
#######################################################
#                                                     #
#                        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   27 (  108),  selected   27 , name T0330AL242_4-D2
# Molecule2: number of CA atoms   72 (  556),  selected   72 , name T0330_D2.pdb
# PARAMETERS: T0330AL242_4-D2.T0330_D2.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    V      17      V      17           -
LGA    -       -      E      18           -
LGA    -       -      S      19           -
LGA    -       -      M      20           -
LGA    -       -      N      21           -
LGA    -       -      R      22           -
LGA    -       -      R      23           -
LGA    -       -      V      24           -
LGA    -       -      L      25           -
LGA    -       -      A      26           -
LGA    E      18      D      27          5.410
LGA    S      19      A      28          1.709
LGA    -       -      L      29           -
LGA    M      20      I      30          2.741
LGA    D      69      E      31          2.749
LGA    K      70      V      32          1.975
LGA    F      71      Y      33          4.290
LGA    -       -      G      34           -
LGA    -       -      T      35           -
LGA    D      72      E      36          2.598
LGA    K      73      G      37          3.608
LGA    -       -      S      38           -
LGA    A      74      T      39          2.226
LGA    K      75      D      43           -
LGA    -       -      F      44           -
LGA    -       -      S      45           -
LGA    -       -      G      46           -
LGA    E      76      K      47           #
LGA    T      77      M      48          3.129
LGA    Y      78      -       -           -
LGA    I      79      -       -           -
LGA    A      80      -       -           -
LGA    L      81      -       -           -
LGA    F      82      D      49          4.516
LGA    R      83      G      50          2.166
LGA    E      84      A      51          3.724
LGA    -       -      I      52           -
LGA    R      85      I      53          2.680
LGA    -       -      Y      54           -
LGA    -       -      E      55           -
LGA    A      86      V      56          2.170
LGA    R      87      L      57          2.311
LGA    R      88      S      58          4.409
LGA    -       -      N      59           -
LGA    -       -      V      60           -
LGA    -       -      G      61           -
LGA    -       -      L      62           -
LGA    -       -      E      63           -
LGA    -       -      R      64           -
LGA    -       -      A      65           -
LGA    -       -      E      66           -
LGA    E      89      I      67          3.318
LGA    D      90      A      68           #
LGA    I      91      D      69           -
LGA    -       -      K      70           -
LGA    -       -      F      71           -
LGA    -       -      D      72           -
LGA    -       -      K      73           -
LGA    -       -      A      74           -
LGA    -       -      K      75           -
LGA    -       -      E      76           -
LGA    -       -      T      77           -
LGA    -       -      Y      78           -
LGA    -       -      I      79           -
LGA    -       -      A      80           -
LGA    -       -      L      81           -
LGA    -       -      F      82           -
LGA    -       -      R      83           -
LGA    -       -      E      84           -
LGA    -       -      R      85           -
LGA    -       -      A      86           -
LGA    -       -      R      87           -
LGA    -       -      R      88           -
LGA    -       -      E      89           -
LGA    -       -      D      90           -
LGA    -       -      I      91           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   27   72    5.0     18    3.26     0.00     15.734     0.537

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.919971 * X  +  -0.036347 * Y  +  -0.390297 * Z  +  14.197649
  Y_new =   0.333095 * X  +   0.452405 * Y  +  -0.827271 * Z  +  50.289371
  Z_new =   0.206642 * X  +  -0.891071 * Y  +  -0.404093 * Z  +   6.548537 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.996549    1.145043  [ DEG:  -114.3939     65.6061 ]
  Theta =  -0.208141   -2.933451  [ DEG:   -11.9256   -168.0744 ]
  Phi   =   2.794205   -0.347388  [ DEG:   160.0962    -19.9038 ]
 
# 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: T0330AL242_4-D2                               
REMARK     2: T0330_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0330AL242_4-D2.T0330_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   27   72   5.0   18   3.26    0.00  15.734
REMARK  ---------------------------------------------------------- 
MOLECULE T0330AL242_4-D2
REMARK Aligment from pdb entry: 1u7p_A
ATOM     65  N   VAL    17      15.640  47.118  -5.060  1.00  0.00              
ATOM     66  CA  VAL    17      16.264  46.309  -6.101  1.00  0.00              
ATOM     67  C   VAL    17      15.705  44.901  -6.071  1.00  0.00              
ATOM     68  O   VAL    17      14.982  44.540  -5.140  1.00  0.00              
ATOM     69  N   GLU    18      16.031  44.117  -7.098  1.00  0.00              
ATOM     70  CA  GLU    18      15.624  42.715  -7.158  1.00  0.00              
ATOM     71  C   GLU    18      16.818  41.935  -6.617  1.00  0.00              
ATOM     72  O   GLU    18      17.932  42.074  -7.127  1.00  0.00              
ATOM     73  N   SER    19      16.592  41.124  -5.591  1.00  0.00              
ATOM     74  CA  SER    19      17.676  40.353  -4.999  1.00  0.00              
ATOM     75  C   SER    19      18.258  39.298  -5.951  1.00  0.00              
ATOM     76  O   SER    19      19.392  38.857  -5.769  1.00  0.00              
ATOM     77  N   MET    20      17.499  38.909  -6.975  1.00  0.00              
ATOM     78  CA  MET    20      17.982  37.906  -7.925  1.00  0.00              
ATOM     79  C   MET    20      18.620  38.535  -9.165  1.00  0.00              
ATOM     80  O   MET    20      18.993  37.826 -10.100  1.00  0.00              
ATOM     81  N   ASP    69      18.769  39.855  -9.161  1.00  0.00              
ATOM     82  CA  ASP    69      19.321  40.546 -10.318  1.00  0.00              
ATOM     83  C   ASP    69      20.403  41.596 -10.072  1.00  0.00              
ATOM     84  O   ASP    69      21.480  41.535 -10.666  1.00  0.00              
ATOM     85  N   LYS    70      20.112  42.562  -9.209  1.00  0.00              
ATOM     86  CA  LYS    70      21.032  43.663  -8.951  1.00  0.00              
ATOM     87  C   LYS    70      22.192  43.430  -7.994  1.00  0.00              
ATOM     88  O   LYS    70      23.098  44.255  -7.910  1.00  0.00              
ATOM     89  N   PHE    71      22.167  42.321  -7.271  1.00  0.00              
ATOM     90  CA  PHE    71      23.223  42.029  -6.318  1.00  0.00              
ATOM     91  C   PHE    71      23.828  40.657  -6.545  1.00  0.00              
ATOM     92  O   PHE    71      23.299  39.850  -7.304  1.00  0.00              
ATOM     93  N   ASP    72      24.943  40.393  -5.876  1.00  0.00              
ATOM     94  CA  ASP    72      25.628  39.115  -6.013  1.00  0.00              
ATOM     95  C   ASP    72      25.897  38.532  -4.623  1.00  0.00              
ATOM     96  O   ASP    72      26.882  38.880  -3.970  1.00  0.00              
ATOM     97  N   LYS    73      24.995  37.652  -4.148  1.00  0.00              
ATOM     98  CA  LYS    73      25.062  36.980  -2.843  1.00  0.00              
ATOM     99  C   LYS    73      26.235  35.998  -2.786  1.00  0.00              
ATOM    100  O   LYS    73      26.738  35.574  -3.819  1.00  0.00              
ATOM    101  N   ALA    74      26.669  35.613  -1.578  1.00  0.00              
ATOM    102  CA  ALA    74      26.143  36.026  -0.271  1.00  0.00              
ATOM    103  C   ALA    74      26.532  37.453   0.105  1.00  0.00              
ATOM    104  O   ALA    74      27.332  38.101  -0.581  1.00  0.00              
ATOM    105  N   LYS    75      25.970  37.928   1.211  1.00  0.00              
ATOM    106  CA  LYS    75      26.249  39.268   1.703  1.00  0.00              
ATOM    107  C   LYS    75      27.023  39.183   3.015  1.00  0.00              
ATOM    108  O   LYS    75      27.188  38.105   3.575  1.00  0.00              
ATOM    109  N   GLU    76      27.486  40.331   3.501  1.00  0.00              
ATOM    110  CA  GLU    76      28.234  40.386   4.755  1.00  0.00              
ATOM    111  C   GLU    76      28.330  41.827   5.244  1.00  0.00              
ATOM    112  O   GLU    76      28.311  42.761   4.444  1.00  0.00              
ATOM    113  N   THR    77      28.436  42.002   6.558  1.00  0.00              
ATOM    114  CA  THR    77      28.571  43.339   7.121  1.00  0.00              
ATOM    115  C   THR    77      30.023  43.771   7.003  1.00  0.00              
ATOM    116  O   THR    77      30.934  43.015   7.330  1.00  0.00              
ATOM    117  N   TYR    78      30.230  44.991   6.526  1.00  0.00              
ATOM    118  CA  TYR    78      31.571  45.529   6.361  1.00  0.00              
ATOM    119  C   TYR    78      32.043  46.120   7.687  1.00  0.00              
ATOM    120  O   TYR    78      31.274  46.214   8.644  1.00  0.00              
ATOM    121  N   ILE    79      33.311  46.516   7.741  1.00  0.00              
ATOM    122  CA  ILE    79      33.876  47.091   8.955  1.00  0.00              
ATOM    123  C   ILE    79      33.207  48.414   9.316  1.00  0.00              
ATOM    124  O   ILE    79      33.172  48.797  10.486  1.00  0.00              
ATOM    125  N   ALA    80      32.678  49.107   8.312  1.00  0.00              
ATOM    126  CA  ALA    80      32.016  50.389   8.535  1.00  0.00              
ATOM    127  C   ALA    80      30.533  50.231   8.866  1.00  0.00              
ATOM    128  O   ALA    80      29.776  51.199   8.833  1.00  0.00              
ATOM    129  N   LEU    81      30.124  49.004   9.177  1.00  0.00              
ATOM    130  CA  LEU    81      28.735  48.746   9.530  1.00  0.00              
ATOM    131  C   LEU    81      27.765  48.502   8.384  1.00  0.00              
ATOM    132  O   LEU    81      26.631  48.088   8.611  1.00  0.00              
ATOM    133  N   PHE    82      28.200  48.754   7.154  1.00  0.00              
ATOM    134  CA  PHE    82      27.331  48.559   6.003  1.00  0.00              
ATOM    135  C   PHE    82      27.173  47.088   5.618  1.00  0.00              
ATOM    136  O   PHE    82      27.947  46.231   6.045  1.00  0.00              
ATOM    137  N   ARG    83      26.149  46.800   4.824  1.00  0.00              
ATOM    138  CA  ARG    83      25.925  45.449   4.332  1.00  0.00              
ATOM    139  C   ARG    83      26.475  45.476   2.913  1.00  0.00              
ATOM    140  O   ARG    83      26.219  46.416   2.157  1.00  0.00              
ATOM    141  N   GLU    84      27.242  44.458   2.554  1.00  0.00              
ATOM    142  CA  GLU    84      27.834  44.421   1.226  1.00  0.00              
ATOM    143  C   GLU    84      27.651  43.071   0.553  1.00  0.00              
ATOM    144  O   GLU    84      27.446  42.060   1.221  1.00  0.00              
ATOM    145  N   ARG    85      27.731  43.067  -0.774  1.00  0.00              
ATOM    146  CA  ARG    85      27.610  41.834  -1.537  1.00  0.00              
ATOM    147  C   ARG    85      28.988  41.549  -2.133  1.00  0.00              
ATOM    148  O   ARG    85      29.916  42.344  -1.961  1.00  0.00              
ATOM    149  N   ALA    86      29.122  40.424  -2.824  1.00  0.00              
ATOM    150  CA  ALA    86      30.396  40.022  -3.418  1.00  0.00              
ATOM    151  C   ALA    86      31.084  41.063  -4.303  1.00  0.00              
ATOM    152  O   ALA    86      32.302  41.018  -4.481  1.00  0.00              
ATOM    153  N   ARG    87      30.317  41.991  -4.864  1.00  0.00              
ATOM    154  CA  ARG    87      30.896  43.009  -5.735  1.00  0.00              
ATOM    155  C   ARG    87      31.114  44.348  -5.041  1.00  0.00              
ATOM    156  O   ARG    87      31.247  45.384  -5.696  1.00  0.00              
ATOM    157  N   ARG    88      31.153  44.314  -3.713  1.00  0.00              
ATOM    158  CA  ARG    88      31.382  45.521  -2.941  1.00  0.00              
ATOM    159  C   ARG    88      30.273  46.558  -2.970  1.00  0.00              
ATOM    160  O   ARG    88      30.502  47.721  -2.631  1.00  0.00              
ATOM    161  N   GLU    89      29.072  46.153  -3.369  1.00  0.00              
ATOM    162  CA  GLU    89      27.949  47.084  -3.416  1.00  0.00              
ATOM    163  C   GLU    89      27.400  47.373  -2.026  1.00  0.00              
ATOM    164  O   GLU    89      27.306  46.487  -1.181  1.00  0.00              
ATOM    165  N   ASP    90      27.033  48.624  -1.801  1.00  0.00              
ATOM    166  CA  ASP    90      26.457  49.015  -0.528  1.00  0.00              
ATOM    167  C   ASP    90      24.984  48.625  -0.629  1.00  0.00              
ATOM    168  O   ASP    90      24.266  49.156  -1.470  1.00  0.00              
ATOM    169  N   ILE    91      24.543  47.694   0.210  1.00  0.00              
ATOM    170  CA  ILE    91      23.152  47.247   0.180  1.00  0.00              
ATOM    171  C   ILE    91      22.357  47.986   1.251  1.00  0.00              
ATOM    172  O   ILE    91      22.702  47.928   2.424  1.00  0.00              
END
