
#######################################################
#                                                     #
#                        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   48 (  192),  selected   48 , name T0348TS550_4
# Molecule2: number of CA atoms   61 (  465),  selected   61 , name T0348.pdb
# PARAMETERS: T0348TS550_4.T0348.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      D       2           -
LGA    -       -      A       3           -
LGA    -       -      K       4           -
LGA    -       -      F       5           -
LGA    -       -      L       6           -
LGA    -       -      E       7           -
LGA    -       -      I       8           -
LGA    -       -      L       9           -
LGA    -       -      V      10           -
LGA    -       -      C      11           -
LGA    -       -      P      12           -
LGA    -       -      L      13           -
LGA    -       -      C      14           -
LGA    -       -      K      15           -
LGA    -       -      G      16           -
LGA    K       4      P      17          3.258
LGA    F       5      L      18          4.475
LGA    L       6      V      19          1.909
LGA    E       7      F      20          1.261
LGA    I       8      D      21          1.606
LGA    -       -      K      22           -
LGA    L       9      S      23          2.341
LGA    V      10      K      24          5.428
LGA    C      11      -       -           -
LGA    P      12      -       -           -
LGA    L      13      -       -           -
LGA    C      14      -       -           -
LGA    K      15      -       -           -
LGA    G      16      -       -           -
LGA    P      17      D      25          2.009
LGA    L      18      E      26          0.842
LGA    V      19      L      27          0.654
LGA    F      20      I      28          1.344
LGA    D      21      C      29          1.522
LGA    K      22      K      30          1.221
LGA    S      23      G      31          0.978
LGA    K      24      D      32          1.237
LGA    D      25      R      33          1.375
LGA    E      26      L      34          0.727
LGA    L      27      A      35          0.443
LGA    I      28      F      36          0.192
LGA    C      29      P      37          0.506
LGA    K      30      I      38          1.967
LGA    G      31      K      39          4.042
LGA    D      32      D      40           -
LGA    -       -      G      41           -
LGA    -       -      I      42           -
LGA    -       -      P      43           -
LGA    -       -      M      44           -
LGA    -       -      M      45           -
LGA    -       -      L      46           -
LGA    -       -      E      47           -
LGA    R      33      S      48          4.415
LGA    L      34      E      49          3.191
LGA    A      35      A      50          3.480
LGA    F      36      R      51          3.578
LGA    P      37      E      52          3.110
LGA    I      38      -       -           -
LGA    K      39      -       -           -
LGA    D      40      -       -           -
LGA    G      41      -       -           -
LGA    I      42      -       -           -
LGA    P      43      -       -           -
LGA    M      44      L      53          2.915
LGA    M      45      A      54          4.872
LGA    L      46      P      55          5.289
LGA    -       -      E      56           -
LGA    -       -      E      57           -
LGA    E      47      E      58          2.568
LGA    S      48      V      59          2.792
LGA    E      49      K      60          2.742
LGA    A      50      L      61          3.231
LGA    R      51      E      62          3.803

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   48   61    5.0     35    2.83     8.57     39.945     1.193

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.140935 * X  +   0.492244 * Y  +   0.858972 * Z  + -20.213459
  Y_new =   0.543989 * X  +   0.763420 * Y  +  -0.348232 * Z  + -53.747074
  Z_new =  -0.827172 * X  +   0.418193 * Y  +  -0.375368 * Z  + 114.218536 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.302281   -0.839312  [ DEG:   131.9110    -48.0890 ]
  Theta =   0.974056    2.167537  [ DEG:    55.8093    124.1907 ]
  Phi   =   1.824300   -1.317292  [ DEG:   104.5247    -75.4753 ]
 
# 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: T0348TS550_4                                  
REMARK     2: T0348.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0348TS550_4.T0348.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   48   61   5.0   35   2.83    8.57  39.945
REMARK  ---------------------------------------------------------- 
MOLECULE T0348TS550_4
PFRMAT TS
TARGET T0348
MODEL 4
PARENT 1nui_A
ATOM      1  N   LYS     4      13.213  28.880  61.083  1.00  0.00
ATOM      2  CA  LYS     4      13.710  28.945  59.707  1.00  0.00
ATOM      3  C   LYS     4      15.208  28.682  59.692  1.00  0.00
ATOM      4  O   LYS     4      15.953  29.307  60.445  1.00  0.00
ATOM      5  N   PHE     5      15.648  27.763  58.839  1.00  0.00
ATOM      6  CA  PHE     5      17.067  27.446  58.737  1.00  0.00
ATOM      7  C   PHE     5      17.686  28.131  57.532  1.00  0.00
ATOM      8  O   PHE     5      18.659  28.862  57.660  1.00  0.00
ATOM      9  N   LEU     6      17.111  27.891  56.361  1.00  0.00
ATOM     10  CA  LEU     6      17.580  28.488  55.123  1.00  0.00
ATOM     11  C   LEU     6      16.778  27.900  53.973  1.00  0.00
ATOM     12  O   LEU     6      16.161  26.850  54.127  1.00  0.00
ATOM     13  N   GLU     7      16.792  28.580  52.829  1.00  0.00
ATOM     14  CA  GLU     7      16.039  28.145  51.660  1.00  0.00
ATOM     15  C   GLU     7      16.539  26.857  51.036  1.00  0.00
ATOM     16  O   GLU     7      17.705  26.485  51.176  1.00  0.00
ATOM     17  N   ILE     8      15.629  26.179  50.348  1.00  0.00
ATOM     18  CA  ILE     8      15.903  24.902  49.705  1.00  0.00
ATOM     19  C   ILE     8      15.119  24.861  48.394  1.00  0.00
ATOM     20  O   ILE     8      14.084  25.512  48.259  1.00  0.00
ATOM     21  N   LEU     9      15.165  24.478  47.191  1.00  0.00
ATOM     22  CA  LEU     9      15.730  23.729  46.063  1.00  0.00
ATOM     23  C   LEU     9      17.058  24.282  45.540  1.00  0.00
ATOM     24  O   LEU     9      17.887  23.549  44.997  1.00  0.00
ATOM     25  N   VAL    10      17.234  25.582  45.708  1.00  0.00
ATOM     26  CA  VAL    10      18.415  26.312  45.273  1.00  0.00
ATOM     27  C   VAL    10      19.776  25.605  45.225  1.00  0.00
ATOM     28  O   VAL    10      20.273  25.275  44.152  1.00  0.00
ATOM     29  N   CYS    11      20.381  25.365  46.374  1.00  0.00
ATOM     30  CA  CYS    11      21.701  24.750  46.401  1.00  0.00
ATOM     31  C   CYS    11      21.934  23.439  45.635  1.00  0.00
ATOM     32  O   CYS    11      22.997  23.265  45.029  1.00  0.00
ATOM     33  N   PRO    12      20.969  22.520  45.637  1.00  0.00
ATOM     34  CA  PRO    12      21.202  21.246  44.966  1.00  0.00
ATOM     35  C   PRO    12      20.309  20.853  43.801  1.00  0.00
ATOM     36  O   PRO    12      20.255  19.672  43.440  1.00  0.00
ATOM     37  N   LEU    13      19.620  21.819  43.201  1.00  0.00
ATOM     38  CA  LEU    13      18.762  21.522  42.048  1.00  0.00
ATOM     39  C   LEU    13      18.625  22.687  41.065  1.00  0.00
ATOM     40  O   LEU    13      19.101  23.810  41.310  1.00  0.00
ATOM     41  N   CYS    14      17.936  22.388  39.964  1.00  0.00
ATOM     42  CA  CYS    14      17.656  23.335  38.893  1.00  0.00
ATOM     43  C   CYS    14      16.575  24.327  39.325  1.00  0.00
ATOM     44  O   CYS    14      16.305  25.307  38.629  1.00  0.00
ATOM     45  N   LYS    15      15.953  24.066  40.473  1.00  0.00
ATOM     46  CA  LYS    15      14.902  24.938  40.956  1.00  0.00
ATOM     47  C   LYS    15      15.307  25.859  42.088  1.00  0.00
ATOM     48  O   LYS    15      16.456  25.874  42.530  1.00  0.00
ATOM     49  N   GLY    16      14.341  26.634  42.567  1.00  0.00
ATOM     50  CA  GLY    16      14.588  27.576  43.646  1.00  0.00
ATOM     51  C   GLY    16      13.410  27.595  44.607  1.00  0.00
ATOM     52  O   GLY    16      12.376  26.983  44.344  1.00  0.00
ATOM     53  N   PRO    17      13.586  28.281  45.730  1.00  0.00
ATOM     54  CA  PRO    17      12.521  28.391  46.706  1.00  0.00
ATOM     55  C   PRO    17      12.287  27.174  47.575  1.00  0.00
ATOM     56  O   PRO    17      12.817  26.095  47.304  1.00  0.00
ATOM     57  N   LEU    18      11.309  27.305  48.487  1.00  0.00
ATOM     58  CA  LEU    18      10.988  26.348  49.535  1.00  0.00
ATOM     59  C   LEU    18      11.914  26.647  50.719  1.00  0.00
ATOM     60  O   LEU    18      13.135  26.667  50.560  1.00  0.00
ATOM     61  N   VAL    19      11.341  26.892  51.899  1.00  0.00
ATOM     62  CA  VAL    19      12.152  27.179  53.087  1.00  0.00
ATOM     63  C   VAL    19      12.191  25.973  54.024  1.00  0.00
ATOM     64  O   VAL    19      11.187  25.286  54.201  1.00  0.00
ATOM     65  N   PHE    20      13.359  25.731  54.615  1.00  0.00
ATOM     66  CA  PHE    20      13.567  24.617  55.541  1.00  0.00
ATOM     67  C   PHE    20      13.632  25.095  56.990  1.00  0.00
ATOM     68  O   PHE    20      14.385  26.011  57.312  1.00  0.00
ATOM     69  N   ASP    21      12.867  24.452  57.868  1.00  0.00
ATOM     70  CA  ASP    21      12.864  24.826  59.278  1.00  0.00
ATOM     71  C   ASP    21      13.457  23.733  60.174  1.00  0.00
ATOM     72  O   ASP    21      13.846  22.670  59.694  1.00  0.00
ATOM     73  N   LYS    22      14.606  23.912  60.506  1.00  0.00
ATOM     74  CA  LYS    22      15.264  22.942  61.387  1.00  0.00
ATOM     75  C   LYS    22      14.541  22.626  62.715  1.00  0.00
ATOM     76  O   LYS    22      14.761  21.568  63.304  1.00  0.00
ATOM     77  N   SER    23      13.654  23.520  63.150  1.00  0.00
ATOM     78  CA  SER    23      12.886  23.362  64.385  1.00  0.00
ATOM     79  C   SER    23      11.691  22.421  64.220  1.00  0.00
ATOM     80  O   SER    23      11.140  21.911  65.200  1.00  0.00
ATOM     81  N   LYS    24      11.283  22.202  62.979  1.00  0.00
ATOM     82  CA  LYS    24      10.136  21.349  62.706  1.00  0.00
ATOM     83  C   LYS    24      10.432  20.330  61.607  1.00  0.00
ATOM     84  O   LYS    24       9.691  19.360  61.436  1.00  0.00
ATOM     85  N   ASP    25      11.536  20.548  60.892  1.00  0.00
ATOM     86  CA  ASP    25      11.931  19.677  59.794  1.00  0.00
ATOM     87  C   ASP    25      11.061  19.838  58.557  1.00  0.00
ATOM     88  O   ASP    25      11.348  19.258  57.502  1.00  0.00
ATOM     89  N   GLU    26      10.013  20.651  58.682  1.00  0.00
ATOM     90  CA  GLU    26       9.072  20.897  57.609  1.00  0.00
ATOM     91  C   GLU    26       9.420  22.131  56.807  1.00  0.00
ATOM     92  O   GLU    26      10.026  23.068  57.324  1.00  0.00
ATOM     93  N   LEU    27       9.048  22.043  55.369  1.00  0.00
ATOM     94  CA  LEU    27       9.299  23.130  54.444  1.00  0.00
ATOM     95  C   LEU    27       8.001  23.738  53.926  1.00  0.00
ATOM     96  O   LEU    27       6.924  23.160  54.065  1.00  0.00
ATOM     97  N   ILE    28       8.118  24.925  53.347  1.00  0.00
ATOM     98  CA  ILE    28       6.975  25.632  52.795  1.00  0.00
ATOM     99  C   ILE    28       7.370  26.271  51.476  1.00  0.00
ATOM    100  O   ILE    28       8.368  26.997  51.413  1.00  0.00
ATOM    101  N   CYS    29       6.585  26.003  50.433  1.00  0.00
ATOM    102  CA  CYS    29       6.851  26.556  49.107  1.00  0.00
ATOM    103  C   CYS    29       5.921  27.712  48.776  1.00  0.00
ATOM    104  O   CYS    29       4.722  27.510  48.554  1.00  0.00
ATOM    105  N   LYS    30       6.534  28.510  47.702  1.00  0.00
ATOM    106  CA  LYS    30       6.247  28.847  46.324  1.00  0.00
ATOM    107  C   LYS    30       4.756  28.700  46.028  1.00  0.00
ATOM    108  O   LYS    30       4.368  28.252  44.960  1.00  0.00
ATOM    109  N   GLY    31       3.922  29.072  46.989  1.00  0.00
ATOM    110  CA  GLY    31       2.488  28.994  46.779  1.00  0.00
ATOM    111  C   GLY    31       1.795  27.782  47.371  1.00  0.00
ATOM    112  O   GLY    31       0.665  27.882  47.869  1.00  0.00
ATOM    113  N   ASP    32       2.470  26.638  47.319  1.00  0.00
ATOM    114  CA  ASP    32       1.916  25.396  47.839  1.00  0.00
ATOM    115  C   ASP    32       2.112  25.228  49.338  1.00  0.00
ATOM    116  O   ASP    32       3.138  25.615  49.889  1.00  0.00
ATOM    117  N   ARG    33       1.112  24.648  49.987  1.00  0.00
ATOM    118  CA  ARG    33       1.171  24.412  51.411  1.00  0.00
ATOM    119  C   ARG    33       2.045  23.197  51.653  1.00  0.00
ATOM    120  O   ARG    33       1.974  22.210  50.930  1.00  0.00
ATOM    121  N   LEU    34       3.048  22.808  52.123  1.00  0.00
ATOM    122  CA  LEU    34       3.635  22.778  53.455  1.00  0.00
ATOM    123  C   LEU    34       3.687  21.352  53.978  1.00  0.00
ATOM    124  O   LEU    34       2.683  20.822  54.429  1.00  0.00
ATOM    125  N   ALA    35       4.859  20.736  53.918  1.00  0.00
ATOM    126  CA  ALA    35       5.022  19.362  54.386  1.00  0.00
ATOM    127  C   ALA    35       5.984  19.298  55.565  1.00  0.00
ATOM    128  O   ALA    35       6.943  20.076  55.628  1.00  0.00
ATOM    129  N   PHE    36       5.188  18.549  56.090  1.00  0.00
ATOM    130  CA  PHE    36       6.307  18.001  56.845  1.00  0.00
ATOM    131  C   PHE    36       6.514  16.531  56.501  1.00  0.00
ATOM    132  O   PHE    36       7.612  16.120  56.121  1.00  0.00
ATOM    133  N   PRO    37       5.452  15.744  56.630  1.00  0.00
ATOM    134  CA  PRO    37       5.518  14.320  56.342  1.00  0.00
ATOM    135  C   PRO    37       5.569  14.065  54.839  1.00  0.00
ATOM    136  O   PRO    37       6.100  13.049  54.392  1.00  0.00
ATOM    137  N   ILE    38       5.019  14.995  54.066  1.00  0.00
ATOM    138  CA  ILE    38       5.014  14.845  52.625  1.00  0.00
ATOM    139  C   ILE    38       3.814  14.051  52.153  1.00  0.00
ATOM    140  O   ILE    38       3.213  13.304  52.925  1.00  0.00
ATOM    141  N   LYS    39       3.461  14.214  50.883  1.00  0.00
ATOM    142  CA  LYS    39       2.327  13.505  50.310  1.00  0.00
ATOM    143  C   LYS    39       2.797  12.619  49.161  1.00  0.00
ATOM    144  O   LYS    39       3.997  12.413  48.982  1.00  0.00
ATOM    145  N   ASP    40       1.852  12.091  48.391  1.00  0.00
ATOM    146  CA  ASP    40       2.188  11.228  47.265  1.00  0.00
ATOM    147  C   ASP    40       3.076  11.982  46.279  1.00  0.00
ATOM    148  O   ASP    40       2.608  12.862  45.557  1.00  0.00
ATOM    149  N   GLY    41       4.358  11.636  46.258  1.00  0.00
ATOM    150  CA  GLY    41       5.287  12.297  45.360  1.00  0.00
ATOM    151  C   GLY    41       6.259  13.187  46.104  1.00  0.00
ATOM    152  O   GLY    41       7.474  13.028  45.988  1.00  0.00
ATOM    153  N   ILE    42       5.722  14.131  46.871  1.00  0.00
ATOM    154  CA  ILE    42       6.550  15.046  47.648  1.00  0.00
ATOM    155  C   ILE    42       7.018  14.358  48.925  1.00  0.00
ATOM    156  O   ILE    42       6.210  14.021  49.791  1.00  0.00
ATOM    157  N   PRO    43       8.325  14.145  49.036  1.00  0.00
ATOM    158  CA  PRO    43       8.889  13.499  50.213  1.00  0.00
ATOM    159  C   PRO    43       8.718  14.392  51.434  1.00  0.00
ATOM    160  O   PRO    43       7.922  15.328  51.420  1.00  0.00
ATOM    161  N   MET    44       9.467  14.101  52.492  1.00  0.00
ATOM    162  CA  MET    44       9.381  14.884  53.716  1.00  0.00
ATOM    163  C   MET    44      10.583  15.805  53.878  1.00  0.00
ATOM    164  O   MET    44      11.668  15.521  53.372  1.00  0.00
ATOM    165  N   MET    45      10.378  16.911  54.586  1.00  0.00
ATOM    166  CA  MET    45      11.442  17.875  54.825  1.00  0.00
ATOM    167  C   MET    45      12.582  17.187  55.564  1.00  0.00
ATOM    168  O   MET    45      12.351  16.477  56.543  1.00  0.00
ATOM    169  N   LEU    46      13.806  17.390  55.089  1.00  0.00
ATOM    170  CA  LEU    46      14.969  16.783  55.719  1.00  0.00
ATOM    171  C   LEU    46      14.944  17.002  57.227  1.00  0.00
ATOM    172  O   LEU    46      14.552  18.066  57.704  1.00  0.00
ATOM    173  N   GLU    47      14.650  16.258  57.695  1.00  0.00
ATOM    174  CA  GLU    47      14.617  16.233  59.153  1.00  0.00
ATOM    175  C   GLU    47      16.042  16.041  59.662  1.00  0.00
ATOM    176  O   GLU    47      16.372  16.401  60.792  1.00  0.00
ATOM    177  N   SER    48      16.886  15.463  58.815  1.00  0.00
ATOM    178  CA  SER    48      18.276  15.250  59.177  1.00  0.00
ATOM    179  C   SER    48      18.964  16.592  59.011  1.00  0.00
ATOM    180  O   SER    48      19.455  17.172  59.981  1.00  0.00
ATOM    181  N   GLU    49      18.977  17.084  57.775  1.00  0.00
ATOM    182  CA  GLU    49      19.584  18.368  57.456  1.00  0.00
ATOM    183  C   GLU    49      19.288  19.377  58.566  1.00  0.00
ATOM    184  O   GLU    49      20.177  20.099  59.021  1.00  0.00
ATOM    185  N   ALA    50      18.032  19.408  59.001  1.00  0.00
ATOM    186  CA  ALA    50      17.590  20.330  60.038  1.00  0.00
ATOM    187  C   ALA    50      18.325  20.164  61.359  1.00  0.00
ATOM    188  O   ALA    50      18.658  21.150  62.021  1.00  0.00
ATOM    189  N   ARG    51      18.576  18.924  61.756  1.00  0.00
ATOM    190  CA  ARG    51      19.266  18.681  63.019  1.00  0.00
ATOM    191  C   ARG    51      20.655  19.314  63.010  1.00  0.00
ATOM    192  O   ARG    51      21.005  20.114  63.887  1.00  0.00
TER
END
