
#######################################################
#                                                     #
#                        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_1
# Molecule2: number of CA atoms   61 (  465),  selected   61 , name T0348.pdb
# PARAMETERS: T0348TS550_1.T0348.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    A       3      D       2           -
LGA    K       4      A       3           -
LGA    F       5      K       4           -
LGA    L       6      F       5           -
LGA    E       7      L       6           -
LGA    I       8      E       7           -
LGA    L       9      I       8           -
LGA    V      10      L       9           -
LGA    C      11      V      10           -
LGA    P      12      -       -           -
LGA    L      13      C      11           #
LGA    -       -      P      12           -
LGA    C      14      L      13          2.547
LGA    K      15      C      14          3.561
LGA    G      16      K      15          2.662
LGA    P      17      G      16          4.026
LGA    L      18      P      17          4.667
LGA    V      19      L      18          2.682
LGA    F      20      V      19          2.332
LGA    -       -      F      20           -
LGA    -       -      D      21           -
LGA    -       -      K      22           -
LGA    -       -      S      23           -
LGA    -       -      K      24           -
LGA    -       -      D      25           -
LGA    -       -      E      26           -
LGA    -       -      L      27           -
LGA    D      21      I      28          1.400
LGA    K      22      C      29          0.658
LGA    S      23      K      30          0.878
LGA    K      24      G      31          3.520
LGA    D      25      D      32          1.539
LGA    E      26      R      33          3.606
LGA    L      27      L      34          3.023
LGA    I      28      A      35          3.306
LGA    C      29      F      36          3.183
LGA    K      30      P      37          3.675
LGA    G      31      I      38          2.256
LGA    D      32      K      39          2.289
LGA    -       -      D      40           -
LGA    -       -      G      41           -
LGA    R      33      I      42          5.028
LGA    L      34      P      43          4.638
LGA    A      35      M      44          3.383
LGA    -       -      M      45           -
LGA    -       -      L      46           -
LGA    -       -      E      47           -
LGA    -       -      S      48           -
LGA    F      36      E      49          4.036
LGA    P      37      A      50          2.120
LGA    I      38      R      51          3.031
LGA    K      39      E      52          2.999
LGA    D      40      L      53          2.951
LGA    G      41      -       -           -
LGA    I      42      -       -           -
LGA    P      43      A      54          0.969
LGA    M      44      P      55          3.607
LGA    M      45      E      56          3.597
LGA    L      46      E      57          2.803
LGA    E      47      E      58           #
LGA    S      48      V      59           -
LGA    E      49      K      60           -
LGA    A      50      L      61           -
LGA    -       -      E      62           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   48   61    5.0     31    3.12     6.45     30.285     0.962

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.134824 * X  +   0.943415 * Y  +   0.302969 * Z  + -123.424301
  Y_new =  -0.772313 * X  +  -0.091503 * Y  +   0.628617 * Z  + 203.888474
  Z_new =   0.620770 * X  +  -0.318740 * Y  +   0.716275 * Z  + -89.569214 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.418685    2.722908  [ DEG:   -23.9889    156.0111 ]
  Theta =  -0.669724   -2.471869  [ DEG:   -38.3724   -141.6276 ]
  Phi   =  -1.397967    1.743626  [ DEG:   -80.0976     99.9024 ]
 
# 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_1                                  
REMARK     2: T0348.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0348TS550_1.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   31   3.12    6.45  30.285
REMARK  ---------------------------------------------------------- 
MOLECULE T0348TS550_1
PFRMAT TS
TARGET T0348
MODEL 1
PARENT 1hnw_S
ATOM      1  N   ALA     3      23.734  26.477  57.937  1.00  0.00
ATOM      2  CA  ALA     3      23.426  26.722  59.340  1.00  0.00
ATOM      3  C   ALA     3      22.548  27.932  59.633  1.00  0.00
ATOM      4  O   ALA     3      22.657  28.542  60.692  1.00  0.00
ATOM      5  N   LYS     4      21.681  28.285  58.692  1.00  0.00
ATOM      6  CA  LYS     4      20.762  29.392  58.913  1.00  0.00
ATOM      7  C   LYS     4      19.719  28.724  59.779  1.00  0.00
ATOM      8  O   LYS     4      19.340  29.223  60.835  1.00  0.00
ATOM      9  N   PHE     5      19.272  27.567  59.305  1.00  0.00
ATOM     10  CA  PHE     5      18.275  26.777  59.997  1.00  0.00
ATOM     11  C   PHE     5      18.914  25.849  61.022  1.00  0.00
ATOM     12  O   PHE     5      18.272  25.448  61.988  1.00  0.00
ATOM     13  N   LEU     6      20.182  25.514  60.819  1.00  0.00
ATOM     14  CA  LEU     6      20.853  24.608  61.739  1.00  0.00
ATOM     15  C   LEU     6      20.969  25.214  63.126  1.00  0.00
ATOM     16  O   LEU     6      20.345  24.729  64.067  1.00  0.00
ATOM     17  N   GLU     7      21.755  26.275  63.263  1.00  0.00
ATOM     18  CA  GLU     7      21.899  26.905  64.566  1.00  0.00
ATOM     19  C   GLU     7      20.575  27.537  64.995  1.00  0.00
ATOM     20  O   GLU     7      20.473  28.096  66.084  1.00  0.00
ATOM     21  N   ILE     8      19.560  27.426  64.137  1.00  0.00
ATOM     22  CA  ILE     8      18.226  27.969  64.416  1.00  0.00
ATOM     23  C   ILE     8      17.232  26.847  64.702  1.00  0.00
ATOM     24  O   ILE     8      16.134  27.090  65.205  1.00  0.00
ATOM     25  N   LEU     9      17.613  25.621  64.359  1.00  0.00
ATOM     26  CA  LEU     9      16.746  24.476  64.591  1.00  0.00
ATOM     27  C   LEU     9      16.954  24.011  66.016  1.00  0.00
ATOM     28  O   LEU     9      16.005  23.628  66.700  1.00  0.00
ATOM     29  N   VAL    10      16.193  24.177  66.967  1.00  0.00
ATOM     30  CA  VAL    10      15.868  23.280  68.067  1.00  0.00
ATOM     31  C   VAL    10      14.370  23.071  68.248  1.00  0.00
ATOM     32  O   VAL    10      13.938  22.073  68.825  1.00  0.00
ATOM     33  N   CYS    11      13.582  23.995  67.710  1.00  0.00
ATOM     34  CA  CYS    11      12.132  23.919  67.801  1.00  0.00
ATOM     35  C   CYS    11      11.453  24.712  66.701  1.00  0.00
ATOM     36  O   CYS    11      11.982  25.713  66.200  1.00  0.00
ATOM     37  N   PRO    12      10.271  24.242  66.331  1.00  0.00
ATOM     38  CA  PRO    12       9.462  24.889  65.318  1.00  0.00
ATOM     39  C   PRO    12       8.011  24.649  65.714  1.00  0.00
ATOM     40  O   PRO    12       7.558  23.504  65.797  1.00  0.00
ATOM     41  N   LEU    13       7.318  25.733  66.054  1.00  0.00
ATOM     42  CA  LEU    13       5.917  25.673  66.448  1.00  0.00
ATOM     43  C   LEU    13       5.170  26.878  65.896  1.00  0.00
ATOM     44  O   LEU    13       5.667  27.551  64.993  1.00  0.00
ATOM     45  N   CYS    14       3.964  27.125  66.398  1.00  0.00
ATOM     46  CA  CYS    14       3.171  28.258  65.936  1.00  0.00
ATOM     47  C   CYS    14       3.737  29.594  66.390  1.00  0.00
ATOM     48  O   CYS    14       3.563  30.614  65.729  1.00  0.00
ATOM     49  N   LYS    15       4.429  29.582  67.518  1.00  0.00
ATOM     50  CA  LYS    15       5.045  30.787  68.043  1.00  0.00
ATOM     51  C   LYS    15       6.356  31.045  67.291  1.00  0.00
ATOM     52  O   LYS    15       6.697  32.193  66.992  1.00  0.00
ATOM     53  N   GLY    16       7.055  29.960  66.949  1.00  0.00
ATOM     54  CA  GLY    16       8.333  30.014  66.241  1.00  0.00
ATOM     55  C   GLY    16       8.318  29.109  65.023  1.00  0.00
ATOM     56  O   GLY    16       8.934  28.054  65.040  1.00  0.00
ATOM     57  N   PRO    17       7.578  29.482  63.968  1.00  0.00
ATOM     58  CA  PRO    17       7.505  28.674  62.750  1.00  0.00
ATOM     59  C   PRO    17       8.846  28.655  62.022  1.00  0.00
ATOM     60  O   PRO    17       9.647  29.574  62.171  1.00  0.00
ATOM     61  N   LEU    18       9.086  27.341  61.059  1.00  0.00
ATOM     62  CA  LEU    18      10.386  27.853  60.678  1.00  0.00
ATOM     63  C   LEU    18      10.200  27.994  59.184  1.00  0.00
ATOM     64  O   LEU    18       9.342  27.327  58.612  1.00  0.00
ATOM     65  N   VAL    19      10.972  28.860  58.546  1.00  0.00
ATOM     66  CA  VAL    19      10.839  29.026  57.109  1.00  0.00
ATOM     67  C   VAL    19      12.165  29.397  56.488  1.00  0.00
ATOM     68  O   VAL    19      12.566  30.558  56.514  1.00  0.00
ATOM     69  N   PHE    20      12.848  28.405  55.929  1.00  0.00
ATOM     70  CA  PHE    20      14.131  28.665  55.310  1.00  0.00
ATOM     71  C   PHE    20      14.035  28.615  53.793  1.00  0.00
ATOM     72  O   PHE    20      13.111  28.037  53.224  1.00  0.00
ATOM     73  N   ASP    21      14.266  27.095  55.445  1.00  0.00
ATOM     74  CA  ASP    21      13.532  25.931  55.918  1.00  0.00
ATOM     75  C   ASP    21      13.360  25.860  57.420  1.00  0.00
ATOM     76  O   ASP    21      14.175  26.375  58.181  1.00  0.00
ATOM     77  N   LYS    22      12.283  25.199  57.858  1.00  0.00
ATOM     78  CA  LYS    22      11.904  25.000  59.259  1.00  0.00
ATOM     79  C   LYS    22      12.933  24.173  60.029  1.00  0.00
ATOM     80  O   LYS    22      13.656  23.369  59.436  1.00  0.00
ATOM     81  N   SER    23      12.992  24.366  61.347  1.00  0.00
ATOM     82  CA  SER    23      13.925  23.618  62.190  1.00  0.00
ATOM     83  C   SER    23      13.707  22.127  61.946  1.00  0.00
ATOM     84  O   SER    23      14.432  21.491  61.184  1.00  0.00
ATOM     85  N   LYS    24      12.691  21.584  62.602  1.00  0.00
ATOM     86  CA  LYS    24      12.341  20.179  62.482  1.00  0.00
ATOM     87  C   LYS    24      10.900  20.043  62.936  1.00  0.00
ATOM     88  O   LYS    24      10.141  19.233  62.408  1.00  0.00
ATOM     89  N   ASP    25      10.527  20.850  63.922  1.00  0.00
ATOM     90  CA  ASP    25       9.175  20.829  64.447  1.00  0.00
ATOM     91  C   ASP    25       8.217  21.245  63.347  1.00  0.00
ATOM     92  O   ASP    25       7.017  21.372  63.580  1.00  0.00
ATOM     93  N   GLU    26       8.781  21.517  62.193  1.00  0.00
ATOM     94  CA  GLU    26       7.954  21.866  61.044  1.00  0.00
ATOM     95  C   GLU    26       8.601  23.005  60.264  1.00  0.00
ATOM     96  O   GLU    26       8.367  24.179  60.549  1.00  0.00
ATOM     97  N   LEU    27       9.411  22.647  59.277  1.00  0.00
ATOM     98  CA  LEU    27      10.101  23.624  58.447  1.00  0.00
ATOM     99  C   LEU    27       9.333  23.916  57.162  1.00  0.00
ATOM    100  O   LEU    27       8.996  23.000  56.414  1.00  0.00
ATOM    101  N   ILE    28       9.065  25.192  56.903  1.00  0.00
ATOM    102  CA  ILE    28       8.358  25.583  55.689  1.00  0.00
ATOM    103  C   ILE    28       9.410  25.860  54.621  1.00  0.00
ATOM    104  O   ILE    28      10.332  26.653  54.834  1.00  0.00
ATOM    105  N   CYS    29       9.280  25.195  53.479  1.00  0.00
ATOM    106  CA  CYS    29      10.243  25.377  52.403  1.00  0.00
ATOM    107  C   CYS    29       9.705  26.253  51.270  1.00  0.00
ATOM    108  O   CYS    29       8.492  26.403  51.090  1.00  0.00
ATOM    109  N   LYS    30      10.629  26.817  50.504  1.00  0.00
ATOM    110  CA  LYS    30      10.300  27.716  49.407  1.00  0.00
ATOM    111  C   LYS    30      10.187  27.011  48.046  1.00  0.00
ATOM    112  O   LYS    30      11.043  26.204  47.676  1.00  0.00
ATOM    113  N   GLY    31       9.289  27.786  47.266  1.00  0.00
ATOM    114  CA  GLY    31       9.385  28.103  45.852  1.00  0.00
ATOM    115  C   GLY    31       8.581  29.340  45.503  1.00  0.00
ATOM    116  O   GLY    31       8.250  30.119  46.378  1.00  0.00
ATOM    117  N   ASP    32       8.251  29.523  44.235  1.00  0.00
ATOM    118  CA  ASP    32       7.516  30.721  43.827  1.00  0.00
ATOM    119  C   ASP    32       6.082  30.807  44.331  1.00  0.00
ATOM    120  O   ASP    32       5.534  31.902  44.439  1.00  0.00
ATOM    121  N   ARG    33       5.463  29.663  44.607  1.00  0.00
ATOM    122  CA  ARG    33       4.086  29.648  45.060  1.00  0.00
ATOM    123  C   ARG    33       3.897  29.237  46.496  1.00  0.00
ATOM    124  O   ARG    33       2.863  29.533  47.087  1.00  0.00
ATOM    125  N   LEU    34       4.906  28.602  47.088  1.00  0.00
ATOM    126  CA  LEU    34       4.788  28.139  48.460  1.00  0.00
ATOM    127  C   LEU    34       5.926  28.534  49.378  1.00  0.00
ATOM    128  O   LEU    34       7.086  28.611  48.967  1.00  0.00
ATOM    129  N   ALA    35       5.712  29.096  50.587  1.00  0.00
ATOM    130  CA  ALA    35       6.386  28.531  51.751  1.00  0.00
ATOM    131  C   ALA    35       5.531  27.398  52.295  1.00  0.00
ATOM    132  O   ALA    35       4.654  27.608  53.136  1.00  0.00
ATOM    133  N   PHE    36       5.793  26.195  51.799  1.00  0.00
ATOM    134  CA  PHE    36       5.038  25.025  52.217  1.00  0.00
ATOM    135  C   PHE    36       5.599  24.346  53.456  1.00  0.00
ATOM    136  O   PHE    36       6.778  23.998  53.509  1.00  0.00
ATOM    137  N   PRO    37       4.746  24.158  54.474  1.00  0.00
ATOM    138  CA  PRO    37       5.088  23.521  55.746  1.00  0.00
ATOM    139  C   PRO    37       5.357  22.026  55.571  1.00  0.00
ATOM    140  O   PRO    37       4.600  21.325  54.898  1.00  0.00
ATOM    141  N   ILE    38       6.427  21.543  56.189  1.00  0.00
ATOM    142  CA  ILE    38       6.789  20.135  56.091  1.00  0.00
ATOM    143  C   ILE    38       7.084  19.518  57.462  1.00  0.00
ATOM    144  O   ILE    38       8.037  19.912  58.135  1.00  0.00
ATOM    145  N   LYS    39       6.259  18.560  57.878  1.00  0.00
ATOM    146  CA  LYS    39       6.471  17.890  59.157  1.00  0.00
ATOM    147  C   LYS    39       7.610  16.902  58.931  1.00  0.00
ATOM    148  O   LYS    39       7.481  15.958  58.150  1.00  0.00
ATOM    149  N   ASP    40       8.639  18.105  58.877  1.00  0.00
ATOM    150  CA  ASP    40       9.933  17.917  58.228  1.00  0.00
ATOM    151  C   ASP    40      10.547  16.544  58.501  1.00  0.00
ATOM    152  O   ASP    40      11.281  16.010  57.670  1.00  0.00
ATOM    153  N   GLY    41      10.242  15.974  59.663  1.00  0.00
ATOM    154  CA  GLY    41      10.793  14.678  60.052  1.00  0.00
ATOM    155  C   GLY    41      10.336  13.478  59.218  1.00  0.00
ATOM    156  O   GLY    41      11.026  12.462  59.162  1.00  0.00
ATOM    157  N   ILE    42       9.187  13.593  58.564  1.00  0.00
ATOM    158  CA  ILE    42       8.665  12.481  57.774  1.00  0.00
ATOM    159  C   ILE    42       9.506  12.129  56.543  1.00  0.00
ATOM    160  O   ILE    42       9.545  10.971  56.123  1.00  0.00
ATOM    161  N   PRO    43      10.191  13.123  55.982  1.00  0.00
ATOM    162  CA  PRO    43      10.997  12.924  54.779  1.00  0.00
ATOM    163  C   PRO    43      12.303  12.164  54.967  1.00  0.00
ATOM    164  O   PRO    43      12.935  12.222  56.021  1.00  0.00
ATOM    165  N   MET    44      12.699  11.454  53.917  1.00  0.00
ATOM    166  CA  MET    44      13.934  10.686  53.913  1.00  0.00
ATOM    167  C   MET    44      14.867  11.304  52.877  1.00  0.00
ATOM    168  O   MET    44      15.820  10.679  52.416  1.00  0.00
ATOM    169  N   MET    45      14.566  12.546  52.519  1.00  0.00
ATOM    170  CA  MET    45      15.357  13.305  51.560  1.00  0.00
ATOM    171  C   MET    45      15.539  14.701  52.147  1.00  0.00
ATOM    172  O   MET    45      14.988  15.006  53.206  1.00  0.00
ATOM    173  N   LEU    46      16.310  15.544  51.471  1.00  0.00
ATOM    174  CA  LEU    46      16.542  16.899  51.955  1.00  0.00
ATOM    175  C   LEU    46      15.275  17.732  51.774  1.00  0.00
ATOM    176  O   LEU    46      14.500  17.502  50.845  1.00  0.00
ATOM    177  N   GLU    47      15.028  18.738  52.667  1.00  0.00
ATOM    178  CA  GLU    47      13.800  19.534  52.638  1.00  0.00
ATOM    179  C   GLU    47      13.248  19.812  51.249  1.00  0.00
ATOM    180  O   GLU    47      12.078  19.546  50.985  1.00  0.00
ATOM    181  N   SER    48      14.088  20.365  50.377  1.00  0.00
ATOM    182  CA  SER    48      13.673  20.657  49.016  1.00  0.00
ATOM    183  C   SER    48      12.859  19.537  48.391  1.00  0.00
ATOM    184  O   SER    48      11.848  19.787  47.735  1.00  0.00
ATOM    185  N   GLU    49      13.295  18.298  48.595  1.00  0.00
ATOM    186  CA  GLU    49      12.593  17.141  48.056  1.00  0.00
ATOM    187  C   GLU    49      11.134  17.115  48.494  1.00  0.00
ATOM    188  O   GLU    49      10.297  16.492  47.848  1.00  0.00
ATOM    189  N   ALA    50      10.825  17.787  49.593  1.00  0.00
ATOM    190  CA  ALA    50       9.462  17.780  50.109  1.00  0.00
ATOM    191  C   ALA    50       8.735  19.082  49.822  1.00  0.00
ATOM    192  O   ALA    50       7.649  19.340  50.345  1.00  0.00
TER
END
