
#######################################################
#                                                     #
#                        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 T0348AL243_3
# Molecule2: number of CA atoms   61 (  465),  selected   61 , name T0348.pdb
# PARAMETERS: T0348AL243_3.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    -       -      P      17           -
LGA    -       -      L      18           -
LGA    L       9      V      19          1.929
LGA    V      10      F      20          0.931
LGA    C      11      D      21          2.429
LGA    P      12      K      22          1.895
LGA    -       -      S      23           -
LGA    -       -      K      24           -
LGA    L      18      D      25          3.034
LGA    V      19      E      26          3.342
LGA    -       -      L      27           -
LGA    F      20      I      28          1.115
LGA    D      21      C      29          1.255
LGA    K      22      K      30          2.439
LGA    S      23      G      31          3.544
LGA    K      24      D      32          3.149
LGA    D      25      R      33          2.089
LGA    E      26      L      34          0.637
LGA    L      27      A      35          2.430
LGA    I      28      -       -           -
LGA    C      29      F      36          3.675
LGA    K      30      P      37          2.546
LGA    G      31      I      38           #
LGA    -       -      K      39           -
LGA    -       -      D      40           -
LGA    -       -      G      41           -
LGA    -       -      I      42           -
LGA    -       -      P      43           -
LGA    -       -      M      44           -
LGA    -       -      M      45           -
LGA    -       -      L      46           -
LGA    -       -      E      47           -
LGA    -       -      S      48           -
LGA    -       -      E      49           -
LGA    D      32      A      50          2.890
LGA    R      33      R      51          1.991
LGA    -       -      E      52           -
LGA    -       -      L      53           -
LGA    L      34      A      54          1.464
LGA    A      35      P      55          3.291
LGA    F      36      E      56          6.170
LGA    P      37      E      57           -
LGA    -       -      E      58           -
LGA    -       -      V      59           -
LGA    -       -      K      60           -
LGA    -       -      L      61           -
LGA    I      38      E      62          5.598
LGA    K      39      -       -           -
LGA    D      40      -       -           -
LGA    G      41      -       -           -
LGA    I      42      -       -           -
LGA    P      43      -       -           -
LGA    M      44      -       -           -
LGA    M      45      -       -           -
LGA    L      46      -       -           -
LGA    E      47      -       -           -
LGA    S      48      -       -           -
LGA    E      49      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   36   61    5.0     22    2.95     9.09     26.702     0.722

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.127629 * X  +   0.389115 * Y  +   0.912305 * Z  + -41.828571
  Y_new =   0.930588 * X  +  -0.365175 * Y  +   0.025567 * Z  +  -2.409332
  Z_new =   0.343100 * X  +   0.845716 * Y  +  -0.408713 * Z  +   6.752783 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.020974   -1.120619  [ DEG:   115.7933    -64.2067 ]
  Theta =  -0.350215   -2.791378  [ DEG:   -20.0658   -159.9342 ]
  Phi   =   1.434497   -1.707095  [ DEG:    82.1907    -97.8093 ]
 
# 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: T0348AL243_3                                  
REMARK     2: T0348.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0348AL243_3.T0348.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   36   61   5.0   22   2.95    9.09  26.702
REMARK  ---------------------------------------------------------- 
MOLECULE T0348AL243_3
REMARK Aligment from pdb entry: 1vckA
ATOM      1  N   LEU     9      15.748  26.701  56.513  1.00  0.00              
ATOM      2  CA  LEU     9      16.517  26.642  55.278  1.00  0.00              
ATOM      3  C   LEU     9      15.638  27.140  54.136  1.00  0.00              
ATOM      4  O   LEU     9      14.536  26.638  53.917  1.00  0.00              
ATOM      5  N   VAL    10      16.123  28.158  53.432  1.00  0.00              
ATOM      6  CA  VAL    10      15.395  28.727  52.310  1.00  0.00              
ATOM      7  C   VAL    10      15.871  28.060  51.035  1.00  0.00              
ATOM      8  O   VAL    10      17.067  28.054  50.738  1.00  0.00              
ATOM      9  N   CYS    11      14.931  27.507  50.281  1.00  0.00              
ATOM     10  CA  CYS    11      15.252  26.844  49.028  1.00  0.00              
ATOM     11  C   CYS    11      15.777  27.869  48.024  1.00  0.00              
ATOM     12  O   CYS    11      15.418  29.047  48.073  1.00  0.00              
ATOM     13  N   PRO    12      16.656  27.436  47.112  1.00  0.00              
ATOM     14  CA  PRO    12      17.200  28.350  46.107  1.00  0.00              
ATOM     15  C   PRO    12      16.097  28.894  45.200  1.00  0.00              
ATOM     16  O   PRO    12      16.310  29.854  44.461  1.00  0.00              
ATOM     17  N   LEU    18      14.917  28.281  45.259  1.00  0.00              
ATOM     18  CA  LEU    18      13.815  28.704  44.400  1.00  0.00              
ATOM     19  C   LEU    18      12.489  29.015  45.081  1.00  0.00              
ATOM     20  O   LEU    18      12.244  28.625  46.223  1.00  0.00              
ATOM     21  N   VAL    19      10.617  27.323  51.885  1.00  0.00              
ATOM     22  CA  VAL    19      11.502  27.138  53.024  1.00  0.00              
ATOM     23  C   VAL    19      10.973  26.079  53.976  1.00  0.00              
ATOM     24  O   VAL    19       9.771  25.794  53.999  1.00  0.00              
ATOM     25  N   PHE    20      11.884  25.506  54.758  1.00  0.00              
ATOM     26  CA  PHE    20      11.541  24.476  55.733  1.00  0.00              
ATOM     27  C   PHE    20      12.259  24.731  57.042  1.00  0.00              
ATOM     28  O   PHE    20      13.309  25.369  57.076  1.00  0.00              
ATOM     29  N   ASP    21      11.685  24.214  58.124  1.00  0.00              
ATOM     30  CA  ASP    21      12.314  24.315  59.427  1.00  0.00              
ATOM     31  C   ASP    21      13.227  23.090  59.418  1.00  0.00              
ATOM     32  O   ASP    21      12.776  21.991  59.090  1.00  0.00              
ATOM     33  N   LYS    22      14.502  23.264  59.752  1.00  0.00              
ATOM     34  CA  LYS    22      15.430  22.137  59.721  1.00  0.00              
ATOM     35  C   LYS    22      15.306  21.168  60.890  1.00  0.00              
ATOM     36  O   LYS    22      15.800  20.045  60.817  1.00  0.00              
ATOM     37  N   SER    23      14.642  21.593  61.961  1.00  0.00              
ATOM     38  CA  SER    23      14.469  20.730  63.128  1.00  0.00              
ATOM     39  C   SER    23      13.343  19.730  62.915  1.00  0.00              
ATOM     40  O   SER    23      13.471  18.550  63.252  1.00  0.00              
ATOM     41  N   LYS    24      12.237  20.215  62.360  1.00  0.00              
ATOM     42  CA  LYS    24      11.058  19.386  62.141  1.00  0.00              
ATOM     43  C   LYS    24      10.843  18.937  60.701  1.00  0.00              
ATOM     44  O   LYS    24      10.078  18.003  60.456  1.00  0.00              
ATOM     45  N   ASP    25      11.500  19.609  59.758  1.00  0.00              
ATOM     46  CA  ASP    25      11.336  19.270  58.353  1.00  0.00              
ATOM     47  C   ASP    25      10.051  19.833  57.768  1.00  0.00              
ATOM     48  O   ASP    25       9.757  19.655  56.583  1.00  0.00              
ATOM     49  N   GLU    26       9.282  20.530  58.598  1.00  0.00              
ATOM     50  CA  GLU    26       8.014  21.108  58.169  1.00  0.00              
ATOM     51  C   GLU    26       8.188  22.354  57.306  1.00  0.00              
ATOM     52  O   GLU    26       9.124  23.130  57.501  1.00  0.00              
ATOM     53  N   LEU    27       7.284  22.559  56.336  1.00  0.00              
ATOM     54  CA  LEU    27       7.364  23.733  55.463  1.00  0.00              
ATOM     55  C   LEU    27       7.283  24.987  56.328  1.00  0.00              
ATOM     56  O   LEU    27       6.522  25.024  57.297  1.00  0.00              
ATOM     57  N   ILE    28       8.065  26.003  55.982  1.00  0.00              
ATOM     58  CA  ILE    28       8.066  27.254  56.734  1.00  0.00              
ATOM     59  C   ILE    28       7.564  28.389  55.850  1.00  0.00              
ATOM     60  O   ILE    28       7.253  29.478  56.335  1.00  0.00              
ATOM     61  N   CYS    29       7.481  28.130  54.550  1.00  0.00              
ATOM     62  CA  CYS    29       7.005  29.139  53.616  1.00  0.00              
ATOM     63  C   CYS    29       6.469  28.521  52.333  1.00  0.00              
ATOM     64  O   CYS    29       6.983  27.507  51.862  1.00  0.00              
ATOM     65  N   LYS    30       5.897  27.948  48.433  1.00  0.00              
ATOM     66  CA  LYS    30       4.883  26.954  48.071  1.00  0.00              
ATOM     67  C   LYS    30       5.092  25.558  48.659  1.00  0.00              
ATOM     68  O   LYS    30       4.393  24.620  48.282  1.00  0.00              
ATOM     69  N   GLY    31       6.041  25.410  49.573  1.00  0.00              
ATOM     70  CA  GLY    31       6.314  24.099  50.163  1.00  0.00              
ATOM     71  C   GLY    31       5.138  23.578  50.987  1.00  0.00              
ATOM     72  O   GLY    31       4.547  24.321  51.765  1.00  0.00              
ATOM     73  N   ASP    32       4.804  22.301  50.808  1.00  0.00              
ATOM     74  CA  ASP    32       3.688  21.685  51.526  1.00  0.00              
ATOM     75  C   ASP    32       4.036  20.303  52.072  1.00  0.00              
ATOM     76  O   ASP    32       3.454  19.850  53.057  1.00  0.00              
ATOM     77  N   ARG    33       4.983  19.634  51.427  1.00  0.00              
ATOM     78  CA  ARG    33       5.399  18.299  51.849  1.00  0.00              
ATOM     79  C   ARG    33       6.600  18.385  52.784  1.00  0.00              
ATOM     80  O   ARG    33       7.637  18.950  52.433  1.00  0.00              
ATOM     81  N   LEU    34      12.139  14.723  55.207  1.00  0.00              
ATOM     82  CA  LEU    34      12.406  13.663  56.152  1.00  0.00              
ATOM     83  C   LEU    34      13.502  14.212  57.045  1.00  0.00              
ATOM     84  O   LEU    34      14.371  14.946  56.572  1.00  0.00              
ATOM     85  N   ALA    35      13.460  13.893  58.334  1.00  0.00              
ATOM     86  CA  ALA    35      14.478  14.377  59.257  1.00  0.00              
ATOM     87  C   ALA    35      15.337  13.206  59.711  1.00  0.00              
ATOM     88  O   ALA    35      14.862  12.074  59.793  1.00  0.00              
ATOM     89  N   PHE    36      16.601  13.483  59.997  1.00  0.00              
ATOM     90  CA  PHE    36      17.530  12.449  60.423  1.00  0.00              
ATOM     91  C   PHE    36      18.261  12.833  61.700  1.00  0.00              
ATOM     92  O   PHE    36      18.706  13.970  61.858  1.00  0.00              
ATOM     93  N   PRO    37      18.383  11.872  62.609  1.00  0.00              
ATOM     94  CA  PRO    37      19.057  12.104  63.877  1.00  0.00              
ATOM     95  C   PRO    37      20.539  12.403  63.688  1.00  0.00              
ATOM     96  O   PRO    37      21.219  11.759  62.890  1.00  0.00              
ATOM     97  N   ILE    38      21.026  13.394  64.426  1.00  0.00              
ATOM     98  CA  ILE    38      22.428  13.785  64.378  1.00  0.00              
ATOM     99  C   ILE    38      23.007  13.634  65.780  1.00  0.00              
ATOM    100  O   ILE    38      22.323  13.888  66.772  1.00  0.00              
ATOM    101  N   LYS    39      24.266  13.218  65.857  1.00  0.00              
ATOM    102  CA  LYS    39      24.917  13.034  67.146  1.00  0.00              
ATOM    103  C   LYS    39      26.391  13.404  67.050  1.00  0.00              
ATOM    104  O   LYS    39      27.056  13.093  66.061  1.00  0.00              
ATOM    105  N   ASP    40      32.826  12.937  70.555  1.00  0.00              
ATOM    106  CA  ASP    40      34.242  13.279  70.596  1.00  0.00              
ATOM    107  C   ASP    40      34.640  14.257  69.493  1.00  0.00              
ATOM    108  O   ASP    40      35.686  14.106  68.861  1.00  0.00              
ATOM    109  N   GLY    41      33.796  15.258  69.270  1.00  0.00              
ATOM    110  CA  GLY    41      34.083  16.262  68.260  1.00  0.00              
ATOM    111  C   GLY    41      33.770  15.869  66.830  1.00  0.00              
ATOM    112  O   GLY    41      34.004  16.652  65.911  1.00  0.00              
ATOM    113  N   ILE    42      30.916  14.729  64.004  1.00  0.00              
ATOM    114  CA  ILE    42      29.488  14.758  63.711  1.00  0.00              
ATOM    115  C   ILE    42      29.059  13.533  62.907  1.00  0.00              
ATOM    116  O   ILE    42      29.635  13.233  61.861  1.00  0.00              
ATOM    117  N   PRO    43      28.050  12.828  63.406  1.00  0.00              
ATOM    118  CA  PRO    43      27.523  11.650  62.727  1.00  0.00              
ATOM    119  C   PRO    43      26.036  11.839  62.457  1.00  0.00              
ATOM    120  O   PRO    43      25.324  12.448  63.257  1.00  0.00              
ATOM    121  N   MET    44      25.567  11.314  61.330  1.00  0.00              
ATOM    122  CA  MET    44      24.159  11.419  60.973  1.00  0.00              
ATOM    123  C   MET    44      23.601  10.042  60.629  1.00  0.00              
ATOM    124  O   MET    44      24.270   9.235  59.985  1.00  0.00              
ATOM    125  N   MET    45      22.376   9.777  61.070  1.00  0.00              
ATOM    126  CA  MET    45      21.728   8.501  60.797  1.00  0.00              
ATOM    127  C   MET    45      21.387   8.408  59.316  1.00  0.00              
ATOM    128  O   MET    45      20.878   9.362  58.728  1.00  0.00              
ATOM    129  N   LEU    46      21.670   7.258  58.715  1.00  0.00              
ATOM    130  CA  LEU    46      21.384   7.075  57.306  1.00  0.00              
ATOM    131  C   LEU    46      19.916   6.804  57.043  1.00  0.00              
ATOM    132  O   LEU    46      19.460   6.883  55.902  1.00  0.00              
ATOM    133  N   GLU    47      19.172   6.489  58.099  1.00  0.00              
ATOM    134  CA  GLU    47      17.748   6.200  57.974  1.00  0.00              
ATOM    135  C   GLU    47      16.884   7.277  58.623  1.00  0.00              
ATOM    136  O   GLU    47      17.190   7.768  59.710  1.00  0.00              
ATOM    137  N   SER    48      15.800   7.632  57.941  1.00  0.00              
ATOM    138  CA  SER    48      14.867   8.648  58.415  1.00  0.00              
ATOM    139  C   SER    48      14.293   8.267  59.779  1.00  0.00              
ATOM    140  O   SER    48      14.362   7.109  60.188  1.00  0.00              
ATOM    141  N   GLU    49      13.733   9.247  60.480  1.00  0.00              
ATOM    142  CA  GLU    49      13.141   8.997  61.788  1.00  0.00              
ATOM    143  C   GLU    49      11.726   9.560  61.845  1.00  0.00              
ATOM    144  O   GLU    49      11.147   9.705  62.921  1.00  0.00              
END
