
#######################################################
#                                                     #
#                        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   39 (  156),  selected   39 , name T0347TS383_4
# Molecule2: number of CA atoms  196 ( 1574),  selected  196 , name T0347.pdb
# PARAMETERS: T0347TS383_4.T0347.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

# WARNING! The change of the parameter DIST cutoff may give you better result.

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      I       4           -
LGA    -       -      Y       5           -
LGA    -       -      E       6           -
LGA    -       -      P       7           -
LGA    -       -      R       8           -
LGA    -       -      L       9           -
LGA    -       -      S      10           -
LGA    -       -      R      11           -
LGA    -       -      I      12           -
LGA    -       -      A      13           -
LGA    -       -      I      14           -
LGA    -       -      D      15           -
LGA    -       -      K      16           -
LGA    -       -      L      17           -
LGA    -       -      R      18           -
LGA    -       -      P      19           -
LGA    -       -      T      20           -
LGA    -       -      Q      21           -
LGA    -       -      I      22           -
LGA    -       -      A      23           -
LGA    -       -      V      24           -
LGA    -       -      G      25           -
LGA    -       -      F      26           -
LGA    -       -      R      27           -
LGA    -       -      E      28           -
LGA    -       -      V      29           -
LGA    -       -      E      30           -
LGA    -       -      L      31           -
LGA    -       -      K      32           -
LGA    -       -      R      33           -
LGA    -       -      K      34           -
LGA    -       -      E      35           -
LGA    -       -      W      36           -
LGA    -       -      R      37           -
LGA    -       -      E      38           -
LGA    -       -      T      39           -
LGA    -       -      R      40           -
LGA    -       -      D      46           -
LGA    -       -      F      47           -
LGA    -       -      L      48           -
LGA    -       -      G      49           -
LGA    -       -      N      50           -
LGA    -       -      H      51           -
LGA    -       -      I      52           -
LGA    -       -      V      53           -
LGA    -       -      P      54           -
LGA    -       -      V      55           -
LGA    -       -      V      56           -
LGA    -       -      A      57           -
LGA    -       -      G      58           -
LGA    -       -      P      59           -
LGA    -       -      K      60           -
LGA    -       -      D      61           -
LGA    -       -      R      62           -
LGA    -       -      A      63           -
LGA    -       -      Y      64           -
LGA    -       -      L      65           -
LGA    -       -      I      66           -
LGA    -       -      D      67           -
LGA    -       -      H      68           -
LGA    -       -      H      69           -
LGA    -       -      H      70           -
LGA    -       -      L      71           -
LGA    -       -      V      72           -
LGA    -       -      L      73           -
LGA    -       -      A      74           -
LGA    -       -      L      75           -
LGA    -       -      S      76           -
LGA    -       -      K      77           -
LGA    -       -      E      78           -
LGA    -       -      G      79           -
LGA    -       -      V      80           -
LGA    -       -      E      81           -
LGA    -       -      H      82           -
LGA    -       -      V      83           -
LGA    -       -      L      84           -
LGA    -       -      T      85           -
LGA    -       -      S      86           -
LGA    -       -      E      87           -
LGA    -       -      V      88           -
LGA    -       -      A      89           -
LGA    -       -      K      90           -
LGA    -       -      F      91           -
LGA    -       -      S      92           -
LGA    -       -      H      93           -
LGA    -       -      L      94           -
LGA    -       -      G      95           -
LGA    -       -      K      96           -
LGA    -       -      D      97           -
LGA    -       -      E      98           -
LGA    -       -      F      99           -
LGA    -       -      W     100           -
LGA    -       -      S     101           -
LGA    -       -      V     102           -
LGA    -       -      M     103           -
LGA    -       -      D     104           -
LGA    -       -      H     105           -
LGA    -       -      R     106           -
LGA    -       -      N     107           -
LGA    -       -      L     108           -
LGA    -       -      I     109           -
LGA    -       -      Y     110           -
LGA    -       -      P     111           -
LGA    -       -      F     112           -
LGA    -       -      D     113           -
LGA    -       -      A     114           -
LGA    -       -      Q     115           -
LGA    -       -      G     116           -
LGA    -       -      L     117           -
LGA    -       -      R     118           -
LGA    -       -      R     119           -
LGA    -       -      Q     120           -
LGA    -       -      S     121           -
LGA    -       -      G     122           -
LGA    -       -      D     123           -
LGA    -       -      I     124           -
LGA    -       -      P     125           -
LGA    -       -      K     126           -
LGA    -       -      N     127           -
LGA    -       -      I     128           -
LGA    -       -      H     129           -
LGA    -       -      D     130           -
LGA    -       -      L     131           -
LGA    -       -      E     132           -
LGA    -       -      D     133           -
LGA    -       -      D     134           -
LGA    -       -      P     135           -
LGA    -       -      F     136           -
LGA    -       -      R     137           -
LGA    G      44      S     138          1.697
LGA    D      45      L     139          3.621
LGA    D      46      A     140          3.763
LGA    -       -      G     141           -
LGA    F      47      A     142          2.220
LGA    -       -      L     143           -
LGA    -       -      R     144           -
LGA    -       -      M     145           -
LGA    L      48      A     146          1.207
LGA    G      49      G     147          1.638
LGA    N      50      G     148           #
LGA    -       -      Y     149           -
LGA    H      51      A     150          2.445
LGA    -       -      K     151           -
LGA    -       -      V     152           -
LGA    -       -      I     153           -
LGA    -       -      I     154           -
LGA    -       -      P     155           -
LGA    -       -      F     156           -
LGA    -       -      S     157           -
LGA    -       -      E     158           -
LGA    I      52      F     159          3.651
LGA    V      53      G     160          2.433
LGA    P      54      W     161          5.227
LGA    -       -      A     162           -
LGA    V      55      D     163          0.554
LGA    V      56      F     164          3.739
LGA    -       -      L     165           -
LGA    A      57      R     166          2.559
LGA    G      58      R     167          4.358
LGA    P      59      R     168           #
LGA    K      60      -       -           -
LGA    D      61      -       -           -
LGA    R      62      -       -           -
LGA    A      63      I     169          3.985
LGA    Y      64      D     170           -
LGA    L      65      R     171           -
LGA    I      66      D     172           -
LGA    D      67      L     173           -
LGA    G      79      L     174           -
LGA    V      80      S     175           -
LGA    E      81      D     176           -
LGA    H      82      S     177           -
LGA    V      83      F     178           -
LGA    L      84      D     179           -
LGA    T      85      D     180           -
LGA    S      86      -       -           -
LGA    E      87      -       -           -
LGA    V      88      A     181          4.351
LGA    A      89      L     182          4.312
LGA    G      95      A     183          4.169
LGA    -       -      E     184           -
LGA    -       -      A     185           -
LGA    K      96      M     186          0.675
LGA    -       -      K     187           -
LGA    -       -      L     188           -
LGA    D      97      A     189          2.215
LGA    E      98      K     190          2.612
LGA    -       -      S     191           -
LGA    -       -      R     192           -
LGA    -       -      E     193           -
LGA    -       -      A     194           -
LGA    -       -      R     195           -
LGA    -       -      H     196           -
LGA    -       -      L     197           -
LGA    -       -      P     198           -
LGA    -       -      G     199           -
LGA    -       -      W     200           -
LGA    -       -      C     201           -
LGA    -       -      G     202           -
LGA    -       -      V     203           -
LGA    -       -      E     204           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   39  196    5.0     21    3.20     4.76      6.039     0.637

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.169176 * X  +  -0.982440 * Y  +   0.078683 * Z  +  15.889130
  Y_new =   0.326449 * X  +  -0.131184 * Y  +  -0.936067 * Z  +  93.119995
  Z_new =   0.929952 * X  +  -0.132674 * Y  +   0.342909 * Z  + -17.839373 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.369169    2.772424  [ DEG:   -21.1518    158.8482 ]
  Theta =  -1.194282   -1.947310  [ DEG:   -68.4273   -111.5727 ]
  Phi   =   2.048923   -1.092670  [ DEG:   117.3946    -62.6054 ]
 
# 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: T0347TS383_4                                  
REMARK     2: T0347.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0347TS383_4.T0347.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   39  196   5.0   21   3.20    4.76   6.039
REMARK  ---------------------------------------------------------- 
MOLECULE T0347TS383_4
PFRMAT TS
TARGET T0347
MODEL 4
PARENT 1rwiB
ATOM      1  N   GLY    44      10.479  55.917  -4.270  1.00  0.00
ATOM      2  CA  GLY    44      11.436  57.001  -4.101  1.00  0.00
ATOM      3  C   GLY    44      12.762  56.677  -4.795  1.00  0.00
ATOM      4  O   GLY    44      13.234  55.540  -4.735  1.00  0.00
ATOM      5  N   ASP    45      13.356  57.670  -5.457  1.00  0.00
ATOM      6  CA  ASP    45      14.593  57.451  -6.211  1.00  0.00
ATOM      7  C   ASP    45      15.830  57.518  -5.317  1.00  0.00
ATOM      8  O   ASP    45      16.488  58.556  -5.243  1.00  0.00
ATOM      9  N   ASP    46      16.131  56.423  -4.629  1.00  0.00
ATOM     10  CA  ASP    46      17.351  56.334  -3.833  1.00  0.00
ATOM     11  C   ASP    46      18.408  55.783  -4.763  1.00  0.00
ATOM     12  O   ASP    46      18.732  54.592  -4.733  1.00  0.00
ATOM     13  N   PHE    47      18.925  56.686  -5.593  1.00  0.00
ATOM     14  CA  PHE    47      19.872  56.374  -6.659  1.00  0.00
ATOM     15  C   PHE    47      21.151  57.193  -6.439  1.00  0.00
ATOM     16  O   PHE    47      21.132  58.227  -5.751  1.00  0.00
ATOM     17  N   LEU    48      22.262  56.724  -7.003  1.00  0.00
ATOM     18  CA  LEU    48      23.534  57.413  -6.871  1.00  0.00
ATOM     19  C   LEU    48      24.271  56.978  -5.620  1.00  0.00
ATOM     20  O   LEU    48      24.857  57.816  -4.921  1.00  0.00
ATOM     21  N   GLY    49      24.217  55.673  -5.327  1.00  0.00
ATOM     22  CA  GLY    49      24.954  55.072  -4.205  1.00  0.00
ATOM     23  C   GLY    49      25.560  53.723  -4.607  1.00  0.00
ATOM     24  O   GLY    49      24.979  52.995  -5.414  1.00  0.00
ATOM     25  N   ASN    50      26.724  53.392  -4.034  1.00  0.00
ATOM     26  CA  ASN    50      27.430  52.139  -4.375  1.00  0.00
ATOM     27  C   ASN    50      26.733  50.902  -3.796  1.00  0.00
ATOM     28  O   ASN    50      26.712  49.827  -4.423  1.00  0.00
ATOM     29  N   HIS    51      26.139  51.090  -2.617  1.00  0.00
ATOM     30  CA  HIS    51      25.784  50.008  -1.703  1.00  0.00
ATOM     31  C   HIS    51      24.301  49.662  -1.784  1.00  0.00
ATOM     32  O   HIS    51      23.486  50.486  -2.197  1.00  0.00
ATOM     33  N   ILE    52      16.945  48.991   3.540  1.00  0.00
ATOM     34  CA  ILE    52      16.299  49.915   4.472  1.00  0.00
ATOM     35  C   ILE    52      15.786  49.196   5.723  1.00  0.00
ATOM     36  O   ILE    52      15.157  48.170   5.559  1.00  0.00
ATOM     37  N   VAL    53      16.018  49.744   6.908  1.00  0.00
ATOM     38  CA  VAL    53      15.475  49.194   8.156  1.00  0.00
ATOM     39  C   VAL    53      14.638  50.190   8.946  1.00  0.00
ATOM     40  O   VAL    53      14.041  49.829   9.942  1.00  0.00
ATOM     41  N   PRO    54      14.606  51.435   8.497  1.00  0.00
ATOM     42  CA  PRO    54      13.923  52.504   9.189  1.00  0.00
ATOM     43  C   PRO    54      13.708  53.633   8.189  1.00  0.00
ATOM     44  O   PRO    54      14.457  53.756   7.234  1.00  0.00
ATOM     45  N   VAL    55      12.646  54.411   8.398  1.00  0.00
ATOM     46  CA  VAL    55      12.306  55.547   7.531  1.00  0.00
ATOM     47  C   VAL    55      11.748  56.686   8.367  1.00  0.00
ATOM     48  O   VAL    55      10.997  56.472   9.315  1.00  0.00
ATOM     49  N   VAL    56      12.116  57.908   7.987  1.00  0.00
ATOM     50  CA  VAL    56      11.652  59.101   8.656  1.00  0.00
ATOM     51  C   VAL    56      11.594  60.258   7.655  1.00  0.00
ATOM     52  O   VAL    56      12.323  60.295   6.678  1.00  0.00
ATOM     53  N   ALA    57      10.695  61.180   7.922  1.00  0.00
ATOM     54  CA  ALA    57      10.467  62.350   7.090  1.00  0.00
ATOM     55  C   ALA    57      10.400  63.590   7.985  1.00  0.00
ATOM     56  O   ALA    57       9.698  63.597   8.981  1.00  0.00
ATOM     57  N   GLY    58      11.160  64.634   7.640  1.00  0.00
ATOM     58  CA  GLY    58      11.187  65.877   8.394  1.00  0.00
ATOM     59  C   GLY    58      10.202  66.894   7.818  1.00  0.00
ATOM     60  O   GLY    58       9.494  66.596   6.858  1.00  0.00
ATOM     61  N   PRO    59      10.176  68.068   8.459  1.00  0.00
ATOM     62  CA  PRO    59       9.394  69.258   8.066  1.00  0.00
ATOM     63  C   PRO    59       9.353  69.553   6.586  1.00  0.00
ATOM     64  O   PRO    59       8.285  69.893   6.059  1.00  0.00
ATOM     65  N   LYS    60      10.517  69.459   5.945  1.00  0.00
ATOM     66  CA  LYS    60      10.748  69.848   4.561  1.00  0.00
ATOM     67  C   LYS    60      10.572  68.747   3.537  1.00  0.00
ATOM     68  O   LYS    60      10.934  68.939   2.374  1.00  0.00
ATOM     69  N   ASP    61      10.054  67.586   3.948  1.00  0.00
ATOM     70  CA  ASP    61       9.937  66.447   3.056  1.00  0.00
ATOM     71  C   ASP    61      11.211  65.704   2.686  1.00  0.00
ATOM     72  O   ASP    61      11.186  64.908   1.753  1.00  0.00
ATOM     73  N   ARG    62      12.321  65.973   3.373  1.00  0.00
ATOM     74  CA  ARG    62      13.539  65.179   3.193  1.00  0.00
ATOM     75  C   ARG    62      13.249  63.762   3.728  1.00  0.00
ATOM     76  O   ARG    62      12.640  63.657   4.727  1.00  0.00
ATOM     77  N   ALA    63      13.681  62.700   3.079  1.00  0.00
ATOM     78  CA  ALA    63      13.396  61.340   3.577  1.00  0.00
ATOM     79  C   ALA    63      14.713  60.707   4.061  1.00  0.00
ATOM     80  O   ALA    63      15.705  60.761   3.364  1.00  0.00
ATOM     81  N   TYR    64      14.699  60.147   5.263  1.00  0.00
ATOM     82  CA  TYR    64      15.886  59.562   5.869  1.00  0.00
ATOM     83  C   TYR    64      15.620  58.062   6.037  1.00  0.00
ATOM     84  O   TYR    64      14.545  57.658   6.507  1.00  0.00
ATOM     85  N   LEU    65      16.610  57.256   5.667  1.00  0.00
ATOM     86  CA  LEU    65      16.518  55.808   5.742  1.00  0.00
ATOM     87  C   LEU    65      17.796  55.274   6.434  1.00  0.00
ATOM     88  O   LEU    65      18.899  55.714   6.121  1.00  0.00
ATOM     89  N   ILE    66      17.633  54.350   7.372  1.00  0.00
ATOM     90  CA  ILE    66      18.759  53.555   7.861  1.00  0.00
ATOM     91  C   ILE    66      19.027  52.434   6.876  1.00  0.00
ATOM     92  O   ILE    66      18.115  51.761   6.420  1.00  0.00
ATOM     93  N   ASP    67      20.295  52.244   6.553  1.00  0.00
ATOM     94  CA  ASP    67      20.747  51.254   5.608  1.00  0.00
ATOM     95  C   ASP    67      21.477  50.202   6.425  1.00  0.00
ATOM     96  O   ASP    67      22.545  50.463   6.974  1.00  0.00
ATOM     97  N   GLY    79      20.860  49.036   6.512  1.00  0.00
ATOM     98  CA  GLY    79      21.241  48.001   7.456  1.00  0.00
ATOM     99  C   GLY    79      22.276  47.074   6.849  1.00  0.00
ATOM    100  O   GLY    79      21.959  46.208   6.032  1.00  0.00
ATOM    101  N   VAL    80      23.527  47.301   7.216  1.00  0.00
ATOM    102  CA  VAL    80      24.612  46.382   6.932  1.00  0.00
ATOM    103  C   VAL    80      25.614  46.390   8.073  1.00  0.00
ATOM    104  O   VAL    80      25.510  47.190   9.021  1.00  0.00
ATOM    105  N   GLU    81      26.594  45.501   8.002  1.00  0.00
ATOM    106  CA  GLU    81      27.693  45.484   9.020  1.00  0.00
ATOM    107  C   GLU    81      28.295  46.910   9.061  1.00  0.00
ATOM    108  O   GLU    81      28.501  47.504  10.132  1.00  0.00
ATOM    109  N   HIS    82      28.550  47.420   7.845  1.00  0.00
ATOM    110  CA  HIS    82      28.715  48.870   7.666  1.00  0.00
ATOM    111  C   HIS    82      27.358  49.614   7.614  1.00  0.00
ATOM    112  O   HIS    82      26.676  49.615   6.607  1.00  0.00
ATOM    113  N   VAL    83      26.988  50.284   8.693  1.00  0.00
ATOM    114  CA  VAL    83      25.707  50.966   8.745  1.00  0.00
ATOM    115  C   VAL    83      25.754  52.372   8.173  1.00  0.00
ATOM    116  O   VAL    83      26.759  53.092   8.305  1.00  0.00
ATOM    117  N   LEU    84      24.651  52.789   7.563  1.00  0.00
ATOM    118  CA  LEU    84      24.519  54.166   7.093  1.00  0.00
ATOM    119  C   LEU    84      23.117  54.741   7.360  1.00  0.00
ATOM    120  O   LEU    84      22.140  54.001   7.526  1.00  0.00
ATOM    121  N   THR    85      23.045  56.067   7.426  1.00  0.00
ATOM    122  CA  THR    85      21.789  56.797   7.333  1.00  0.00
ATOM    123  C   THR    85      21.899  57.598   6.039  1.00  0.00
ATOM    124  O   THR    85      22.811  58.429   5.884  1.00  0.00
ATOM    125  N   SER    86      20.992  57.305   5.105  1.00  0.00
ATOM    126  CA  SER    86      20.915  57.954   3.802  1.00  0.00
ATOM    127  C   SER    86      19.780  58.985   3.799  1.00  0.00
ATOM    128  O   SER    86      18.706  58.755   4.369  1.00  0.00
ATOM    129  N   GLU    87      20.011  60.120   3.152  1.00  0.00
ATOM    130  CA  GLU    87      19.010  61.175   3.050  1.00  0.00
ATOM    131  C   GLU    87      18.700  61.468   1.576  1.00  0.00
ATOM    132  O   GLU    87      19.603  61.658   0.773  1.00  0.00
ATOM    133  N   VAL    88      17.412  61.498   1.234  1.00  0.00
ATOM    134  CA  VAL    88      16.938  61.926  -0.085  1.00  0.00
ATOM    135  C   VAL    88      16.326  63.320   0.065  1.00  0.00
ATOM    136  O   VAL    88      15.265  63.470   0.660  1.00  0.00
ATOM    137  N   ALA    89      17.020  64.347  -0.433  1.00  0.00
ATOM    138  CA  ALA    89      16.541  65.735  -0.323  1.00  0.00
ATOM    139  C   ALA    89      15.576  66.064  -1.452  1.00  0.00
ATOM    140  O   ALA    89      15.297  65.213  -2.299  1.00  0.00
ATOM    141  N   GLY    95      20.459  62.534  -3.056  1.00  0.00
ATOM    142  CA  GLY    95      21.020  61.469  -2.207  1.00  0.00
ATOM    143  C   GLY    95      22.362  61.829  -1.530  1.00  0.00
ATOM    144  O   GLY    95      23.360  62.038  -2.217  1.00  0.00
ATOM    145  N   LYS    96      22.379  61.908  -0.196  1.00  0.00
ATOM    146  CA  LYS    96      23.629  61.970   0.563  1.00  0.00
ATOM    147  C   LYS    96      23.670  60.897   1.664  1.00  0.00
ATOM    148  O   LYS    96      22.640  60.503   2.202  1.00  0.00
ATOM    149  N   ASP    97      24.872  60.436   1.990  1.00  0.00
ATOM    150  CA  ASP    97      25.084  59.626   3.177  1.00  0.00
ATOM    151  C   ASP    97      25.477  60.574   4.308  1.00  0.00
ATOM    152  O   ASP    97      26.445  61.325   4.194  1.00  0.00
ATOM    153  N   GLU    98      24.700  60.573   5.386  1.00  0.00
ATOM    154  CA  GLU    98      24.937  61.430   6.540  1.00  0.00
ATOM    155  C   GLU    98      26.254  61.029   7.265  1.00  0.00
ATOM    156  O   GLU    98      26.601  59.846   7.268  1.00  0.00
TER
END
