
#######################################################
#                                                     #
#                        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   41 (  164),  selected   41 , name T0385AL586_1-D1
# Molecule2: number of CA atoms  135 ( 1000),  selected  135 , name T0385_D1.pdb
# PARAMETERS: T0385AL586_1-D1.T0385_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      S      17           -
LGA    -       -      E      18           -
LGA    -       -      G      19           -
LGA    -       -      S      20           -
LGA    -       -      A      21           -
LGA    -       -      D      22           -
LGA    -       -      N      23           -
LGA    -       -      A      24           -
LGA    -       -      A      25           -
LGA    -       -      L      26           -
LGA    -       -      C      27           -
LGA    -       -      D      28           -
LGA    -       -      A      29           -
LGA    -       -      L      30           -
LGA    -       -      A      31           -
LGA    -       -      V      32           -
LGA    R      65      E      33          4.195
LGA    R      66      H      34          2.345
LGA    D      67      A      35          0.861
LGA    -       -      T      36           -
LGA    -       -      I      37           -
LGA    D      68      Y      38          2.823
LGA    -       -      G      39           -
LGA    -       -      Y      40           -
LGA    -       -      G      41           -
LGA    -       -      I      42           -
LGA    -       -      V      43           -
LGA    -       -      S      44           -
LGA    -       -      A      45           -
LGA    -       -      L      46           -
LGA    -       -      S      47           -
LGA    -       -      P      48           -
LGA    -       -      P      49           -
LGA    -       -      G      50           -
LGA    -       -      V      51           -
LGA    -       -      N      52           -
LGA    -       -      F      53           -
LGA    -       -      L      54           -
LGA    -       -      V      55           -
LGA    -       -      A      56           -
LGA    -       -      D      57           -
LGA    -       -      A      58           -
LGA    -       -      L      59           -
LGA    -       -      K      60           -
LGA    -       -      Q      61           -
LGA    -       -      H      62           -
LGA    -       -      R      63           -
LGA    -       -      H      64           -
LGA    -       -      R      65           -
LGA    -       -      R      66           -
LGA    -       -      D      67           -
LGA    -       -      D      68           -
LGA    -       -      V      69           -
LGA    -       -      I      70           -
LGA    -       -      V      71           -
LGA    -       -      M      72           -
LGA    -       -      L      73           -
LGA    -       -      S      74           -
LGA    -       -      A      75           -
LGA    -       -      R      76           -
LGA    -       -      G      77           -
LGA    -       -      V      78           -
LGA    -       -      T      79           -
LGA    -       -      A      80           -
LGA    -       -      P      81           -
LGA    V      69      I      82           #
LGA    I      70      A      83          2.671
LGA    V      71      A      84          2.877
LGA    M      72      A      85          2.625
LGA    L      73      -       -           -
LGA    S      74      -       -           -
LGA    A      75      G      86          5.360
LGA    R      76      Y      87           -
LGA    G      77      Q      88           -
LGA    V      78      L      89           -
LGA    -       -      P      90           -
LGA    -       -      M      91           -
LGA    -       -      Q      92           -
LGA    -       -      V      93           -
LGA    T      79      S      94          3.906
LGA    A      80      S      95          2.505
LGA    P      81      A      96          2.775
LGA    I      82      A      97          2.759
LGA    -       -      D      98           -
LGA    -       -      A      99           -
LGA    A      83      A     100          1.123
LGA    A      84      R     101          1.062
LGA    A      85      L     102          0.716
LGA    G      86      A     103           #
LGA    Y      87      V     104           -
LGA    -       -      R     105           -
LGA    Q      88      M     106          4.099
LGA    L      89      E     107          1.794
LGA    P      90      N     108           #
LGA    M      91      D     109          5.086
LGA    Q      92      G     110          3.941
LGA    V      93      A     111          1.246
LGA    S      94      T     112          2.402
LGA    -       -      A     113           -
LGA    S      95      W     114           #
LGA    A      96      R     115          4.313
LGA    A      97      A     116          3.694
LGA    D      98      V     117          3.232
LGA    A      99      V     118          4.047
LGA    A     100      E     119          3.593
LGA    -       -      H     120           -
LGA    R     101      A     121          2.407
LGA    -       -      E     122           -
LGA    -       -      T     123           -
LGA    -       -      A     124           -
LGA    L     102      D     125           #
LGA    A     103      D     126          4.795
LGA    V     104      R     127          1.502
LGA    R     105      V     128          4.622
LGA    -       -      F     129           -
LGA    -       -      A     130           -
LGA    -       -      S     131           -
LGA    -       -      T     132           -
LGA    -       -      A     133           -
LGA    -       -      L     134           -
LGA    -       -      T     135           -
LGA    -       -      E     136           -
LGA    -       -      S     137           -
LGA    -       -      A     138           -
LGA    -       -      V     139           -
LGA    -       -      M     140           -
LGA    -       -      A     141           -
LGA    -       -      T     142           -
LGA    -       -      R     143           -
LGA    -       -      W     144           -
LGA    -       -      N     145           -
LGA    -       -      R     146           -
LGA    -       -      V     147           -
LGA    -       -      L     148           -
LGA    -       -      G     149           -
LGA    -       -      A     150           -
LGA    -       -      W     151           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   41  135    5.0     30    3.24     6.67     12.582     0.897

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.481981 * X  +  -0.210629 * Y  +   0.850488 * Z  + -82.324348
  Y_new =  -0.872152 * X  +   0.022348 * Y  +  -0.488724 * Z  +  -8.564878
  Z_new =   0.083933 * X  +  -0.977311 * Y  +  -0.194471 * Z  +  59.609776 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.767217    1.374376  [ DEG:  -101.2541     78.7459 ]
  Theta =  -0.084032   -3.057561  [ DEG:    -4.8147   -175.1853 ]
  Phi   =  -2.075660    1.065933  [ DEG:  -118.9266     61.0734 ]
 
# 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: T0385AL586_1-D1                               
REMARK     2: T0385_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0385AL586_1-D1.T0385_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   41  135   5.0   30   3.24    6.67  12.582
REMARK  ---------------------------------------------------------- 
MOLECULE T0385AL586_1-D1
REMARK Aligment from pdb entry: 1b35_D
ATOM      1  N   ARG    65      26.682  11.191  20.937  1.00  0.00              
ATOM      2  CA  ARG    65      27.982  10.590  21.374  1.00  0.00              
ATOM      3  C   ARG    65      27.815   9.865  22.706  1.00  0.00              
ATOM      4  O   ARG    65      28.067   8.658  22.800  1.00  0.00              
ATOM      5  N   ARG    66      27.396  10.596  23.736  1.00  0.00              
ATOM      6  CA  ARG    66      27.183   9.995  25.050  1.00  0.00              
ATOM      7  C   ARG    66      26.250   8.789  24.905  1.00  0.00              
ATOM      8  O   ARG    66      26.493   7.726  25.476  1.00  0.00              
ATOM      9  N   ASP    67      25.187   8.983  24.127  1.00  0.00              
ATOM     10  CA  ASP    67      24.172   7.969  23.868  1.00  0.00              
ATOM     11  C   ASP    67      24.792   6.723  23.242  1.00  0.00              
ATOM     12  O   ASP    67      24.508   5.594  23.659  1.00  0.00              
ATOM     13  N   ASP    68      25.646   6.935  22.244  1.00  0.00              
ATOM     14  CA  ASP    68      26.320   5.836  21.562  1.00  0.00              
ATOM     15  C   ASP    68      27.307   5.108  22.473  1.00  0.00              
ATOM     16  O   ASP    68      27.397   3.882  22.444  1.00  0.00              
ATOM     17  N   VAL    69      28.058   5.860  23.273  1.00  0.00              
ATOM     18  CA  VAL    69      29.011   5.251  24.193  1.00  0.00              
ATOM     19  C   VAL    69      28.260   4.344  25.168  1.00  0.00              
ATOM     20  O   VAL    69      28.723   3.250  25.499  1.00  0.00              
ATOM     21  N   ILE    70      27.097   4.805  25.624  1.00  0.00              
ATOM     22  CA  ILE    70      26.279   4.043  26.569  1.00  0.00              
ATOM     23  C   ILE    70      25.784   2.723  25.972  1.00  0.00              
ATOM     24  O   ILE    70      25.930   1.663  26.585  1.00  0.00              
ATOM     25  N   VAL    71      25.206   2.789  24.774  1.00  0.00              
ATOM     26  CA  VAL    71      24.691   1.599  24.100  1.00  0.00              
ATOM     27  C   VAL    71      25.817   0.607  23.811  1.00  0.00              
ATOM     28  O   VAL    71      25.619  -0.609  23.872  1.00  0.00              
ATOM     29  N   MET    72      26.996   1.131  23.494  1.00  0.00              
ATOM     30  CA  MET    72      28.142   0.281  23.196  1.00  0.00              
ATOM     31  C   MET    72      28.537  -0.563  24.408  1.00  0.00              
ATOM     32  O   MET    72      29.037  -1.681  24.258  1.00  0.00              
ATOM     33  N   LEU    73      28.303  -0.039  25.608  1.00  0.00              
ATOM     34  CA  LEU    73      28.639  -0.771  26.828  1.00  0.00              
ATOM     35  C   LEU    73      27.604  -1.846  27.170  1.00  0.00              
ATOM     36  O   LEU    73      27.961  -2.972  27.487  1.00  0.00              
ATOM     37  N   SER    74      26.326  -1.485  27.097  1.00  0.00              
ATOM     38  CA  SER    74      25.222  -2.395  27.414  1.00  0.00              
ATOM     39  C   SER    74      25.161  -3.630  26.513  1.00  0.00              
ATOM     40  O   SER    74      24.915  -4.741  26.976  1.00  0.00              
ATOM     41  N   ALA    75      25.373  -3.427  25.220  1.00  0.00              
ATOM     42  CA  ALA    75      25.330  -4.522  24.262  1.00  0.00              
ATOM     43  C   ALA    75      26.729  -5.011  23.908  1.00  0.00              
ATOM     44  O   ALA    75      26.876  -6.006  23.206  1.00  0.00              
ATOM     45  N   ARG    76      27.749  -4.327  24.431  1.00  0.00              
ATOM     46  CA  ARG    76      29.143  -4.622  24.104  1.00  0.00              
ATOM     47  C   ARG    76      29.238  -4.939  22.619  1.00  0.00              
ATOM     48  O   ARG    76      29.726  -5.992  22.202  1.00  0.00              
ATOM     49  N   GLY    77      15.678   0.510   0.320  1.00  0.00              
ATOM     50  CA  GLY    77      15.824   1.176  -0.972  1.00  0.00              
ATOM     51  C   GLY    77      15.217   2.580  -1.057  1.00  0.00              
ATOM     52  O   GLY    77      15.775   3.461  -1.722  1.00  0.00              
ATOM     53  N   VAL    78      14.081   2.788  -0.397  1.00  0.00              
ATOM     54  CA  VAL    78      13.414   4.091  -0.429  1.00  0.00              
ATOM     55  C   VAL    78      13.824   5.014   0.714  1.00  0.00              
ATOM     56  O   VAL    78      13.490   6.198   0.708  1.00  0.00              
ATOM     57  N   THR    79      14.549   4.474   1.690  1.00  0.00              
ATOM     58  CA  THR    79      14.993   5.251   2.844  1.00  0.00              
ATOM     59  C   THR    79      15.887   6.435   2.479  1.00  0.00              
ATOM     60  O   THR    79      16.908   6.273   1.819  1.00  0.00              
ATOM     61  N   ALA    80      15.498   7.626   2.921  1.00  0.00              
ATOM     62  CA  ALA    80      16.282   8.830   2.663  1.00  0.00              
ATOM     63  C   ALA    80      16.652   9.484   3.995  1.00  0.00              
ATOM     64  O   ALA    80      15.794  10.021   4.697  1.00  0.00              
ATOM     65  N   PRO    81      17.943   9.437   4.364  1.00  0.00              
ATOM     66  CA  PRO    81      18.416  10.027   5.619  1.00  0.00              
ATOM     67  C   PRO    81      18.422  11.558   5.618  1.00  0.00              
ATOM     68  O   PRO    81      18.723  12.193   4.602  1.00  0.00              
ATOM     69  N   ILE    82      18.081  12.142   6.763  1.00  0.00              
ATOM     70  CA  ILE    82      18.065  13.595   6.906  1.00  0.00              
ATOM     71  C   ILE    82      19.034  14.002   8.020  1.00  0.00              
ATOM     72  O   ILE    82      19.270  13.242   8.958  1.00  0.00              
ATOM     73  N   ALA    83      19.599  15.200   7.910  1.00  0.00              
ATOM     74  CA  ALA    83      20.562  15.690   8.893  1.00  0.00              
ATOM     75  C   ALA    83      20.120  15.639  10.364  1.00  0.00              
ATOM     76  O   ALA    83      20.943  15.400  11.246  1.00  0.00              
ATOM     77  N   ALA    84      18.836  15.860  10.635  1.00  0.00              
ATOM     78  CA  ALA    84      18.363  15.824  12.012  1.00  0.00              
ATOM     79  C   ALA    84      17.908  14.436  12.425  1.00  0.00              
ATOM     80  O   ALA    84      16.935  13.921  11.875  1.00  0.00              
ATOM     81  N   ALA    85      18.594  13.829  13.392  1.00  0.00              
ATOM     82  CA  ALA    85      18.240  12.479  13.836  1.00  0.00              
ATOM     83  C   ALA    85      18.326  12.269  15.344  1.00  0.00              
ATOM     84  O   ALA    85      18.343  13.217  16.132  1.00  0.00              
ATOM     85  N   GLY    86      18.397  10.995  15.721  1.00  0.00              
ATOM     86  CA  GLY    86      18.489  10.571  17.112  1.00  0.00              
ATOM     87  C   GLY    86      19.868  10.856  17.716  1.00  0.00              
ATOM     88  O   GLY    86      19.997  11.010  18.927  1.00  0.00              
ATOM     89  N   TYR    87      20.896  10.924  16.873  1.00  0.00              
ATOM     90  CA  TYR    87      22.250  11.187  17.360  1.00  0.00              
ATOM     91  C   TYR    87      22.773  12.569  16.970  1.00  0.00              
ATOM     92  O   TYR    87      23.944  12.878  17.183  1.00  0.00              
ATOM     93  N   GLN    88      21.905  13.404  16.411  1.00  0.00              
ATOM     94  CA  GLN    88      22.310  14.742  15.991  1.00  0.00              
ATOM     95  C   GLN    88      22.425  15.783  17.114  1.00  0.00              
ATOM     96  O   GLN    88      23.057  16.828  16.928  1.00  0.00              
ATOM     97  N   LEU    89      21.831  15.499  18.273  1.00  0.00              
ATOM     98  CA  LEU    89      21.862  16.436  19.401  1.00  0.00              
ATOM     99  C   LEU    89      22.743  15.983  20.569  1.00  0.00              
ATOM    100  O   LEU    89      22.376  15.081  21.324  1.00  0.00              
ATOM    101  N   PRO    90      23.918  16.611  20.736  1.00  0.00              
ATOM    102  CA  PRO    90      24.824  16.245  21.832  1.00  0.00              
ATOM    103  C   PRO    90      24.245  16.491  23.232  1.00  0.00              
ATOM    104  O   PRO    90      23.626  17.521  23.495  1.00  0.00              
ATOM    105  N   MET    91      24.458  15.526  24.121  1.00  0.00              
ATOM    106  CA  MET    91      23.950  15.573  25.490  1.00  0.00              
ATOM    107  C   MET    91      24.357  16.751  26.387  1.00  0.00              
ATOM    108  O   MET    91      23.685  17.010  27.382  1.00  0.00              
ATOM    109  N   GLN    92      25.436  17.461  26.064  1.00  0.00              
ATOM    110  CA  GLN    92      25.852  18.581  26.911  1.00  0.00              
ATOM    111  C   GLN    92      24.966  19.818  26.773  1.00  0.00              
ATOM    112  O   GLN    92      25.084  20.764  27.559  1.00  0.00              
ATOM    113  N   VAL    93      24.080  19.813  25.781  1.00  0.00              
ATOM    114  CA  VAL    93      23.189  20.948  25.565  1.00  0.00              
ATOM    115  C   VAL    93      21.917  20.818  26.397  1.00  0.00              
ATOM    116  O   VAL    93      20.857  20.452  25.874  1.00  0.00              
ATOM    117  N   SER    94      22.020  21.105  27.693  1.00  0.00              
ATOM    118  CA  SER    94      20.855  21.025  28.569  1.00  0.00              
ATOM    119  C   SER    94      20.997  21.951  29.767  1.00  0.00              
ATOM    120  O   SER    94      22.101  22.362  30.119  1.00  0.00              
ATOM    121  N   SER    95      19.868  22.263  30.400  1.00  0.00              
ATOM    122  CA  SER    95      19.853  23.152  31.555  1.00  0.00              
ATOM    123  C   SER    95      19.340  22.487  32.829  1.00  0.00              
ATOM    124  O   SER    95      18.961  23.171  33.781  1.00  0.00              
ATOM    125  N   ALA    96      19.315  21.160  32.855  1.00  0.00              
ATOM    126  CA  ALA    96      18.862  20.467  34.054  1.00  0.00              
ATOM    127  C   ALA    96      19.809  20.841  35.197  1.00  0.00              
ATOM    128  O   ALA    96      21.017  20.965  34.994  1.00  0.00              
ATOM    129  N   ALA    97      19.253  21.041  36.389  1.00  0.00              
ATOM    130  CA  ALA    97      20.040  21.432  37.560  1.00  0.00              
ATOM    131  C   ALA    97      21.422  20.779  37.644  1.00  0.00              
ATOM    132  O   ALA    97      22.435  21.472  37.717  1.00  0.00              
ATOM    133  N   ASP    98      21.461  19.451  37.628  1.00  0.00              
ATOM    134  CA  ASP    98      22.722  18.714  37.714  1.00  0.00              
ATOM    135  C   ASP    98      23.748  19.122  36.653  1.00  0.00              
ATOM    136  O   ASP    98      24.931  19.270  36.958  1.00  0.00              
ATOM    137  N   ALA    99      23.294  19.299  35.413  1.00  0.00              
ATOM    138  CA  ALA    99      24.182  19.685  34.318  1.00  0.00              
ATOM    139  C   ALA    99      24.759  21.091  34.441  1.00  0.00              
ATOM    140  O   ALA    99      25.942  21.297  34.162  1.00  0.00              
ATOM    141  N   ALA   100      23.932  22.052  34.847  1.00  0.00              
ATOM    142  CA  ALA   100      24.386  23.433  34.991  1.00  0.00              
ATOM    143  C   ALA   100      25.421  23.594  36.099  1.00  0.00              
ATOM    144  O   ALA   100      26.347  24.400  35.973  1.00  0.00              
ATOM    145  N   ARG   101      25.261  22.845  37.186  1.00  0.00              
ATOM    146  CA  ARG   101      26.222  22.926  38.276  1.00  0.00              
ATOM    147  C   ARG   101      27.580  22.460  37.739  1.00  0.00              
ATOM    148  O   ARG   101      28.582  23.148  37.898  1.00  0.00              
ATOM    149  N   LEU   102      27.611  21.305  37.079  1.00  0.00              
ATOM    150  CA  LEU   102      28.869  20.803  36.526  1.00  0.00              
ATOM    151  C   LEU   102      29.452  21.775  35.513  1.00  0.00              
ATOM    152  O   LEU   102      30.666  21.975  35.464  1.00  0.00              
ATOM    153  N   ALA   103      28.581  22.369  34.703  1.00  0.00              
ATOM    154  CA  ALA   103      29.004  23.316  33.681  1.00  0.00              
ATOM    155  C   ALA   103      29.813  24.456  34.296  1.00  0.00              
ATOM    156  O   ALA   103      30.835  24.862  33.741  1.00  0.00              
ATOM    157  N   VAL   104      29.361  24.971  35.437  1.00  0.00              
ATOM    158  CA  VAL   104      30.075  26.064  36.091  1.00  0.00              
ATOM    159  C   VAL   104      31.282  25.615  36.923  1.00  0.00              
ATOM    160  O   VAL   104      31.848  26.407  37.678  1.00  0.00              
ATOM    161  N   ARG   105      31.666  24.346  36.777  1.00  0.00              
ATOM    162  CA  ARG   105      32.827  23.828  37.480  1.00  0.00              
ATOM    163  C   ARG   105      32.653  23.198  38.852  1.00  0.00              
ATOM    164  O   ARG   105      33.645  22.826  39.486  1.00  0.00              
END
