
#######################################################
#                                                     #
#                        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   47 (  188),  selected   47 , name T0323AL243_4-D1
# Molecule2: number of CA atoms  101 (  777),  selected  101 , name T0323_D1.pdb
# PARAMETERS: T0323AL243_4-D1.T0323_D1.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    -       -      Y       3           -
LGA    -       -      F       4           -
LGA    -       -      S       5           -
LGA    -       -      T       6           -
LGA    -       -      D       7           -
LGA    -       -      S       8           -
LGA    -       -      P       9           -
LGA    -       -      E      10           -
LGA    -       -      V      11           -
LGA    -       -      K      12           -
LGA    -       -      T      13           -
LGA    -       -      I      14           -
LGA    -       -      V      15           -
LGA    -       -      A      16           -
LGA    -       -      Q      17           -
LGA    -       -      D      18           -
LGA    S      19      S      19          3.052
LGA    R      20      R      20          3.364
LGA    L      21      L      21          1.788
LGA    F      22      F      22          0.753
LGA    Q      23      Q      23          2.451
LGA    F      24      F      24          2.357
LGA    I      25      I      25          0.945
LGA    E      26      E      26          1.030
LGA    I      27      I      27          1.844
LGA    A      28      A      28          3.377
LGA    -       -      G      29           -
LGA    G      29      E      30           #
LGA    E      30      V      31           #
LGA    V      31      Q      32          5.338
LGA    Q      32      -       -           -
LGA    L      33      L      33          1.852
LGA    -       -      L     150           -
LGA    L     150      D     151          2.452
LGA    V     152      V     152          2.605
LGA    L     153      L     153          2.302
LGA    S     154      S     154          2.947
LGA    V     155      V     155          4.174
LGA    -       -      G     156           -
LGA    D     157      D     157          1.514
LGA    V     158      V     158          1.014
LGA    G     159      G     159          1.796
LGA    L     160      L     160          2.250
LGA    Q     161      Q     161          1.751
LGA    R     162      R     162          2.069
LGA    G     163      G     163          2.707
LGA    A     164      A     164          3.089
LGA    K     165      K     165          3.056
LGA    W     166      W     166          4.037
LGA    -       -      L     167           -
LGA    -       -      Y     168           -
LGA    -       -      G     169           -
LGA    -       -      N     170           -
LGA    L     167      G     171          3.125
LGA    G     169      E     172          3.075
LGA    N     170      G     173          2.705
LGA    G     171      D     174          1.692
LGA    E     172      G     175          3.519
LGA    D     174      K     176          4.039
LGA    G     175      -       -           -
LGA    K     176      -       -           -
LGA    K     177      -       -           -
LGA    L     178      K     177          3.701
LGA    L     179      L     178          4.306
LGA    I     180      L     179          3.772
LGA    Y     181      I     180          2.084
LGA    H     182      Y     181          1.809
LGA    G     183      H     182          3.059
LGA    K     184      G     183          1.674
LGA    A     185      K     184          1.906
LGA    -       -      A     185           -
LGA    -       -      W     186           -
LGA    -       -      A     187           -
LGA    -       -      P     188           -
LGA    -       -      Y     189           -
LGA    -       -      E     190           -
LGA    -       -      T     191           -
LGA    -       -      V     192           -
LGA    -       -      A     193           -
LGA    -       -      C     194           -
LGA    -       -      L     195           -
LGA    -       -      Y     196           -
LGA    -       -      L     197           -
LGA    -       -      W     198           -
LGA    -       -      K     199           -
LGA    -       -      A     200           -
LGA    -       -      A     201           -
LGA    -       -      G     202           -
LGA    -       -      T     203           -
LGA    -       -      F     204           -
LGA    -       -      A     205           -
LGA    -       -      E     206           -
LGA    -       -      E     207           -
LGA    -       -      Y     208           -
LGA    -       -      R     209           -
LGA    -       -      S     210           -
LGA    -       -      L     211           -
LGA    -       -      E     212           -
LGA    -       -      E     213           -
LGA    -       -      L     214           -
LGA    -       -      L     215           -
LGA    -       -      H     216           -
LGA    -       -      H     217           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   47  101    5.0     41    2.79    63.41     25.129     1.421

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.410836 * X  +   0.911274 * Y  +  -0.028160 * Z  + -41.938366
  Y_new =  -0.909908 * X  +   0.411769 * Y  +   0.050137 * Z  + 133.249649
  Z_new =   0.057283 * X  +   0.005025 * Y  +   0.998345 * Z  + -45.055557 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.005033   -3.136559  [ DEG:     0.2884   -179.7116 ]
  Theta =  -0.057315   -3.084278  [ DEG:    -3.2839   -176.7161 ]
  Phi   =  -1.146684    1.994908  [ DEG:   -65.7002    114.2998 ]
 
# 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: T0323AL243_4-D1                               
REMARK     2: T0323_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0323AL243_4-D1.T0323_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   47  101   5.0   41   2.79   63.41  25.129
REMARK  ---------------------------------------------------------- 
MOLECULE T0323AL243_4-D1
REMARK Aligment from pdb entry: 1pu6A
ATOM      1  N   SER    19      27.815  36.537  25.342  1.00  0.00              
ATOM      2  CA  SER    19      27.277  35.477  26.236  1.00  0.00              
ATOM      3  C   SER    19      26.087  34.699  25.650  1.00  0.00              
ATOM      4  O   SER    19      26.034  33.445  25.777  1.00  0.00              
ATOM      5  N   ARG    20      25.190  35.425  24.974  1.00  0.00              
ATOM      6  CA  ARG    20      24.017  34.827  24.344  1.00  0.00              
ATOM      7  C   ARG    20      24.492  33.931  23.187  1.00  0.00              
ATOM      8  O   ARG    20      23.992  32.810  23.044  1.00  0.00              
ATOM      9  N   LEU    21      25.428  34.436  22.362  1.00  0.00              
ATOM     10  CA  LEU    21      25.974  33.641  21.251  1.00  0.00              
ATOM     11  C   LEU    21      26.555  32.312  21.766  1.00  0.00              
ATOM     12  O   LEU    21      26.229  31.223  21.228  1.00  0.00              
ATOM     13  N   PHE    22      27.394  32.370  22.806  1.00  0.00              
ATOM     14  CA  PHE    22      27.930  31.115  23.357  1.00  0.00              
ATOM     15  C   PHE    22      26.811  30.154  23.821  1.00  0.00              
ATOM     16  O   PHE    22      26.870  28.919  23.567  1.00  0.00              
ATOM     17  N   GLN    23      25.814  30.689  24.531  1.00  0.00              
ATOM     18  CA  GLN    23      24.712  29.847  25.033  1.00  0.00              
ATOM     19  C   GLN    23      23.931  29.184  23.907  1.00  0.00              
ATOM     20  O   GLN    23      23.639  27.959  23.953  1.00  0.00              
ATOM     21  N   PHE    24      23.628  29.945  22.873  1.00  0.00              
ATOM     22  CA  PHE    24      22.860  29.381  21.769  1.00  0.00              
ATOM     23  C   PHE    24      23.711  28.379  20.970  1.00  0.00              
ATOM     24  O   PHE    24      23.205  27.296  20.528  1.00  0.00              
ATOM     25  N   ILE    25      24.999  28.706  20.801  1.00  0.00              
ATOM     26  CA  ILE    25      25.912  27.820  20.106  1.00  0.00              
ATOM     27  C   ILE    25      25.933  26.424  20.781  1.00  0.00              
ATOM     28  O   ILE    25      25.992  25.366  20.100  1.00  0.00              
ATOM     29  N   GLU    26      25.882  26.429  22.100  1.00  0.00              
ATOM     30  CA  GLU    26      25.957  25.167  22.868  1.00  0.00              
ATOM     31  C   GLU    26      24.739  24.254  22.651  1.00  0.00              
ATOM     32  O   GLU    26      24.777  23.073  22.983  1.00  0.00              
ATOM     33  N   ILE    27      23.652  24.792  22.098  1.00  0.00              
ATOM     34  CA  ILE    27      22.444  23.968  21.863  1.00  0.00              
ATOM     35  C   ILE    27      22.400  23.227  20.515  1.00  0.00              
ATOM     36  O   ILE    27      21.501  22.386  20.292  1.00  0.00              
ATOM     37  N   ALA    28      23.341  23.528  19.607  1.00  0.00              
ATOM     38  CA  ALA    28      23.385  22.908  18.263  1.00  0.00              
ATOM     39  C   ALA    28      22.055  23.063  17.461  1.00  0.00              
ATOM     40  O   ALA    28      21.562  22.126  16.810  1.00  0.00              
ATOM     41  N   GLY    29      20.756  22.762   9.314  1.00  0.00              
ATOM     42  CA  GLY    29      20.635  23.963   8.488  1.00  0.00              
ATOM     43  C   GLY    29      21.812  24.131   7.525  1.00  0.00              
ATOM     44  O   GLY    29      22.912  23.625   7.792  1.00  0.00              
ATOM     45  N   GLU    30      21.604  24.847   6.417  1.00  0.00              
ATOM     46  CA  GLU    30      22.730  25.173   5.519  1.00  0.00              
ATOM     47  C   GLU    30      23.733  26.202   6.161  1.00  0.00              
ATOM     48  O   GLU    30      23.467  26.747   7.195  1.00  0.00              
ATOM     49  N   VAL    31      24.904  26.365   5.559  1.00  0.00              
ATOM     50  CA  VAL    31      26.054  27.066   6.155  1.00  0.00              
ATOM     51  C   VAL    31      25.757  28.520   6.591  1.00  0.00              
ATOM     52  O   VAL    31      26.328  29.001   7.563  1.00  0.00              
ATOM     53  N   GLN    32      24.930  29.205   5.815  1.00  0.00              
ATOM     54  CA  GLN    32      24.555  30.598   6.158  1.00  0.00              
ATOM     55  C   GLN    32      23.109  30.677   6.717  1.00  0.00              
ATOM     56  O   GLN    32      22.543  31.745   6.753  1.00  0.00              
ATOM     57  N   LEU    33      22.545  29.512   7.113  1.00  0.00              
ATOM     58  CA  LEU    33      21.197  29.321   7.683  1.00  0.00              
ATOM     59  C   LEU    33      20.072  29.535   6.664  1.00  0.00              
ATOM     60  O   LEU    33      19.208  28.650   6.473  1.00  0.00              
ATOM    513  N   LEU   150      28.661  42.662   6.845  1.00  0.00              
ATOM    514  CA  LEU   150      28.740  42.468   8.313  1.00  0.00              
ATOM    515  C   LEU   150      27.608  43.206   8.997  1.00  0.00              
ATOM    516  O   LEU   150      27.796  44.276   9.542  1.00  0.00              
ATOM    517  N   VAL   152      26.407  42.637   8.888  1.00  0.00              
ATOM    518  CA  VAL   152      25.169  43.201   9.452  1.00  0.00              
ATOM    519  C   VAL   152      24.430  42.074  10.156  1.00  0.00              
ATOM    520  O   VAL   152      24.252  40.967   9.573  1.00  0.00              
ATOM    521  N   LEU   153      23.961  42.305  11.390  1.00  0.00              
ATOM    522  CA  LEU   153      23.103  41.301  12.058  1.00  0.00              
ATOM    523  C   LEU   153      21.610  41.710  12.002  1.00  0.00              
ATOM    524  O   LEU   153      21.241  42.756  12.518  1.00  0.00              
ATOM    525  N   SER   154      20.761  40.873  11.418  1.00  0.00              
ATOM    526  CA  SER   154      19.323  41.131  11.330  1.00  0.00              
ATOM    527  C   SER   154      18.741  40.960  12.737  1.00  0.00              
ATOM    528  O   SER   154      19.164  40.043  13.469  1.00  0.00              
ATOM    529  N   VAL   155      17.804  41.847  13.105  1.00  0.00              
ATOM    530  CA  VAL   155      16.935  41.631  14.287  1.00  0.00              
ATOM    531  C   VAL   155      15.474  41.744  13.897  1.00  0.00              
ATOM    532  O   VAL   155      15.167  42.092  12.751  1.00  0.00              
ATOM    533  N   ASP   157      14.565  41.398  14.813  1.00  0.00              
ATOM    534  CA  ASP   157      13.134  41.168  14.441  1.00  0.00              
ATOM    535  C   ASP   157      12.333  40.992  15.749  1.00  0.00              
ATOM    536  O   ASP   157      12.907  41.065  16.836  1.00  0.00              
ATOM    537  N   VAL   158      11.019  40.765  15.632  1.00  0.00              
ATOM    538  CA  VAL   158      10.159  40.549  16.801  1.00  0.00              
ATOM    539  C   VAL   158      10.680  39.363  17.642  1.00  0.00              
ATOM    540  O   VAL   158      10.694  39.429  18.882  1.00  0.00              
ATOM    541  N   GLY   159      11.155  38.294  16.992  1.00  0.00              
ATOM    542  CA  GLY   159      11.678  37.169  17.775  1.00  0.00              
ATOM    543  C   GLY   159      12.826  37.615  18.675  1.00  0.00              
ATOM    544  O   GLY   159      12.897  37.216  19.825  1.00  0.00              
ATOM    545  N   LEU   160      13.754  38.428  18.136  1.00  0.00              
ATOM    546  CA  LEU   160      14.954  38.836  18.891  1.00  0.00              
ATOM    547  C   LEU   160      14.527  39.713  20.053  1.00  0.00              
ATOM    548  O   LEU   160      15.107  39.649  21.143  1.00  0.00              
ATOM    549  N   GLN   161      13.594  40.629  19.783  1.00  0.00              
ATOM    550  CA  GLN   161      13.052  41.480  20.832  1.00  0.00              
ATOM    551  C   GLN   161      12.484  40.663  21.989  1.00  0.00              
ATOM    552  O   GLN   161      12.792  40.950  23.141  1.00  0.00              
ATOM    553  N   ARG   162      11.620  39.700  21.680  1.00  0.00              
ATOM    554  CA  ARG   162      10.932  38.906  22.699  1.00  0.00              
ATOM    555  C   ARG   162      11.899  38.017  23.421  1.00  0.00              
ATOM    556  O   ARG   162      11.751  37.840  24.638  1.00  0.00              
ATOM    557  N   GLY   163      12.885  37.454  22.685  1.00  0.00              
ATOM    558  CA  GLY   163      13.960  36.628  23.260  1.00  0.00              
ATOM    559  C   GLY   163      14.765  37.433  24.302  1.00  0.00              
ATOM    560  O   GLY   163      14.998  36.964  25.428  1.00  0.00              
ATOM    561  N   ALA   164      15.174  38.651  23.960  1.00  0.00              
ATOM    562  CA  ALA   164      15.954  39.473  24.900  1.00  0.00              
ATOM    563  C   ALA   164      15.102  39.941  26.073  1.00  0.00              
ATOM    564  O   ALA   164      15.577  39.929  27.214  1.00  0.00              
ATOM    565  N   LYS   165      13.835  40.274  25.804  1.00  0.00              
ATOM    566  CA  LYS   165      12.878  40.692  26.846  1.00  0.00              
ATOM    567  C   LYS   165      12.723  39.597  27.892  1.00  0.00              
ATOM    568  O   LYS   165      12.650  39.897  29.100  1.00  0.00              
ATOM    569  N   TRP   166      12.688  38.331  27.467  1.00  0.00              
ATOM    570  CA  TRP   166      12.549  37.219  28.420  1.00  0.00              
ATOM    571  C   TRP   166      13.779  37.135  29.324  1.00  0.00              
ATOM    572  O   TRP   166      13.676  36.727  30.500  1.00  0.00              
ATOM    573  N   LEU   167      14.935  37.541  28.794  1.00  0.00              
ATOM    574  CA  LEU   167      16.178  37.589  29.583  1.00  0.00              
ATOM    575  C   LEU   167      16.326  38.871  30.420  1.00  0.00              
ATOM    576  O   LEU   167      17.317  39.021  31.138  1.00  0.00              
ATOM    577  N   GLY   169      15.367  39.797  30.312  1.00  0.00              
ATOM    578  CA  GLY   169      15.307  41.004  31.117  1.00  0.00              
ATOM    579  C   GLY   169      15.880  42.279  30.541  1.00  0.00              
ATOM    580  O   GLY   169      16.144  43.251  31.277  1.00  0.00              
ATOM    581  N   ASN   170      16.057  42.306  29.235  1.00  0.00              
ATOM    582  CA  ASN   170      16.512  43.515  28.553  1.00  0.00              
ATOM    583  C   ASN   170      15.465  43.851  27.492  1.00  0.00              
ATOM    584  O   ASN   170      15.201  43.029  26.625  1.00  0.00              
ATOM    585  N   GLY   171      14.858  45.033  27.575  1.00  0.00              
ATOM    586  CA  GLY   171      13.833  45.456  26.606  1.00  0.00              
ATOM    587  C   GLY   171      14.385  46.576  25.738  1.00  0.00              
ATOM    588  O   GLY   171      14.680  47.647  26.250  1.00  0.00              
ATOM    589  N   GLU   172      14.549  46.330  24.441  1.00  0.00              
ATOM    590  CA  GLU   172      15.027  47.355  23.530  1.00  0.00              
ATOM    591  C   GLU   172      14.066  47.374  22.369  1.00  0.00              
ATOM    592  O   GLU   172      14.151  46.537  21.469  1.00  0.00              
ATOM    593  N   ASP   174      13.156  48.338  22.383  1.00  0.00              
ATOM    594  CA  ASP   174      12.097  48.353  21.381  1.00  0.00              
ATOM    595  C   ASP   174      12.567  48.927  20.048  1.00  0.00              
ATOM    596  O   ASP   174      11.993  48.575  19.006  1.00  0.00              
ATOM    597  N   GLY   175      13.608  49.770  20.045  1.00  0.00              
ATOM    598  CA  GLY   175      14.030  50.410  18.812  1.00  0.00              
ATOM    599  C   GLY   175      14.894  49.476  17.976  1.00  0.00              
ATOM    600  O   GLY   175      15.868  48.907  18.510  1.00  0.00              
ATOM    601  N   LYS   176      14.564  49.336  16.685  1.00  0.00              
ATOM    602  CA  LYS   176      15.288  48.353  15.834  1.00  0.00              
ATOM    603  C   LYS   176      16.806  48.596  15.862  1.00  0.00              
ATOM    604  O   LYS   176      17.558  47.649  16.053  1.00  0.00              
ATOM    605  N   LYS   177      17.275  49.825  15.621  1.00  0.00              
ATOM    606  CA  LYS   177      18.728  50.037  15.454  1.00  0.00              
ATOM    607  C   LYS   177      19.531  49.832  16.751  1.00  0.00              
ATOM    608  O   LYS   177      20.704  49.412  16.748  1.00  0.00              
ATOM    609  N   LEU   178      18.893  50.140  17.870  1.00  0.00              
ATOM    610  CA  LEU   178      19.517  49.925  19.184  1.00  0.00              
ATOM    611  C   LEU   178      19.551  48.453  19.576  1.00  0.00              
ATOM    612  O   LEU   178      20.531  47.994  20.118  1.00  0.00              
ATOM    613  N   LEU   179      18.511  47.714  19.196  1.00  0.00              
ATOM    614  CA  LEU   179      18.466  46.270  19.396  1.00  0.00              
ATOM    615  C   LEU   179      19.570  45.592  18.545  1.00  0.00              
ATOM    616  O   LEU   179      20.336  44.737  18.998  1.00  0.00              
ATOM    617  N   ILE   180      19.653  46.010  17.282  1.00  0.00              
ATOM    618  CA  ILE   180      20.746  45.564  16.429  1.00  0.00              
ATOM    619  C   ILE   180      22.163  45.894  17.011  1.00  0.00              
ATOM    620  O   ILE   180      23.093  45.071  16.968  1.00  0.00              
ATOM    621  N   TYR   181      22.341  47.125  17.491  1.00  0.00              
ATOM    622  CA  TYR   181      23.643  47.500  17.997  1.00  0.00              
ATOM    623  C   TYR   181      24.005  46.698  19.233  1.00  0.00              
ATOM    624  O   TYR   181      25.163  46.296  19.391  1.00  0.00              
ATOM    625  N   HIS   182      23.016  46.419  20.099  1.00  0.00              
ATOM    626  CA  HIS   182      23.266  45.536  21.238  1.00  0.00              
ATOM    627  C   HIS   182      23.799  44.192  20.749  1.00  0.00              
ATOM    628  O   HIS   182      24.811  43.659  21.280  1.00  0.00              
ATOM    629  N   GLY   183      23.145  43.596  19.732  1.00  0.00              
ATOM    630  CA  GLY   183      23.600  42.263  19.247  1.00  0.00              
ATOM    631  C   GLY   183      24.983  42.323  18.561  1.00  0.00              
ATOM    632  O   GLY   183      25.865  41.488  18.837  1.00  0.00              
ATOM    633  N   LYS   184      25.221  43.365  17.766  1.00  0.00              
ATOM    634  CA  LYS   184      26.521  43.496  17.072  1.00  0.00              
ATOM    635  C   LYS   184      27.675  43.790  18.019  1.00  0.00              
ATOM    636  O   LYS   184      28.769  43.210  17.881  1.00  0.00              
ATOM    637  N   ALA   185      27.473  44.755  18.914  1.00  0.00              
ATOM    638  CA  ALA   185      28.614  45.238  19.695  1.00  0.00              
ATOM    639  C   ALA   185      29.244  44.179  20.629  1.00  0.00              
ATOM    640  O   ALA   185      30.463  44.189  20.842  1.00  0.00              
END
