
#######################################################
#                                                     #
#                        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   52 (  208),  selected   52 , name T0330AL509_1-D2
# Molecule2: number of CA atoms   72 (  556),  selected   72 , name T0330_D2.pdb
# PARAMETERS: T0330AL509_1-D2.T0330_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    G      34      -       -           -
LGA    T      35      V      17           #
LGA    E      36      E      18          2.405
LGA    G      37      S      19          3.351
LGA    S      38      M      20          2.430
LGA    T      39      N      21          1.392
LGA    G      40      R      22          1.462
LGA    S      41      R      23          0.458
LGA    H      42      V      24          0.308
LGA    D      49      L      25          0.540
LGA    G      50      A      26          0.849
LGA    A      51      D      27          0.728
LGA    I      52      A      28          0.640
LGA    I      53      L      29          0.550
LGA    Y      54      I      30          0.824
LGA    E      55      E      31          0.679
LGA    V      56      V      32          0.752
LGA    L      57      Y      33          1.586
LGA    S      58      G      34          4.813
LGA    N      59      -       -           -
LGA    V      60      -       -           -
LGA    G      61      -       -           -
LGA    L      62      -       -           -
LGA    E      63      -       -           -
LGA    R      64      T      35          3.249
LGA    A      65      -       -           -
LGA    E      66      -       -           -
LGA    I      67      -       -           -
LGA    A      68      -       -           -
LGA    D      69      E      36          2.080
LGA    K      70      G      37          5.448
LGA    F      71      S      38          3.084
LGA    D      72      T      39          2.546
LGA    K      73      D      43           -
LGA    A      74      F      44           #
LGA    -       -      S      45           -
LGA    -       -      G      46           -
LGA    -       -      K      47           -
LGA    -       -      M      48           -
LGA    -       -      D      49           -
LGA    -       -      G      50           -
LGA    -       -      A      51           -
LGA    -       -      I      52           -
LGA    -       -      I      53           -
LGA    -       -      Y      54           -
LGA    -       -      E      55           -
LGA    K      75      V      56          5.140
LGA    -       -      L      57           -
LGA    -       -      S      58           -
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    -       -      I      67           -
LGA    -       -      A      68           -
LGA    -       -      D      69           -
LGA    E      76      K      70          0.795
LGA    T      77      F      71          0.670
LGA    Y      78      D      72          0.454
LGA    I      79      K      73          0.544
LGA    A      80      A      74          0.277
LGA    L      81      K      75          0.264
LGA    F      82      E      76          0.437
LGA    R      83      T      77          0.402
LGA    E      84      Y      78          0.447
LGA    R      85      I      79          0.770
LGA    A      86      A      80          1.011
LGA    R      87      L      81          0.605
LGA    R      88      F      82          0.545
LGA    E      89      R      83          1.535
LGA    D      90      E      84          2.739
LGA    -       -      R      85           -
LGA    I      91      A      86          2.541
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)   52   72    5.0     39    2.06    12.82     42.252     1.809

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.446138 * X  +  -0.611281 * Y  +   0.653679 * Z  +  -3.668478
  Y_new =   0.129269 * X  +   0.766752 * Y  +   0.628794 * Z  +  18.070444
  Z_new =  -0.885579 * X  +  -0.196029 * Y  +   0.421097 * Z  +  65.802986 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.435685    2.705908  [ DEG:   -24.9629    155.0371 ]
  Theta =   1.087739    2.053853  [ DEG:    62.3229    117.6771 ]
  Phi   =   0.282027   -2.859565  [ DEG:    16.1590   -163.8410 ]
 
# 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: T0330AL509_1-D2                               
REMARK     2: T0330_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0330AL509_1-D2.T0330_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   52   72   5.0   39   2.06   12.82  42.252
REMARK  ---------------------------------------------------------- 
MOLECULE T0330AL509_1-D2
REMARK Aligment from pdb entry: 2fi1_A
ATOM     41  N   GLY    34      18.789  35.434  11.620  1.00  0.00              
ATOM     42  CA  GLY    34      19.390  35.438  10.289  1.00  0.00              
ATOM     43  C   GLY    34      20.289  34.241  10.079  1.00  0.00              
ATOM     44  O   GLY    34      21.167  33.970  10.897  1.00  0.00              
ATOM     45  N   THR    35      19.526  31.095  10.187  1.00  0.00              
ATOM     46  CA  THR    35      19.076  29.905  10.908  1.00  0.00              
ATOM     47  C   THR    35      17.566  29.745  10.721  1.00  0.00              
ATOM     48  O   THR    35      17.116  28.782  10.109  1.00  0.00              
ATOM     49  N   GLU    36      16.779  30.689  11.227  1.00  0.00              
ATOM     50  CA  GLU    36      15.329  30.678  10.982  1.00  0.00              
ATOM     51  C   GLU    36      14.954  31.487   9.744  1.00  0.00              
ATOM     52  O   GLU    36      14.099  31.078   8.965  1.00  0.00              
ATOM     53  N   GLY    37      15.596  32.641   9.593  1.00  0.00              
ATOM     54  CA  GLY    37      15.307  33.577   8.503  1.00  0.00              
ATOM     55  C   GLY    37      16.367  33.454   7.420  1.00  0.00              
ATOM     56  O   GLY    37      17.558  33.583   7.706  1.00  0.00              
ATOM     57  N   SER    38      15.927  33.195   6.186  1.00  0.00              
ATOM     58  CA  SER    38      16.830  33.147   5.039  1.00  0.00              
ATOM     59  C   SER    38      17.007  34.577   4.511  1.00  0.00              
ATOM     60  O   SER    38      16.504  34.941   3.442  1.00  0.00              
ATOM     61  N   THR    39      17.724  35.395   5.275  1.00  0.00              
ATOM     62  CA  THR    39      17.943  36.778   4.870  1.00  0.00              
ATOM     63  C   THR    39      18.763  36.867   3.590  1.00  0.00              
ATOM     64  O   THR    39      18.604  37.823   2.825  1.00  0.00              
ATOM     65  N   GLY    40      19.639  35.902   3.333  1.00  0.00              
ATOM     66  CA  GLY    40      20.427  35.985   2.104  1.00  0.00              
ATOM     67  C   GLY    40      19.568  35.760   0.874  1.00  0.00              
ATOM     68  O   GLY    40      19.922  36.226  -0.206  1.00  0.00              
ATOM     69  N   SER    41      18.425  35.093   1.014  1.00  0.00              
ATOM     70  CA  SER    41      17.538  34.915  -0.143  1.00  0.00              
ATOM     71  C   SER    41      16.880  36.226  -0.565  1.00  0.00              
ATOM     72  O   SER    41      16.853  36.562  -1.752  1.00  0.00              
ATOM     73  N   HIS    42      16.340  36.966   0.394  1.00  0.00              
ATOM     74  CA  HIS    42      15.732  38.246   0.075  1.00  0.00              
ATOM     75  C   HIS    42      16.786  39.244  -0.428  1.00  0.00              
ATOM     76  O   HIS    42      16.537  40.016  -1.360  1.00  0.00              
ATOM     77  N   ASP    49      17.975  39.223   0.167  1.00  0.00              
ATOM     78  CA  ASP    49      19.046  40.100  -0.279  1.00  0.00              
ATOM     79  C   ASP    49      19.515  39.734  -1.683  1.00  0.00              
ATOM     80  O   ASP    49      19.734  40.617  -2.511  1.00  0.00              
ATOM     81  N   GLY    50      19.625  38.441  -1.970  1.00  0.00              
ATOM     82  CA  GLY    50      20.015  37.989  -3.310  1.00  0.00              
ATOM     83  C   GLY    50      18.992  38.429  -4.352  1.00  0.00              
ATOM     84  O   GLY    50      19.356  38.931  -5.417  1.00  0.00              
ATOM     85  N   ALA    51      17.716  38.260  -4.049  1.00  0.00              
ATOM     86  CA  ALA    51      16.678  38.682  -4.974  1.00  0.00              
ATOM     87  C   ALA    51      16.827  40.164  -5.285  1.00  0.00              
ATOM     88  O   ALA    51      16.800  40.566  -6.454  1.00  0.00              
ATOM     89  N   ILE    52      17.021  40.975  -4.251  1.00  0.00              
ATOM     90  CA  ILE    52      17.208  42.422  -4.430  1.00  0.00              
ATOM     91  C   ILE    52      18.496  42.752  -5.198  1.00  0.00              
ATOM     92  O   ILE    52      18.515  43.655  -6.029  1.00  0.00              
ATOM     93  N   ILE    53      19.573  42.020  -4.934  1.00  0.00              
ATOM     94  CA  ILE    53      20.859  42.289  -5.568  1.00  0.00              
ATOM     95  C   ILE    53      20.800  41.955  -7.064  1.00  0.00              
ATOM     96  O   ILE    53      21.260  42.726  -7.911  1.00  0.00              
ATOM     97  N   TYR    54      20.210  40.812  -7.388  1.00  0.00              
ATOM     98  CA  TYR    54      20.051  40.392  -8.783  1.00  0.00              
ATOM     99  C   TYR    54      19.163  41.389  -9.536  1.00  0.00              
ATOM    100  O   TYR    54      19.488  41.793 -10.658  1.00  0.00              
ATOM    101  N   GLU    55      18.059  41.815  -8.932  1.00  0.00              
ATOM    102  CA  GLU    55      17.181  42.758  -9.620  1.00  0.00              
ATOM    103  C   GLU    55      17.852  44.120  -9.801  1.00  0.00              
ATOM    104  O   GLU    55      17.657  44.784 -10.829  1.00  0.00              
ATOM    105  N   VAL    56      18.670  44.532  -8.837  1.00  0.00              
ATOM    106  CA  VAL    56      19.406  45.796  -8.953  1.00  0.00              
ATOM    107  C   VAL    56      20.466  45.712 -10.068  1.00  0.00              
ATOM    108  O   VAL    56      20.598  46.645 -10.866  1.00  0.00              
ATOM    109  N   LEU    57      21.199  44.603 -10.151  1.00  0.00              
ATOM    110  CA  LEU    57      22.123  44.378 -11.270  1.00  0.00              
ATOM    111  C   LEU    57      21.429  44.510 -12.627  1.00  0.00              
ATOM    112  O   LEU    57      21.997  45.091 -13.564  1.00  0.00              
ATOM    113  N   SER    58      20.206  44.001 -12.726  1.00  0.00              
ATOM    114  CA  SER    58      19.474  44.020 -13.997  1.00  0.00              
ATOM    115  C   SER    58      19.182  45.446 -14.457  1.00  0.00              
ATOM    116  O   SER    58      19.099  45.696 -15.662  1.00  0.00              
ATOM    117  N   ASN    59      19.042  46.376 -13.516  1.00  0.00              
ATOM    118  CA  ASN    59      18.840  47.797 -13.848  1.00  0.00              
ATOM    119  C   ASN    59      20.012  48.361 -14.642  1.00  0.00              
ATOM    120  O   ASN    59      19.843  49.311 -15.418  1.00  0.00              
ATOM    121  N   VAL    60      21.197  47.791 -14.440  1.00  0.00              
ATOM    122  CA  VAL    60      22.403  48.205 -15.154  1.00  0.00              
ATOM    123  C   VAL    60      22.707  47.303 -16.360  1.00  0.00              
ATOM    124  O   VAL    60      23.780  47.408 -16.964  1.00  0.00              
ATOM    125  N   GLY    61      21.767  46.428 -16.714  1.00  0.00              
ATOM    126  CA  GLY    61      21.943  45.515 -17.840  1.00  0.00              
ATOM    127  C   GLY    61      22.829  44.318 -17.547  1.00  0.00              
ATOM    128  O   GLY    61      23.338  43.676 -18.470  1.00  0.00              
ATOM    129  N   LEU    62      23.001  43.998 -16.265  1.00  0.00              
ATOM    130  CA  LEU    62      23.882  42.918 -15.850  1.00  0.00              
ATOM    131  C   LEU    62      23.075  41.752 -15.298  1.00  0.00              
ATOM    132  O   LEU    62      22.167  41.943 -14.494  1.00  0.00              
ATOM    133  N   GLU    63      23.417  40.547 -15.756  1.00  0.00              
ATOM    134  CA  GLU    63      22.823  39.313 -15.264  1.00  0.00              
ATOM    135  C   GLU    63      23.869  38.521 -14.488  1.00  0.00              
ATOM    136  O   GLU    63      24.956  38.268 -14.989  1.00  0.00              
ATOM    137  N   ARG    64      23.538  38.146 -13.252  1.00  0.00              
ATOM    138  CA  ARG    64      24.346  37.195 -12.493  1.00  0.00              
ATOM    139  C   ARG    64      23.420  36.177 -11.862  1.00  0.00              
ATOM    140  O   ARG    64      22.266  36.476 -11.546  1.00  0.00              
ATOM    141  N   ALA    65      23.937  34.972 -11.677  1.00  0.00              
ATOM    142  CA  ALA    65      23.138  33.866 -11.176  1.00  0.00              
ATOM    143  C   ALA    65      22.913  33.934  -9.663  1.00  0.00              
ATOM    144  O   ALA    65      23.743  34.442  -8.902  1.00  0.00              
ATOM    145  N   GLU    66      21.785  33.378  -9.247  1.00  0.00              
ATOM    146  CA  GLU    66      21.381  33.326  -7.851  1.00  0.00              
ATOM    147  C   GLU    66      22.461  32.786  -6.922  1.00  0.00              
ATOM    148  O   GLU    66      22.799  33.417  -5.919  1.00  0.00              
ATOM    149  N   ILE    67      22.993  31.605  -7.227  1.00  0.00              
ATOM    150  CA  ILE    67      23.866  30.929  -6.276  1.00  0.00              
ATOM    151  C   ILE    67      25.176  31.688  -6.065  1.00  0.00              
ATOM    152  O   ILE    67      25.693  31.715  -4.953  1.00  0.00              
ATOM    153  N   ALA    68      25.703  32.307  -7.117  1.00  0.00              
ATOM    154  CA  ALA    68      26.936  33.094  -6.995  1.00  0.00              
ATOM    155  C   ALA    68      26.728  34.321  -6.130  1.00  0.00              
ATOM    156  O   ALA    68      27.565  34.638  -5.285  1.00  0.00              
ATOM    157  N   ASP    69      25.625  35.018  -6.373  1.00  0.00              
ATOM    158  CA  ASP    69      25.307  36.231  -5.629  1.00  0.00              
ATOM    159  C   ASP    69      25.044  35.901  -4.155  1.00  0.00              
ATOM    160  O   ASP    69      25.536  36.594  -3.259  1.00  0.00              
ATOM    161  N   LYS    70      24.309  34.829  -3.907  1.00  0.00              
ATOM    162  CA  LYS    70      23.982  34.399  -2.555  1.00  0.00              
ATOM    163  C   LYS    70      25.261  34.104  -1.776  1.00  0.00              
ATOM    164  O   LYS    70      25.449  34.566  -0.644  1.00  0.00              
ATOM    165  N   PHE    71      26.163  33.335  -2.377  1.00  0.00              
ATOM    166  CA  PHE    71      27.406  32.995  -1.710  1.00  0.00              
ATOM    167  C   PHE    71      28.257  34.230  -1.468  1.00  0.00              
ATOM    168  O   PHE    71      28.867  34.371  -0.401  1.00  0.00              
ATOM    169  N   ASP    72      28.310  35.127  -2.446  1.00  0.00              
ATOM    170  CA  ASP    72      29.086  36.355  -2.285  1.00  0.00              
ATOM    171  C   ASP    72      28.558  37.206  -1.133  1.00  0.00              
ATOM    172  O   ASP    72      29.347  37.738  -0.344  1.00  0.00              
ATOM    173  N   LYS    73      27.243  37.368  -1.052  1.00  0.00              
ATOM    174  CA  LYS    73      26.636  38.119   0.055  1.00  0.00              
ATOM    175  C   LYS    73      26.917  37.468   1.403  1.00  0.00              
ATOM    176  O   LYS    73      27.096  38.161   2.407  1.00  0.00              
ATOM    177  N   ALA    74      26.992  36.140   1.435  1.00  0.00              
ATOM    178  CA  ALA    74      27.315  35.420   2.672  1.00  0.00              
ATOM    179  C   ALA    74      28.726  35.724   3.150  1.00  0.00              
ATOM    180  O   ALA    74      29.001  35.659   4.363  1.00  0.00              
ATOM    181  N   LYS    75      29.623  36.035   2.221  1.00  0.00              
ATOM    182  CA  LYS    75      30.948  36.544   2.574  1.00  0.00              
ATOM    183  C   LYS    75      30.760  37.942   3.173  1.00  0.00              
ATOM    184  O   LYS    75      30.971  38.139   4.380  1.00  0.00              
ATOM    185  N   GLU    76      24.660  52.088  -6.961  1.00  0.00              
ATOM    186  CA  GLU    76      24.202  50.700  -6.849  1.00  0.00              
ATOM    187  C   GLU    76      23.750  50.373  -5.433  1.00  0.00              
ATOM    188  O   GLU    76      22.647  49.863  -5.239  1.00  0.00              
ATOM    189  N   THR    77      24.601  50.659  -4.451  1.00  0.00              
ATOM    190  CA  THR    77      24.297  50.291  -3.059  1.00  0.00              
ATOM    191  C   THR    77      22.977  50.889  -2.607  1.00  0.00              
ATOM    192  O   THR    77      22.146  50.209  -2.015  1.00  0.00              
ATOM    193  N   TYR    78      22.786  52.173  -2.877  1.00  0.00              
ATOM    194  CA  TYR    78      21.574  52.851  -2.463  1.00  0.00              
ATOM    195  C   TYR    78      20.330  52.194  -3.047  1.00  0.00              
ATOM    196  O   TYR    78      19.346  51.969  -2.343  1.00  0.00              
ATOM    197  N   ILE    79      20.376  51.889  -4.342  1.00  0.00              
ATOM    198  CA  ILE    79      19.257  51.255  -5.021  1.00  0.00              
ATOM    199  C   ILE    79      19.063  49.823  -4.533  1.00  0.00              
ATOM    200  O   ILE    79      17.935  49.379  -4.343  1.00  0.00              
ATOM    201  N   ALA    80      20.169  49.118  -4.315  1.00  0.00              
ATOM    202  CA  ALA    80      20.113  47.766  -3.751  1.00  0.00              
ATOM    203  C   ALA    80      19.415  47.752  -2.386  1.00  0.00              
ATOM    204  O   ALA    80      18.543  46.913  -2.144  1.00  0.00              
ATOM    205  N   LEU    81      19.789  48.679  -1.500  1.00  0.00              
ATOM    206  CA  LEU    81      19.196  48.722  -0.157  1.00  0.00              
ATOM    207  C   LEU    81      17.700  49.022  -0.207  1.00  0.00              
ATOM    208  O   LEU    81      16.923  48.474   0.582  1.00  0.00              
ATOM    209  N   PHE    82      17.293  49.880  -1.136  1.00  0.00              
ATOM    210  CA  PHE    82      15.872  50.149  -1.321  1.00  0.00              
ATOM    211  C   PHE    82      15.136  48.893  -1.792  1.00  0.00              
ATOM    212  O   PHE    82      14.080  48.548  -1.268  1.00  0.00              
ATOM    213  N   ARG    83      15.714  48.187  -2.760  1.00  0.00              
ATOM    214  CA  ARG    83      15.120  46.943  -3.238  1.00  0.00              
ATOM    215  C   ARG    83      15.096  45.856  -2.161  1.00  0.00              
ATOM    216  O   ARG    83      14.151  45.075  -2.087  1.00  0.00              
ATOM    217  N   GLU    84      16.126  45.824  -1.319  1.00  0.00              
ATOM    218  CA  GLU    84      16.183  44.861  -0.223  1.00  0.00              
ATOM    219  C   GLU    84      15.075  45.129   0.798  1.00  0.00              
ATOM    220  O   GLU    84      14.426  44.202   1.269  1.00  0.00              
ATOM    221  N   ARG    85      14.866  46.396   1.144  1.00  0.00              
ATOM    222  CA  ARG    85      13.784  46.751   2.061  1.00  0.00              
ATOM    223  C   ARG    85      12.437  46.301   1.510  1.00  0.00              
ATOM    224  O   ARG    85      11.595  45.786   2.251  1.00  0.00              
ATOM    225  N   ALA    86      12.236  46.477   0.207  1.00  0.00              
ATOM    226  CA  ALA    86      11.014  45.999  -0.441  1.00  0.00              
ATOM    227  C   ALA    86      10.848  44.484  -0.343  1.00  0.00              
ATOM    228  O   ALA    86       9.767  43.990  -0.036  1.00  0.00              
ATOM    229  N   ARG    87      11.916  43.740  -0.603  1.00  0.00              
ATOM    230  CA  ARG    87      11.868  42.289  -0.441  1.00  0.00              
ATOM    231  C   ARG    87      11.495  41.891   0.983  1.00  0.00              
ATOM    232  O   ARG    87      10.742  40.929   1.185  1.00  0.00              
ATOM    233  N   ARG    88      12.022  42.625   1.961  1.00  0.00              
ATOM    234  CA  ARG    88      11.787  42.319   3.373  1.00  0.00              
ATOM    235  C   ARG    88      10.382  42.696   3.847  1.00  0.00              
ATOM    236  O   ARG    88      10.030  42.422   4.992  1.00  0.00              
ATOM    237  N   GLU    89       9.575  43.305   2.978  1.00  0.00              
ATOM    238  CA  GLU    89       8.141  43.391   3.270  1.00  0.00              
ATOM    239  C   GLU    89       7.532  41.989   3.349  1.00  0.00              
ATOM    240  O   GLU    89       6.501  41.790   3.995  1.00  0.00              
ATOM    241  N   ASP    90       8.172  41.021   2.692  1.00  0.00              
ATOM    242  CA  ASP    90       7.768  39.624   2.760  1.00  0.00              
ATOM    243  C   ASP    90       9.003  38.762   2.998  1.00  0.00              
ATOM    244  O   ASP    90       9.523  38.135   2.072  1.00  0.00              
ATOM    245  N   ILE    91       9.473  38.723   4.256  1.00  0.00              
ATOM    246  CA  ILE    91      10.683  37.948   4.534  1.00  0.00              
ATOM    247  C   ILE    91      10.471  36.459   4.277  1.00  0.00              
ATOM    248  O   ILE    91       9.333  35.981   4.288  1.00  0.00              
END
