.908 -26.557  1.00  0.00              
ATOM    135  C   GLN    35      11.814  -3.669 -26.992  1.00  0.00              
ATOM    136  O   GLN    35      12.097  -3.777 -28.187  1.00  0.00              
ATOM    137  N   GLU    36      12.551  -4.195 -26.020  1.00  0.00              
ATOM    138  CA  GLU    36      13.757  -4.947 -26.328  1.00  0.00              
ATOM    139  C   GLU    36      13.374  -6.161 -27.184  1.00  0.00              
ATOM    140  O   GLU    36      13.931  -6.359 -28.257  1.00  0.00              
ATOM    141  N   TYR    37      12.412  -6.952 -26.717  1.00  0.00              
ATOM    142  CA  TYR    37      11.987  -8.129 -27.453  1.00  0.00              
ATOM    143  C   TYR    37      11.634  -7.772 -28.891  1.00  0.00              
ATOM    144  O   TYR    37      11.788  -8.574 -29.804  1.00  0.00              
ATOM    145  N   LEU    38      11.166  -6.549 -29.082  1.00  0.00              
ATOM    146  CA  LEU    38      10.785  -6.049 -30.399  1.00  0.00              
ATOM    147  C   LEU    38      12.065  -5.659 -31.147  1.00  0.00              
ATOM    148  O   LEU    38      12.151  -5.798 -32.364  1.00  0.00              
ATOM    149  N   LYS    39      13.060  -5.184 -30.401  1.00  0.00              
ATOM    150  CA  LYS    39      14.342  -4.786 -30.977  1.00  0.00              
ATOM    151  C   LYS    39      15.202  -5.975 -31.417  1.00  0.00              
ATOM    152  O   LYS    39      15.956  -5.861 -32.381  1.00  0.00              
ATOM    153  N   GLY    40      15.100  -7.113 -30.732  1.00  0.00              
ATOM    154  CA  GLY    40      15.908  -8.275 -31.112  1.00  0.00              
ATOM    155  C   GLY    40      15.071  -9.293 -31.904  1.00  0.00              
ATOM    156  O   GLY    40      15.618 -10.221 -32.504  1.00  0.00              
ATOM    157  N   PHE    41      13.750  -9.107 -31.928  1.00  0.00              
ATOM    158  CA  PHE    41      12.867 -10.021 -32.659  1.00  0.00              
ATOM    159  C   PHE    41      11.770  -9.263 -33.403  1.00  0.00              
ATOM    160  O   PHE    41      10.581  -9.524 -33.213  1.00  0.00              
ATOM    161  N   ARG    42      12.164  -8.343 -34.303  1.00  0.00              
ATOM    162  CA  ARG    42      11.194  -7.550 -35.068  1.00  0.00              
ATOM    163  C   ARG    42      10.169  -8.349 -35.844  1.00  0.00              
ATOM    164  O   ARG    42      10.520  -9.224 -36.624  1.00  0.00              
ATOM    165  N   SER    43       8.896  -8.049 -35.602  1.00  0.00              
ATOM    166  CA  SER    43       7.822  -8.734 -36.295  1.00  0.00              
ATOM    167  C   SER    43       7.259  -9.942 -35.575  1.00  0.00              
ATOM    168  O   SER    43       6.089 -10.272 -35.767  1.00  0.00              
END
