
#######################################################
#                                                     #
#                        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 T0349AL509_2
# Molecule2: number of CA atoms   75 ( 1131),  selected   75 , name T0349.pdb
# PARAMETERS: T0349AL509_2.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    G      26      E       3          3.317
LGA    H      27      L       4          2.736
LGA    L      28      L       5          3.796
LGA    V      29      R       6          3.188
LGA    L      30      T       7          1.382
LGA    D      31      N       8          2.841
LGA    E      38      D       9          2.919
LGA    -       -      A      10           -
LGA    -       -      V      11           -
LGA    -       -      L      12           -
LGA    -       -      L      13           -
LGA    -       -      S      14           -
LGA    -       -      A      15           -
LGA    -       -      V      16           -
LGA    G      39      G      17          1.474
LGA    S      40      A      18          1.015
LGA    L      41      L      19          0.564
LGA    -       -      L      20           -
LGA    -       -      D      21           -
LGA    -       -      G      22           -
LGA    -       -      A      23           -
LGA    -       -      D      24           -
LGA    G      42      I      25          0.963
LGA    V      43      G      26          1.727
LGA    I      44      H      27          0.998
LGA    P      45      L      28          0.969
LGA    R      46      V      29          1.102
LGA    -       -      L      30           -
LGA    -       -      D      31           -
LGA    -       -      Q      32           -
LGA    -       -      N      33           -
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    -       -      V      43           -
LGA    -       -      I      44           -
LGA    -       -      P      45           -
LGA    -       -      R      46           -
LGA    -       -      R      47           -
LGA    -       -      V      48           -
LGA    L      49      L      49          0.807
LGA    V      50      V      50          0.875
LGA    H      51      H      51          0.952
LGA    E      52      E      52          1.035
LGA    D      53      D      53          1.441
LGA    D      54      D      54          0.859
LGA    L      55      L      55          0.373
LGA    A      56      A      56          0.984
LGA    G      57      G      57          0.753
LGA    A      58      A      58          0.461
LGA    R      59      R      59          0.902
LGA    R      60      R      60          0.837
LGA    L      61      L      61          0.309
LGA    L      62      L      62          0.559
LGA    T      63      T      63          0.745
LGA    D      64      D      64          0.849
LGA    A      65      A      65          2.383
LGA    -       -      G      66           -
LGA    G      66      L      67          2.097
LGA    L      67      A      68          2.587
LGA    D      74      H      69           -
LGA    D      75      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)   36   75    5.0     34    1.72    58.82     41.632     1.871

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.655020 * X  +  -0.654672 * Y  +   0.377297 * Z  +   9.246201
  Y_new =   0.723109 * X  +   0.687980 * Y  +  -0.061623 * Z  + -62.112377
  Z_new =  -0.219230 * X  +   0.313191 * Y  +   0.924040 * Z  + -46.356831 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.326785   -2.814808  [ DEG:    18.7234   -161.2766 ]
  Theta =   0.221025    2.920568  [ DEG:    12.6638    167.3362 ]
  Phi   =   0.834765   -2.306828  [ DEG:    47.8285   -132.1715 ]
 
# 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: T0349AL509_2                                  
REMARK     2: T0349.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0349AL509_2.T0349.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   36   75   5.0   34   1.72   58.82  41.632
REMARK  ---------------------------------------------------------- 
MOLECULE T0349AL509_2
REMARK Aligment from pdb entry: 1yj7A_
ATOM      1  N   GLY    26       4.276   5.216  -2.114  1.00  0.00              
ATOM      2  CA  GLY    26       5.030   5.039  -0.856  1.00  0.00              
ATOM      3  C   GLY    26       5.561   3.610  -0.769  1.00  0.00              
ATOM      4  O   GLY    26       6.767   3.377  -0.826  1.00  0.00              
ATOM      5  N   HIS    27       4.647   2.651  -0.684  1.00  0.00              
ATOM      6  CA  HIS    27       4.979   1.249  -0.503  1.00  0.00              
ATOM      7  C   HIS    27       4.062   0.343  -1.333  1.00  0.00              
ATOM      8  O   HIS    27       2.873   0.608  -1.460  1.00  0.00              
ATOM      9  N   LEU    28       4.640  -0.718  -1.879  1.00  0.00              
ATOM     10  CA  LEU    28       3.902  -1.844  -2.458  1.00  0.00              
ATOM     11  C   LEU    28       4.118  -3.117  -1.636  1.00  0.00              
ATOM     12  O   LEU    28       4.931  -3.150  -0.692  1.00  0.00              
ATOM     13  N   VAL    29       3.398  -4.176  -2.003  1.00  0.00              
ATOM     14  CA  VAL    29       3.577  -5.480  -1.387  1.00  0.00              
ATOM     15  C   VAL    29       3.006  -5.602   0.010  1.00  0.00              
ATOM     16  O   VAL    29       3.382  -6.505   0.765  1.00  0.00              
ATOM     17  N   LEU    30       2.109  -4.692   0.395  1.00  0.00              
ATOM     18  CA  LEU    30       1.578  -4.690   1.758  1.00  0.00              
ATOM     19  C   LEU    30       0.405  -5.667   1.903  1.00  0.00              
ATOM     20  O   LEU    30      -0.368  -5.868   0.963  1.00  0.00              
ATOM     21  N   ASP    31       0.259  -6.255   3.091  1.00  0.00              
ATOM     22  CA  ASP    31      -0.972  -6.969   3.430  1.00  0.00              
ATOM     23  C   ASP    31      -2.117  -5.980   3.536  1.00  0.00              
ATOM     24  O   ASP    31      -1.913  -4.777   3.719  1.00  0.00              
ATOM     25  N   GLU    38      -3.336  -6.491   3.433  1.00  0.00              
ATOM     26  CA  GLU    38      -4.498  -5.638   3.576  1.00  0.00              
ATOM     27  C   GLU    38      -4.524  -5.000   4.969  1.00  0.00              
ATOM     28  O   GLU    38      -4.764  -3.802   5.095  1.00  0.00              
ATOM     29  N   GLY    39      -2.809   3.539   6.135  1.00  0.00              
ATOM     30  CA  GLY    39      -3.752   4.461   5.520  1.00  0.00              
ATOM     31  C   GLY    39      -4.530   5.224   6.584  1.00  0.00              
ATOM     32  O   GLY    39      -4.648   6.446   6.528  1.00  0.00              
ATOM     33  N   SER    40      -5.014   4.522   7.604  1.00  0.00              
ATOM     34  CA  SER    40      -5.739   5.190   8.674  1.00  0.00              
ATOM     35  C   SER    40      -4.833   6.130   9.468  1.00  0.00              
ATOM     36  O   SER    40      -5.250   7.222   9.830  1.00  0.00              
ATOM     37  N   LEU    41      -3.589   5.729   9.714  1.00  0.00              
ATOM     38  CA  LEU    41      -2.633   6.582  10.400  1.00  0.00              
ATOM     39  C   LEU    41      -2.387   7.900   9.646  1.00  0.00              
ATOM     40  O   LEU    41      -2.388   8.984  10.228  1.00  0.00              
ATOM     41  N   GLY    42      -2.932  13.658   6.256  1.00  0.00              
ATOM     42  CA  GLY    42      -2.314  13.384   4.973  1.00  0.00              
ATOM     43  C   GLY    42      -3.234  12.503   4.139  1.00  0.00              
ATOM     44  O   GLY    42      -3.589  11.390   4.544  1.00  0.00              
ATOM     45  N   VAL    43      -3.615  13.001   2.965  1.00  0.00              
ATOM     46  CA  VAL    43      -4.401  12.232   2.012  1.00  0.00              
ATOM     47  C   VAL    43      -3.626  11.024   1.525  1.00  0.00              
ATOM     48  O   VAL    43      -2.407  11.073   1.425  1.00  0.00              
ATOM     49  N   ILE    44      -4.328   9.941   1.228  1.00  0.00              
ATOM     50  CA  ILE    44      -3.675   8.753   0.701  1.00  0.00              
ATOM     51  C   ILE    44      -4.623   7.995  -0.226  1.00  0.00              
ATOM     52  O   ILE    44      -5.855   8.013  -0.050  1.00  0.00              
ATOM     53  N   PRO    45      -4.041   7.373  -1.252  1.00  0.00              
ATOM     54  CA  PRO    45      -4.771   6.531  -2.164  1.00  0.00              
ATOM     55  C   PRO    45      -4.208   5.118  -2.105  1.00  0.00              
ATOM     56  O   PRO    45      -3.040   4.912  -1.798  1.00  0.00              
ATOM     57  N   ARG    46      -5.058   4.141  -2.393  1.00  0.00              
ATOM     58  CA  ARG    46      -4.714   2.745  -2.264  1.00  0.00              
ATOM     59  C   ARG    46      -5.152   1.981  -3.499  1.00  0.00              
ATOM     60  O   ARG    46      -6.207   2.277  -4.066  1.00  0.00              
ATOM     61  N   LEU    49      -0.138   5.275  -2.013  1.00  0.00              
ATOM     62  CA  LEU    49       0.461   6.455  -2.641  1.00  0.00              
ATOM     63  C   LEU    49      -0.046   7.729  -1.985  1.00  0.00              
ATOM     64  O   LEU    49      -1.088   7.725  -1.335  1.00  0.00              
ATOM     65  N   VAL    50       0.678   8.823  -2.181  1.00  0.00              
ATOM     66  CA  VAL    50       0.256  10.140  -1.730  1.00  0.00              
ATOM     67  C   VAL    50       0.467  11.153  -2.852  1.00  0.00              
ATOM     68  O   VAL    50       1.171  10.888  -3.822  1.00  0.00              
ATOM     69  N   HIS    51      -0.134  12.322  -2.705  1.00  0.00              
ATOM     70  CA  HIS    51       0.187  13.439  -3.586  1.00  0.00              
ATOM     71  C   HIS    51       1.660  13.734  -3.391  1.00  0.00              
ATOM     72  O   HIS    51       2.174  13.657  -2.262  1.00  0.00              
ATOM     73  N   GLU    52       2.378  14.036  -4.475  1.00  0.00              
ATOM     74  CA  GLU    52       3.832  14.183  -4.370  1.00  0.00              
ATOM     75  C   GLU    52       4.287  15.204  -3.341  1.00  0.00              
ATOM     76  O   GLU    52       5.312  15.002  -2.692  1.00  0.00              
ATOM     77  N   ASP    53       3.528  16.288  -3.172  1.00  0.00              
ATOM     78  CA  ASP    53       3.890  17.358  -2.270  1.00  0.00              
ATOM     79  C   ASP    53       3.849  16.901  -0.823  1.00  0.00              
ATOM     80  O   ASP    53       4.485  17.508   0.032  1.00  0.00              
ATOM     81  N   ASP    54       3.114  15.823  -0.569  1.00  0.00              
ATOM     82  CA  ASP    54       2.926  15.296   0.777  1.00  0.00              
ATOM     83  C   ASP    54       3.922  14.190   1.141  1.00  0.00              
ATOM     84  O   ASP    54       3.841  13.609   2.242  1.00  0.00              
ATOM     85  N   LEU    55       4.857  13.884   0.241  1.00  0.00              
ATOM     86  CA  LEU    55       5.709  12.725   0.433  1.00  0.00              
ATOM     87  C   LEU    55       6.536  12.805   1.732  1.00  0.00              
ATOM     88  O   LEU    55       6.576  11.842   2.504  1.00  0.00              
ATOM     89  N   ALA    56       7.166  13.934   1.984  1.00  0.00              
ATOM     90  CA  ALA    56       8.021  14.046   3.183  1.00  0.00              
ATOM     91  C   ALA    56       7.193  13.925   4.470  1.00  0.00              
ATOM     92  O   ALA    56       7.554  13.174   5.368  1.00  0.00              
ATOM     93  N   GLY    57       6.069  14.625   4.549  1.00  0.00              
ATOM     94  CA  GLY    57       5.161  14.539   5.692  1.00  0.00              
ATOM     95  C   GLY    57       4.708  13.108   5.923  1.00  0.00              
ATOM     96  O   GLY    57       4.690  12.623   7.059  1.00  0.00              
ATOM     97  N   ALA    58       4.349  12.417   4.837  1.00  0.00              
ATOM     98  CA  ALA    58       3.896  11.030   4.920  1.00  0.00              
ATOM     99  C   ALA    58       4.954  10.066   5.436  1.00  0.00              
ATOM    100  O   ALA    58       4.684   9.266   6.337  1.00  0.00              
ATOM    101  N   ARG    59       6.158  10.132   4.876  1.00  0.00              
ATOM    102  CA  ARG    59       7.237   9.263   5.315  1.00  0.00              
ATOM    103  C   ARG    59       7.601   9.575   6.774  1.00  0.00              
ATOM    104  O   ARG    59       7.898   8.653   7.528  1.00  0.00              
ATOM    105  N   ARG    60       7.539  10.835   7.156  1.00  0.00              
ATOM    106  CA  ARG    60       7.803  11.242   8.544  1.00  0.00              
ATOM    107  C   ARG    60       6.844  10.563   9.517  1.00  0.00              
ATOM    108  O   ARG    60       7.277   9.931  10.492  1.00  0.00              
ATOM    109  N   LEU    61       5.542  10.644   9.222  1.00  0.00              
ATOM    110  CA  LEU    61       4.513  10.023  10.023  1.00  0.00              
ATOM    111  C   LEU    61       4.697   8.501  10.085  1.00  0.00              
ATOM    112  O   LEU    61       4.583   7.899  11.155  1.00  0.00              
ATOM    113  N   LEU    62       4.960   7.880   8.939  1.00  0.00              
ATOM    114  CA  LEU    62       5.135   6.441   8.902  1.00  0.00              
ATOM    115  C   LEU    62       6.374   6.028   9.715  1.00  0.00              
ATOM    116  O   LEU    62       6.277   5.089  10.530  1.00  0.00              
ATOM    117  N   THR    63       7.491   6.717   9.495  1.00  0.00              
ATOM    118  CA  THR    63       8.750   6.450  10.211  1.00  0.00              
ATOM    119  C   THR    63       8.532   6.567  11.723  1.00  0.00              
ATOM    120  O   THR    63       9.000   5.708  12.501  1.00  0.00              
ATOM    121  N   ASP    64       7.817   7.615  12.128  1.00  0.00              
ATOM    122  CA  ASP    64       7.542   7.882  13.548  1.00  0.00              
ATOM    123  C   ASP    64       6.654   6.851  14.200  1.00  0.00              
ATOM    124  O   ASP    64       6.558   6.816  15.432  1.00  0.00              
ATOM    125  N   ALA    65       5.966   6.030  13.401  1.00  0.00              
ATOM    126  CA  ALA    65       5.121   4.970  13.910  1.00  0.00              
ATOM    127  C   ALA    65       5.630   3.573  13.586  1.00  0.00              
ATOM    128  O   ALA    65       4.936   2.586  13.806  1.00  0.00              
ATOM    129  N   GLY    66       6.855   3.492  13.068  1.00  0.00              
ATOM    130  CA  GLY    66       7.499   2.224  12.782  1.00  0.00              
ATOM    131  C   GLY    66       6.963   1.441  11.595  1.00  0.00              
ATOM    132  O   GLY    66       7.057   0.226  11.577  1.00  0.00              
ATOM    133  N   LEU    67       6.365   2.135  10.624  1.00  0.00              
ATOM    134  CA  LEU    67       5.825   1.487   9.425  1.00  0.00              
ATOM    135  C   LEU    67       6.757   1.718   8.247  1.00  0.00              
ATOM    136  O   LEU    67       7.346   2.799   8.132  1.00  0.00              
ATOM    137  N   ASP    74       2.183 -25.429  32.764  1.00  0.00              
ATOM    138  CA  ASP    74       2.815 -26.198  33.830  1.00  0.00              
ATOM    139  C   ASP    74       3.627 -25.364  34.834  1.00  0.00              
ATOM    140  O   ASP    74       4.480 -24.558  34.448  1.00  0.00              
ATOM    141  N   ASP    75       3.314 -25.570  36.110  1.00  0.00              
ATOM    142  CA  ASP    75       4.064 -25.077  37.275  1.00  0.00              
ATOM    143  C   ASP    75       4.271 -23.563  37.296  1.00  0.00              
ATOM    144  O   ASP    75       5.384 -23.079  37.479  1.00  0.00              
END
