
#######################################################
#                                                     #
#                        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   53 (  212),  selected   53 , name T0381AL044_5-D1
# Molecule2: number of CA atoms   61 (  477),  selected   61 , name T0381_D1.pdb
# PARAMETERS: T0381AL044_5-D1.T0381_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      V      17           -
LGA    L      20      Q      18          1.945
LGA    -       -      S      19           -
LGA    -       -      L      20           -
LGA    A      21      A      21          1.317
LGA    R      22      R      22          1.370
LGA    G      23      G      23          0.930
LGA    L      24      L      24          0.864
LGA    A      25      A      25          1.311
LGA    V      26      V      26          0.909
LGA    I      27      I      27          0.671
LGA    R      28      R      28          1.543
LGA    C      29      C      29          1.515
LGA    F      30      F      30          2.373
LGA    D      31      D      31          4.743
LGA    H      32      H      32          4.038
LGA    R      33      R      33          5.360
LGA    -       -      N      34           -
LGA    Q      35      Q      35          3.065
LGA    R      36      R      36          1.431
LGA    R      37      R      37          0.969
LGA    T      38      T      38          1.342
LGA    L      39      L      39          0.987
LGA    S      40      S      40          0.473
LGA    D      41      D      41          1.273
LGA    V      42      V      42          1.340
LGA    A      43      A      43          1.008
LGA    R      44      R      44          1.593
LGA    A      45      A      45          2.081
LGA    T      46      T      46          1.845
LGA    D      47      D      47          2.145
LGA    L      48      L      48          1.860
LGA    T      49      T      49          1.542
LGA    R      50      R      50          0.383
LGA    A      51      A      51          1.383
LGA    T      52      T      52          1.250
LGA    A      53      A      53          1.378
LGA    R      54      R      54          1.372
LGA    R      55      R      55          1.077
LGA    F      56      F      56          0.571
LGA    L      57      L      57          1.056
LGA    L      58      L      58          1.350
LGA    T      59      T      59          1.055
LGA    L      60      L      60          1.396
LGA    V      61      V      61          2.274
LGA    E      62      E      62          2.456
LGA    L      63      L      63          2.448
LGA    G      64      G      64          2.823
LGA    Y      65      Y      65          0.730
LGA    V      66      V      66          3.659
LGA    A      67      A      67          2.074
LGA    T      68      T      68          2.336
LGA    D      69      D      69          3.192
LGA    G      70      G      70          5.530
LGA    L      75      S      71          5.136
LGA    T      76      A      72          2.018
LGA    P      77      F      73          1.211
LGA    -       -      W      74           -
LGA    -       -      L      75           -
LGA    -       -      T      76           -
LGA    -       -      P      77           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   53   61    5.0     53    2.24    92.45     74.655     2.261

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.646715 * X  +  -0.117936 * Y  +  -0.753559 * Z  +   0.614973
  Y_new =  -0.762137 * X  +  -0.138925 * Y  +  -0.632334 * Z  +  93.896599
  Z_new =  -0.030113 * X  +   0.983255 * Y  +  -0.179728 * Z  +   8.288613 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.751589   -1.390003  [ DEG:   100.3587    -79.6413 ]
  Theta =   0.030117    3.111475  [ DEG:     1.7256    178.2744 ]
  Phi   =  -0.867142    2.274450  [ DEG:   -49.6836    130.3164 ]
 
# 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: T0381AL044_5-D1                               
REMARK     2: T0381_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0381AL044_5-D1.T0381_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   53   61   5.0   53   2.24   92.45  74.655
REMARK  ---------------------------------------------------------- 
MOLECULE T0381AL044_5-D1
REMARK Aligment from pdb entry: 1j5y_A
ATOM      1  N   LEU    20       6.527  55.864  33.502  1.00  0.00              
ATOM      2  CA  LEU    20       5.589  56.037  32.408  1.00  0.00              
ATOM      3  C   LEU    20       6.369  56.423  31.152  1.00  0.00              
ATOM      4  O   LEU    20       6.103  55.932  30.064  1.00  0.00              
ATOM      5  N   ALA    21       8.518  53.576  29.664  1.00  0.00              
ATOM      6  CA  ALA    21       7.648  52.693  28.908  1.00  0.00              
ATOM      7  C   ALA    21       7.283  53.294  27.534  1.00  0.00              
ATOM      8  O   ALA    21       7.248  52.585  26.536  1.00  0.00              
ATOM      9  N   ARG    22       7.015  54.593  27.471  1.00  0.00              
ATOM     10  CA  ARG    22       6.688  55.188  26.190  1.00  0.00              
ATOM     11  C   ARG    22       7.895  55.183  25.256  1.00  0.00              
ATOM     12  O   ARG    22       7.757  54.929  24.061  1.00  0.00              
ATOM     13  N   GLY    23       9.078  55.456  25.792  1.00  0.00              
ATOM     14  CA  GLY    23      10.282  55.483  24.960  1.00  0.00              
ATOM     15  C   GLY    23      10.551  54.093  24.369  1.00  0.00              
ATOM     16  O   GLY    23      10.932  53.975  23.199  1.00  0.00              
ATOM     17  N   LEU    24      10.349  53.050  25.177  1.00  0.00              
ATOM     18  CA  LEU    24      10.557  51.687  24.703  1.00  0.00              
ATOM     19  C   LEU    24       9.549  51.379  23.604  1.00  0.00              
ATOM     20  O   LEU    24       9.889  50.744  22.617  1.00  0.00              
ATOM     21  N   ALA    25       8.312  51.838  23.757  1.00  0.00              
ATOM     22  CA  ALA    25       7.299  51.580  22.736  1.00  0.00              
ATOM     23  C   ALA    25       7.631  52.286  21.418  1.00  0.00              
ATOM     24  O   ALA    25       7.422  51.732  20.350  1.00  0.00              
ATOM     25  N   VAL    26       8.143  53.508  21.494  1.00  0.00              
ATOM     26  CA  VAL    26       8.474  54.247  20.293  1.00  0.00              
ATOM     27  C   VAL    26       9.536  53.469  19.522  1.00  0.00              
ATOM     28  O   VAL    26       9.435  53.271  18.313  1.00  0.00              
ATOM     29  N   ILE    27      10.558  53.027  20.243  1.00  0.00              
ATOM     30  CA  ILE    27      11.627  52.305  19.603  1.00  0.00              
ATOM     31  C   ILE    27      11.091  51.052  18.938  1.00  0.00              
ATOM     32  O   ILE    27      11.426  50.774  17.793  1.00  0.00              
ATOM     33  N   ARG    28      10.255  50.300  19.643  1.00  0.00              
ATOM     34  CA  ARG    28       9.685  49.086  19.067  1.00  0.00              
ATOM     35  C   ARG    28       8.836  49.381  17.833  1.00  0.00              
ATOM     36  O   ARG    28       8.948  48.697  16.817  1.00  0.00              
ATOM     37  N   CYS    29       7.987  50.400  17.909  1.00  0.00              
ATOM     38  CA  CYS    29       7.132  50.731  16.770  1.00  0.00              
ATOM     39  C   CYS    29       7.941  51.151  15.557  1.00  0.00              
ATOM     40  O   CYS    29       7.643  50.752  14.439  1.00  0.00              
ATOM     41  N   PHE    30       8.963  51.976  15.770  1.00  0.00              
ATOM     42  CA  PHE    30       9.770  52.416  14.649  1.00  0.00              
ATOM     43  C   PHE    30      10.550  51.271  14.052  1.00  0.00              
ATOM     44  O   PHE    30      10.719  51.223  12.849  1.00  0.00              
ATOM     45  N   ASP    31      11.018  50.353  14.888  1.00  0.00              
ATOM     46  CA  ASP    31      11.803  49.226  14.393  1.00  0.00              
ATOM     47  C   ASP    31      10.987  48.199  13.642  1.00  0.00              
ATOM     48  O   ASP    31      11.430  47.684  12.626  1.00  0.00              
ATOM     49  N   HIS    32       8.204  48.736  11.991  1.00  0.00              
ATOM     50  CA  HIS    32       7.661  49.299  10.761  1.00  0.00              
ATOM     51  C   HIS    32       8.574  49.351   9.541  1.00  0.00              
ATOM     52  O   HIS    32       9.659  49.871   9.598  1.00  0.00              
ATOM     53  N   ARG    33       8.116  48.832   8.414  1.00  0.00              
ATOM     54  CA  ARG    33       8.931  48.858   7.204  1.00  0.00              
ATOM     55  C   ARG    33       8.988  50.276   6.631  1.00  0.00              
ATOM     56  O   ARG    33       9.958  50.660   5.984  1.00  0.00              
ATOM     57  N   GLN    35       7.940  51.049   6.876  1.00  0.00              
ATOM     58  CA  GLN    35       7.861  52.413   6.371  1.00  0.00              
ATOM     59  C   GLN    35       8.030  53.483   7.450  1.00  0.00              
ATOM     60  O   GLN    35       8.024  53.202   8.644  1.00  0.00              
ATOM     61  N   ARG    36       8.197  54.739   7.025  1.00  0.00              
ATOM     62  CA  ARG    36       8.339  55.758   8.064  1.00  0.00              
ATOM     63  C   ARG    36       7.013  55.917   8.827  1.00  0.00              
ATOM     64  O   ARG    36       5.919  55.737   8.262  1.00  0.00              
ATOM     65  N   ARG    37       7.116  56.233  10.117  1.00  0.00              
ATOM     66  CA  ARG    37       5.944  56.402  10.960  1.00  0.00              
ATOM     67  C   ARG    37       5.823  57.868  11.342  1.00  0.00              
ATOM     68  O   ARG    37       6.696  58.405  12.020  1.00  0.00              
ATOM     69  N   THR    38       4.743  58.523  10.940  1.00  0.00              
ATOM     70  CA  THR    38       4.629  59.931  11.258  1.00  0.00              
ATOM     71  C   THR    38       4.514  60.221  12.751  1.00  0.00              
ATOM     72  O   THR    38       4.066  59.384  13.545  1.00  0.00              
ATOM     73  N   LEU    39       4.960  61.408  13.129  1.00  0.00              
ATOM     74  CA  LEU    39       4.865  61.821  14.511  1.00  0.00              
ATOM     75  C   LEU    39       3.404  61.910  14.940  1.00  0.00              
ATOM     76  O   LEU    39       3.094  61.696  16.112  1.00  0.00              
ATOM     77  N   SER    40       2.510  62.236  14.008  1.00  0.00              
ATOM     78  CA  SER    40       1.090  62.311  14.336  1.00  0.00              
ATOM     79  C   SER    40       0.586  60.916  14.690  1.00  0.00              
ATOM     80  O   SER    40      -0.243  60.767  15.581  1.00  0.00              
ATOM     81  N   ASP    41       1.092  59.895  13.997  1.00  0.00              
ATOM     82  CA  ASP    41       0.670  58.531  14.295  1.00  0.00              
ATOM     83  C   ASP    41       1.239  58.058  15.626  1.00  0.00              
ATOM     84  O   ASP    41       0.543  57.381  16.387  1.00  0.00              
ATOM     85  N   VAL    42       2.495  58.386  15.917  1.00  0.00              
ATOM     86  CA  VAL    42       3.071  57.977  17.192  1.00  0.00              
ATOM     87  C   VAL    42       2.267  58.635  18.313  1.00  0.00              
ATOM     88  O   VAL    42       1.991  57.997  19.322  1.00  0.00              
ATOM     89  N   ALA    43       1.902  59.908  18.125  1.00  0.00              
ATOM     90  CA  ALA    43       1.120  60.660  19.116  1.00  0.00              
ATOM     91  C   ALA    43      -0.245  60.005  19.327  1.00  0.00              
ATOM     92  O   ALA    43      -0.699  59.855  20.446  1.00  0.00              
ATOM     93  N   ARG    44      -0.898  59.619  18.236  1.00  0.00              
ATOM     94  CA  ARG    44      -2.203  58.962  18.312  1.00  0.00              
ATOM     95  C   ARG    44      -2.044  57.609  18.996  1.00  0.00              
ATOM     96  O   ARG    44      -2.767  57.276  19.923  1.00  0.00              
ATOM     97  N   ALA    45      -1.077  56.831  18.543  1.00  0.00              
ATOM     98  CA  ALA    45      -0.841  55.511  19.103  1.00  0.00              
ATOM     99  C   ALA    45      -0.437  55.516  20.591  1.00  0.00              
ATOM    100  O   ALA    45      -0.805  54.625  21.352  1.00  0.00              
ATOM    101  N   THR    46       0.317  56.517  21.014  1.00  0.00              
ATOM    102  CA  THR    46       0.760  56.579  22.410  1.00  0.00              
ATOM    103  C   THR    46      -0.055  57.516  23.291  1.00  0.00              
ATOM    104  O   THR    46       0.245  57.669  24.457  1.00  0.00              
ATOM    105  N   ASP    47      -1.090  58.144  22.733  1.00  0.00              
ATOM    106  CA  ASP    47      -1.923  59.059  23.499  1.00  0.00              
ATOM    107  C   ASP    47      -1.173  60.216  24.154  1.00  0.00              
ATOM    108  O   ASP    47      -1.392  60.523  25.331  1.00  0.00              
ATOM    109  N   LEU    48      -0.276  60.854  23.408  1.00  0.00              
ATOM    110  CA  LEU    48       0.441  62.019  23.929  1.00  0.00              
ATOM    111  C   LEU    48       0.424  63.010  22.784  1.00  0.00              
ATOM    112  O   LEU    48       0.073  62.645  21.662  1.00  0.00              
ATOM    113  N   THR    49       0.782  64.257  23.061  1.00  0.00              
ATOM    114  CA  THR    49       0.777  65.293  22.029  1.00  0.00              
ATOM    115  C   THR    49       1.937  65.143  21.048  1.00  0.00              
ATOM    116  O   THR    49       2.940  64.485  21.336  1.00  0.00              
ATOM    117  N   ARG    50       1.796  65.768  19.889  1.00  0.00              
ATOM    118  CA  ARG    50       2.834  65.733  18.873  1.00  0.00              
ATOM    119  C   ARG    50       4.146  66.269  19.450  1.00  0.00              
ATOM    120  O   ARG    50       5.223  65.767  19.143  1.00  0.00              
ATOM    121  N   ALA    51       4.040  67.303  20.279  1.00  0.00              
ATOM    122  CA  ALA    51       5.204  67.926  20.886  1.00  0.00              
ATOM    123  C   ALA    51       5.938  66.976  21.836  1.00  0.00              
ATOM    124  O   ALA    51       7.176  66.990  21.904  1.00  0.00              
ATOM    125  N   THR    52       5.192  66.161  22.581  1.00  0.00              
ATOM    126  CA  THR    52       5.826  65.186  23.467  1.00  0.00              
ATOM    127  C   THR    52       6.661  64.223  22.621  1.00  0.00              
ATOM    128  O   THR    52       7.758  63.837  23.013  1.00  0.00              
ATOM    129  N   ALA    53       6.150  63.838  21.454  1.00  0.00              
ATOM    130  CA  ALA    53       6.904  62.937  20.605  1.00  0.00              
ATOM    131  C   ALA    53       8.200  63.601  20.109  1.00  0.00              
ATOM    132  O   ALA    53       9.256  62.980  20.118  1.00  0.00              
ATOM    133  N   ARG    54       8.117  64.860  19.681  1.00  0.00              
ATOM    134  CA  ARG    54       9.301  65.586  19.207  1.00  0.00              
ATOM    135  C   ARG    54      10.389  65.578  20.277  1.00  0.00              
ATOM    136  O   ARG    54      11.563  65.360  19.977  1.00  0.00              
ATOM    137  N   ARG    55       9.997  65.779  21.529  1.00  0.00              
ATOM    138  CA  ARG    55      10.952  65.793  22.626  1.00  0.00              
ATOM    139  C   ARG    55      11.476  64.395  22.918  1.00  0.00              
ATOM    140  O   ARG    55      12.662  64.232  23.164  1.00  0.00              
ATOM    141  N   PHE    56      10.607  63.386  22.881  1.00  0.00              
ATOM    142  CA  PHE    56      11.039  62.015  23.137  1.00  0.00              
ATOM    143  C   PHE    56      12.067  61.576  22.098  1.00  0.00              
ATOM    144  O   PHE    56      13.086  60.956  22.427  1.00  0.00              
ATOM    145  N   LEU    57      11.782  61.877  20.835  1.00  0.00              
ATOM    146  CA  LEU    57      12.690  61.494  19.760  1.00  0.00              
ATOM    147  C   LEU    57      14.061  62.177  19.894  1.00  0.00              
ATOM    148  O   LEU    57      15.092  61.547  19.641  1.00  0.00              
ATOM    149  N   LEU    58      14.079  63.455  20.278  1.00  0.00              
ATOM    150  CA  LEU    58      15.344  64.164  20.430  1.00  0.00              
ATOM    151  C   LEU    58      16.131  63.499  21.556  1.00  0.00              
ATOM    152  O   LEU    58      17.351  63.316  21.457  1.00  0.00              
ATOM    153  N   THR    59      15.418  63.121  22.614  1.00  0.00              
ATOM    154  CA  THR    59      16.035  62.456  23.750  1.00  0.00              
ATOM    155  C   THR    59      16.600  61.102  23.308  1.00  0.00              
ATOM    156  O   THR    59      17.757  60.804  23.573  1.00  0.00              
ATOM    157  N   LEU    60      15.783  60.287  22.640  1.00  0.00              
ATOM    158  CA  LEU    60      16.240  58.991  22.151  1.00  0.00              
ATOM    159  C   LEU    60      17.495  59.138  21.264  1.00  0.00              
ATOM    160  O   LEU    60      18.416  58.340  21.348  1.00  0.00              
ATOM    161  N   VAL    61      17.549  60.171  20.436  1.00  0.00              
ATOM    162  CA  VAL    61      18.716  60.332  19.577  1.00  0.00              
ATOM    163  C   VAL    61      19.976  60.681  20.369  1.00  0.00              
ATOM    164  O   VAL    61      21.060  60.191  20.064  1.00  0.00              
ATOM    165  N   GLU    62      19.825  61.508  21.395  1.00  0.00              
ATOM    166  CA  GLU    62      20.969  61.898  22.182  1.00  0.00              
ATOM    167  C   GLU    62      21.494  60.694  22.960  1.00  0.00              
ATOM    168  O   GLU    62      22.638  60.698  23.401  1.00  0.00              
ATOM    169  N   LEU    63      20.664  59.666  23.127  1.00  0.00              
ATOM    170  CA  LEU    63      21.098  58.458  23.820  1.00  0.00              
ATOM    171  C   LEU    63      21.822  57.515  22.847  1.00  0.00              
ATOM    172  O   LEU    63      22.525  56.619  23.278  1.00  0.00              
ATOM    173  N   GLY    64      21.642  57.699  21.545  1.00  0.00              
ATOM    174  CA  GLY    64      22.308  56.824  20.591  1.00  0.00              
ATOM    175  C   GLY    64      21.414  56.189  19.541  1.00  0.00              
ATOM    176  O   GLY    64      21.900  55.567  18.601  1.00  0.00              
ATOM    177  N   TYR    65      20.100  56.330  19.678  1.00  0.00              
ATOM    178  CA  TYR    65      19.199  55.736  18.693  1.00  0.00              
ATOM    179  C   TYR    65      19.317  56.399  17.335  1.00  0.00              
ATOM    180  O   TYR    65      19.187  57.621  17.212  1.00  0.00              
ATOM    181  N   VAL    66      19.546  55.591  16.313  1.00  0.00              
ATOM    182  CA  VAL    66      19.723  56.109  14.972  1.00  0.00              
ATOM    183  C   VAL    66      18.420  56.455  14.277  1.00  0.00              
ATOM    184  O   VAL    66      18.104  55.912  13.223  1.00  0.00              
ATOM    185  N   ALA    67      17.678  57.393  14.860  1.00  0.00              
ATOM    186  CA  ALA    67      16.402  57.801  14.299  1.00  0.00              
ATOM    187  C   ALA    67      16.529  59.024  13.407  1.00  0.00              
ATOM    188  O   ALA    67      17.271  59.949  13.717  1.00  0.00              
ATOM    189  N   THR    68      14.161  61.926  11.190  1.00  0.00              
ATOM    190  CA  THR    68      12.842  62.498  10.936  1.00  0.00              
ATOM    191  C   THR    68      12.770  62.876   9.450  1.00  0.00              
ATOM    192  O   THR    68      13.427  63.809   9.032  1.00  0.00              
ATOM    193  N   ASP    69      11.995  62.149   8.651  1.00  0.00              
ATOM    194  CA  ASP    69      11.874  62.454   7.229  1.00  0.00              
ATOM    195  C   ASP    69      10.497  63.074   7.012  1.00  0.00              
ATOM    196  O   ASP    69       9.650  63.000   7.886  1.00  0.00              
ATOM    197  N   GLY    70      10.251  63.693   5.843  1.00  0.00              
ATOM    198  CA  GLY    70       8.933  64.304   5.628  1.00  0.00              
ATOM    199  C   GLY    70       7.752  63.362   5.804  1.00  0.00              
ATOM    200  O   GLY    70       6.664  63.787   6.193  1.00  0.00              
ATOM    201  N   LEU    75       7.950  62.087   5.512  1.00  0.00              
ATOM    202  CA  LEU    75       6.858  61.130   5.652  1.00  0.00              
ATOM    203  C   LEU    75       6.830  60.430   7.015  1.00  0.00              
ATOM    204  O   LEU    75       5.974  59.574   7.266  1.00  0.00              
ATOM    205  N   THR    76       7.751  60.794   7.901  1.00  0.00              
ATOM    206  CA  THR    76       7.758  60.184   9.223  1.00  0.00              
ATOM    207  C   THR    76       9.123  59.806   9.747  1.00  0.00              
ATOM    208  O   THR    76      10.125  59.982   9.063  1.00  0.00              
ATOM    209  N   PRO    77       9.158  59.295  10.973  1.00  0.00              
ATOM    210  CA  PRO    77      10.397  58.888  11.603  1.00  0.00              
ATOM    211  C   PRO    77      10.860  57.553  11.096  1.00  0.00              
ATOM    212  O   PRO    77      10.061  56.659  10.876  1.00  0.00              
END
