
#######################################################
#                                                     #
#                        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   45 (  180),  selected   45 , name T0349AL381_5
# Molecule2: number of CA atoms   75 ( 1131),  selected   75 , name T0349.pdb
# PARAMETERS: T0349AL381_5.T0349.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      M       1           -
LGA    -       -      R       2           -
LGA    -       -      E       3           -
LGA    -       -      L       4           -
LGA    -       -      L       5           -
LGA    -       -      R       6           -
LGA    -       -      T       7           -
LGA    -       -      N       8           -
LGA    -       -      D       9           -
LGA    -       -      A      10           -
LGA    -       -      V      11           -
LGA    -       -      L      12           -
LGA    L      13      L      13          0.730
LGA    S      14      S      14          0.794
LGA    A      15      A      15          1.022
LGA    V      16      V      16          0.775
LGA    G      17      G      17          1.264
LGA    A      18      A      18          1.161
LGA    L      19      L      19          1.152
LGA    L      20      L      20          0.872
LGA    D      21      D      21          0.781
LGA    G      22      G      22          0.506
LGA    A      23      A      23          0.658
LGA    D      24      D      24          1.488
LGA    I      25      I      25          0.227
LGA    G      26      G      26          1.808
LGA    H      27      H      27          2.013
LGA    L      28      L      28          1.818
LGA    V      29      V      29          1.702
LGA    M      34      L      30          2.336
LGA    -       -      D      31           -
LGA    -       -      Q      32           -
LGA    S      35      N      33          4.310
LGA    -       -      M      34           -
LGA    -       -      S      35           -
LGA    -       -      I      36           -
LGA    -       -      L      37           -
LGA    -       -      E      38           -
LGA    -       -      G      39           -
LGA    -       -      S      40           -
LGA    -       -      L      41           -
LGA    -       -      G      42           -
LGA    I      36      V      43          6.122
LGA    L      37      I      44          1.701
LGA    E      38      -       -           -
LGA    G      39      P      45          1.805
LGA    R      46      R      46          1.040
LGA    R      47      R      47          0.814
LGA    V      48      V      48          1.615
LGA    L      49      L      49          2.092
LGA    V      50      V      50          1.218
LGA    H      51      H      51          0.765
LGA    E      52      E      52          1.287
LGA    D      53      D      53          1.701
LGA    D      54      D      54          1.214
LGA    L      55      L      55          0.692
LGA    A      56      A      56          0.439
LGA    G      57      G      57          0.359
LGA    A      58      A      58          0.668
LGA    R      59      R      59          0.720
LGA    R      60      R      60          0.706
LGA    L      61      L      61          0.591
LGA    L      62      L      62          0.436
LGA    T      63      T      63          0.606
LGA    D      64      D      64          2.100
LGA    -       -      A      65           -
LGA    A      65      G      66          0.799
LGA    G      66      L      67          1.200
LGA    L      67      A      68          2.345
LGA    -       -      H      69           -
LGA    -       -      E      70           -
LGA    -       -      L      71           -
LGA    -       -      R      72           -
LGA    -       -      S      73           -
LGA    -       -      D      74           -
LGA    -       -      D      75           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   45   75    5.0     44    1.68    81.82     54.854     2.468

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.931741 * X  +   0.016313 * Y  +  -0.362758 * Z  +  32.768059
  Y_new =   0.351075 * X  +  -0.214746 * Y  +  -0.911389 * Z  +  36.872112
  Z_new =  -0.092768 * X  +  -0.976534 * Y  +   0.194360 * Z  +   5.489551 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.374333    1.767259  [ DEG:   -78.7435    101.2565 ]
  Theta =   0.092902    3.048691  [ DEG:     5.3229    174.6771 ]
  Phi   =   2.781250   -0.360343  [ DEG:   159.3539    -20.6461 ]
 
# 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: T0349AL381_5                                  
REMARK     2: T0349.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0349AL381_5.T0349.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   45   75   5.0   44   1.68   81.82  54.854
REMARK  ---------------------------------------------------------- 
MOLECULE T0349AL381_5
REMARK Aligment from pdb entry: 1zhvA
ATOM      1  N   LEU    13      -4.286  -2.735   5.929  1.00  0.00              
ATOM      2  CA  LEU    13      -4.527  -1.452   5.281  1.00  0.00              
ATOM      3  C   LEU    13      -4.803  -0.388   6.340  1.00  0.00              
ATOM      4  O   LEU    13      -4.266   0.716   6.279  1.00  0.00              
ATOM      5  N   SER    14      -5.638  -0.724   7.318  1.00  0.00              
ATOM      6  CA  SER    14      -5.963   0.214   8.384  1.00  0.00              
ATOM      7  C   SER    14      -4.710   0.745   9.081  1.00  0.00              
ATOM      8  O   SER    14      -4.579   1.950   9.303  1.00  0.00              
ATOM      9  N   ALA    15      -3.789  -0.157   9.408  1.00  0.00              
ATOM     10  CA  ALA    15      -2.566   0.218  10.113  1.00  0.00              
ATOM     11  C   ALA    15      -1.742   1.242   9.344  1.00  0.00              
ATOM     12  O   ALA    15      -1.028   2.053   9.940  1.00  0.00              
ATOM     13  N   VAL    16      -1.854   1.215   8.022  1.00  0.00              
ATOM     14  CA  VAL    16      -1.103   2.137   7.188  1.00  0.00              
ATOM     15  C   VAL    16      -1.836   3.454   6.934  1.00  0.00              
ATOM     16  O   VAL    16      -1.259   4.525   7.083  1.00  0.00              
ATOM     17  N   GLY    17      -3.115   3.387   6.582  1.00  0.00              
ATOM     18  CA  GLY    17      -3.837   4.623   6.302  1.00  0.00              
ATOM     19  C   GLY    17      -4.273   5.427   7.523  1.00  0.00              
ATOM     20  O   GLY    17      -4.477   6.635   7.422  1.00  0.00              
ATOM     21  N   ALA    18      -4.397   4.784   8.681  1.00  0.00              
ATOM     22  CA  ALA    18      -4.822   5.516   9.876  1.00  0.00              
ATOM     23  C   ALA    18      -3.910   6.707  10.193  1.00  0.00              
ATOM     24  O   ALA    18      -4.388   7.829  10.379  1.00  0.00              
ATOM     25  N   LEU    19      -2.587   6.484  10.267  1.00  0.00              
ATOM     26  CA  LEU    19      -1.706   7.621  10.569  1.00  0.00              
ATOM     27  C   LEU    19      -1.690   8.704   9.495  1.00  0.00              
ATOM     28  O   LEU    19      -1.374   9.861   9.773  1.00  0.00              
ATOM     29  N   LEU    20      -2.038   8.339   8.268  1.00  0.00              
ATOM     30  CA  LEU    20      -2.057   9.313   7.186  1.00  0.00              
ATOM     31  C   LEU    20      -3.357  10.117   7.177  1.00  0.00              
ATOM     32  O   LEU    20      -3.344  11.351   7.197  1.00  0.00              
ATOM     33  N   ASP    21      -4.484   9.411   7.170  1.00  0.00              
ATOM     34  CA  ASP    21      -5.792  10.052   7.140  1.00  0.00              
ATOM     35  C   ASP    21      -6.080  10.930   8.351  1.00  0.00              
ATOM     36  O   ASP    21      -6.709  11.981   8.218  1.00  0.00              
ATOM     37  N   GLY    22      -5.621  10.504   9.523  1.00  0.00              
ATOM     38  CA  GLY    22      -5.841  11.272  10.746  1.00  0.00              
ATOM     39  C   GLY    22      -4.949  12.506  10.775  1.00  0.00              
ATOM     40  O   GLY    22      -5.149  13.403  11.593  1.00  0.00              
ATOM     41  N   ALA    23      -3.977  12.566   9.872  1.00  0.00              
ATOM     42  CA  ALA    23      -3.073  13.708   9.833  1.00  0.00              
ATOM     43  C   ALA    23      -3.097  14.527   8.541  1.00  0.00              
ATOM     44  O   ALA    23      -2.080  15.077   8.116  1.00  0.00              
ATOM     45  N   ASP    24      -4.271  14.603   7.920  1.00  0.00              
ATOM     46  CA  ASP    24      -4.438  15.397   6.714  1.00  0.00              
ATOM     47  C   ASP    24      -3.832  14.918   5.408  1.00  0.00              
ATOM     48  O   ASP    24      -3.696  15.706   4.469  1.00  0.00              
ATOM     49  N   ILE    25      -3.467  13.645   5.326  1.00  0.00              
ATOM     50  CA  ILE    25      -2.887  13.130   4.092  1.00  0.00              
ATOM     51  C   ILE    25      -3.919  12.309   3.323  1.00  0.00              
ATOM     52  O   ILE    25      -4.426  11.310   3.824  1.00  0.00              
ATOM     53  N   GLY    26      -4.238  12.750   2.112  1.00  0.00              
ATOM     54  CA  GLY    26      -5.198  12.025   1.302  1.00  0.00              
ATOM     55  C   GLY    26      -4.593  10.715   0.848  1.00  0.00              
ATOM     56  O   GLY    26      -3.398  10.647   0.541  1.00  0.00              
ATOM     57  N   HIS    27      -5.412   9.670   0.813  1.00  0.00              
ATOM     58  CA  HIS    27      -4.949   8.351   0.397  1.00  0.00              
ATOM     59  C   HIS    27      -5.764   7.766  -0.750  1.00  0.00              
ATOM     60  O   HIS    27      -6.948   8.061  -0.909  1.00  0.00              
ATOM     61  N   LEU    28      -5.105   6.931  -1.545  1.00  0.00              
ATOM     62  CA  LEU    28      -5.726   6.276  -2.692  1.00  0.00              
ATOM     63  C   LEU    28      -5.232   4.839  -2.586  1.00  0.00              
ATOM     64  O   LEU    28      -4.045   4.569  -2.746  1.00  0.00              
ATOM     65  N   VAL    29      -6.144   3.917  -2.304  1.00  0.00              
ATOM     66  CA  VAL    29      -5.770   2.523  -2.122  1.00  0.00              
ATOM     67  C   VAL    29      -6.269   1.597  -3.204  1.00  0.00              
ATOM     68  O   VAL    29      -7.419   1.673  -3.613  1.00  0.00              
ATOM     69  N   MET    34      -5.393   0.719  -3.668  1.00  0.00              
ATOM     70  CA  MET    34      -5.781  -0.261  -4.665  1.00  0.00              
ATOM     71  C   MET    34      -5.380  -1.641  -4.169  1.00  0.00              
ATOM     72  O   MET    34      -4.205  -2.018  -4.205  1.00  0.00              
ATOM     73  N   SER    35      -6.359  -2.390  -3.677  1.00  0.00              
ATOM     74  CA  SER    35      -6.111  -3.745  -3.214  1.00  0.00              
ATOM     75  C   SER    35      -6.027  -4.625  -4.453  1.00  0.00              
ATOM     76  O   SER    35      -6.626  -4.323  -5.485  1.00  0.00              
ATOM     77  N   ILE    36      -5.255  -5.695  -4.351  1.00  0.00              
ATOM     78  CA  ILE    36      -5.105  -6.645  -5.443  1.00  0.00              
ATOM     79  C   ILE    36      -5.133  -8.032  -4.827  1.00  0.00              
ATOM     80  O   ILE    36      -5.123  -8.183  -3.603  1.00  0.00              
ATOM     81  N   LEU    37      -5.159  -9.047  -5.676  1.00  0.00              
ATOM     82  CA  LEU    37      -5.162 -10.418  -5.190  1.00  0.00              
ATOM     83  C   LEU    37      -4.014 -10.627  -4.186  1.00  0.00              
ATOM     84  O   LEU    37      -4.237 -11.105  -3.071  1.00  0.00              
ATOM     85  N   GLU    38      -2.798 -10.241  -4.571  1.00  0.00              
ATOM     86  CA  GLU    38      -1.626 -10.407  -3.702  1.00  0.00              
ATOM     87  C   GLU    38      -1.596  -9.528  -2.459  1.00  0.00              
ATOM     88  O   GLU    38      -1.125  -9.955  -1.405  1.00  0.00              
ATOM     89  N   GLY    39      -2.070  -8.296  -2.575  1.00  0.00              
ATOM     90  CA  GLY    39      -2.032  -7.416  -1.423  1.00  0.00              
ATOM     91  C   GLY    39      -2.626  -6.051  -1.682  1.00  0.00              
ATOM     92  O   GLY    39      -3.807  -5.937  -1.999  1.00  0.00              
ATOM     93  N   ARG    46      -1.809  -5.010  -1.550  1.00  0.00              
ATOM     94  CA  ARG    46      -2.292  -3.651  -1.755  1.00  0.00              
ATOM     95  C   ARG    46      -1.199  -2.701  -2.201  1.00  0.00              
ATOM     96  O   ARG    46      -0.014  -2.926  -1.958  1.00  0.00              
ATOM     97  N   ARG    47      -1.635  -1.630  -2.851  1.00  0.00              
ATOM     98  CA  ARG    47      -0.759  -0.546  -3.263  1.00  0.00              
ATOM     99  C   ARG    47      -1.420   0.709  -2.714  1.00  0.00              
ATOM    100  O   ARG    47      -2.641   0.765  -2.564  1.00  0.00              
ATOM    101  N   VAL    48      -0.610   1.707  -2.390  1.00  0.00              
ATOM    102  CA  VAL    48      -1.107   2.961  -1.840  1.00  0.00              
ATOM    103  C   VAL    48      -0.495   4.124  -2.592  1.00  0.00              
ATOM    104  O   VAL    48       0.704   4.126  -2.851  1.00  0.00              
ATOM    105  N   LEU    49      -1.313   5.099  -2.961  1.00  0.00              
ATOM    106  CA  LEU    49      -0.778   6.284  -3.602  1.00  0.00              
ATOM    107  C   LEU    49      -1.139   7.491  -2.746  1.00  0.00              
ATOM    108  O   LEU    49      -2.203   7.541  -2.128  1.00  0.00              
ATOM    109  N   VAL    50      -0.216   8.439  -2.681  1.00  0.00              
ATOM    110  CA  VAL    50      -0.424   9.679  -1.956  1.00  0.00              
ATOM    111  C   VAL    50       0.112  10.741  -2.898  1.00  0.00              
ATOM    112  O   VAL    50       0.883  10.428  -3.807  1.00  0.00              
ATOM    113  N   HIS    51      -0.304  11.986  -2.706  1.00  0.00              
ATOM    114  CA  HIS    51       0.192  13.049  -3.563  1.00  0.00              
ATOM    115  C   HIS    51       1.689  13.152  -3.333  1.00  0.00              
ATOM    116  O   HIS    51       2.170  13.008  -2.201  1.00  0.00              
ATOM    117  N   GLU    52       2.431  13.389  -4.406  1.00  0.00              
ATOM    118  CA  GLU    52       3.874  13.486  -4.306  1.00  0.00              
ATOM    119  C   GLU    52       4.353  14.564  -3.353  1.00  0.00              
ATOM    120  O   GLU    52       5.398  14.416  -2.733  1.00  0.00              
ATOM    121  N   ASP    53       3.594  15.642  -3.229  1.00  0.00              
ATOM    122  CA  ASP    53       3.986  16.711  -2.324  1.00  0.00              
ATOM    123  C   ASP    53       3.831  16.283  -0.864  1.00  0.00              
ATOM    124  O   ASP    53       4.324  16.962   0.039  1.00  0.00              
ATOM    125  N   ASP    54       3.157  15.155  -0.638  1.00  0.00              
ATOM    126  CA  ASP    54       2.958  14.621   0.713  1.00  0.00              
ATOM    127  C   ASP    54       3.929  13.484   1.029  1.00  0.00              
ATOM    128  O   ASP    54       3.846  12.866   2.091  1.00  0.00              
ATOM    129  N   LEU    55       4.858  13.225   0.116  1.00  0.00              
ATOM    130  CA  LEU    55       5.811  12.133   0.282  1.00  0.00              
ATOM    131  C   LEU    55       6.655  12.190   1.555  1.00  0.00              
ATOM    132  O   LEU    55       6.781  11.188   2.270  1.00  0.00              
ATOM    133  N   ALA    56       7.228  13.352   1.846  1.00  0.00              
ATOM    134  CA  ALA    56       8.067  13.506   3.032  1.00  0.00              
ATOM    135  C   ALA    56       7.276  13.345   4.328  1.00  0.00              
ATOM    136  O   ALA    56       7.725  12.677   5.257  1.00  0.00              
ATOM    137  N   GLY    57       6.095  13.952   4.390  1.00  0.00              
ATOM    138  CA  GLY    57       5.262  13.834   5.582  1.00  0.00              
ATOM    139  C   GLY    57       4.766  12.398   5.735  1.00  0.00              
ATOM    140  O   GLY    57       4.709  11.868   6.841  1.00  0.00              
ATOM    141  N   ALA    58       4.433  11.765   4.614  1.00  0.00              
ATOM    142  CA  ALA    58       3.949  10.393   4.646  1.00  0.00              
ATOM    143  C   ALA    58       5.011   9.468   5.229  1.00  0.00              
ATOM    144  O   ALA    58       4.719   8.627   6.083  1.00  0.00              
ATOM    145  N   ARG    59       6.248   9.631   4.778  1.00  0.00              
ATOM    146  CA  ARG    59       7.332   8.799   5.284  1.00  0.00              
ATOM    147  C   ARG    59       7.556   9.001   6.783  1.00  0.00              
ATOM    148  O   ARG    59       7.763   8.027   7.513  1.00  0.00              
ATOM    149  N   ARG    60       7.498  10.250   7.253  1.00  0.00              
ATOM    150  CA  ARG    60       7.695  10.519   8.678  1.00  0.00              
ATOM    151  C   ARG    60       6.583   9.880   9.503  1.00  0.00              
ATOM    152  O   ARG    60       6.846   9.250  10.525  1.00  0.00              
ATOM    153  N   LEU    61       5.344  10.043   9.050  1.00  0.00              
ATOM    154  CA  LEU    61       4.199   9.497   9.763  1.00  0.00              
ATOM    155  C   LEU    61       4.186   7.977   9.795  1.00  0.00              
ATOM    156  O   LEU    61       3.874   7.386  10.824  1.00  0.00              
ATOM    157  N   LEU    62       4.532   7.342   8.682  1.00  0.00              
ATOM    158  CA  LEU    62       4.535   5.886   8.647  1.00  0.00              
ATOM    159  C   LEU    62       5.652   5.300   9.507  1.00  0.00              
ATOM    160  O   LEU    62       5.458   4.284  10.173  1.00  0.00              
ATOM    161  N   THR    63       6.818   5.935   9.504  1.00  0.00              
ATOM    162  CA  THR    63       7.921   5.437  10.322  1.00  0.00              
ATOM    163  C   THR    63       7.560   5.550  11.802  1.00  0.00              
ATOM    164  O   THR    63       7.774   4.619  12.577  1.00  0.00              
ATOM    165  N   ASP    64       7.000   6.688  12.198  1.00  0.00              
ATOM    166  CA  ASP    64       6.620   6.877  13.594  1.00  0.00              
ATOM    167  C   ASP    64       5.585   5.832  14.013  1.00  0.00              
ATOM    168  O   ASP    64       5.546   5.411  15.172  1.00  0.00              
ATOM    169  N   ALA    65       4.767   5.399  13.054  1.00  0.00              
ATOM    170  CA  ALA    65       3.732   4.398  13.308  1.00  0.00              
ATOM    171  C   ALA    65       4.302   2.975  13.369  1.00  0.00              
ATOM    172  O   ALA    65       3.570   2.010  13.602  1.00  0.00              
ATOM    173  N   GLY    66       5.607   2.853  13.150  1.00  0.00              
ATOM    174  CA  GLY    66       6.258   1.558  13.223  1.00  0.00              
ATOM    175  C   GLY    66       6.465   0.806  11.925  1.00  0.00              
ATOM    176  O   GLY    66       6.976  -0.316  11.932  1.00  0.00              
ATOM    177  N   LEU    67       6.066   1.398  10.807  1.00  0.00              
ATOM    178  CA  LEU    67       6.233   0.735   9.524  1.00  0.00              
ATOM    179  C   LEU    67       7.636   0.917   8.971  1.00  0.00              
ATOM    180  O   LEU    67       8.340   1.858   9.334  1.00  0.00              
END
