
#######################################################
#                                                     #
#                        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   46 (  184),  selected   46 , name T0324AL333_3-D2
# Molecule2: number of CA atoms   65 (  494),  selected   65 , name T0324_D2.pdb
# PARAMETERS: T0324AL333_3-D2.T0324_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    S      17      S      17          2.640
LGA    Q      18      Q      18          3.258
LGA    V      24      P      19           -
LGA    M      25      A      20           -
LGA    R      26      Y      21          3.040
LGA    -       -      T      22           -
LGA    E      27      T      23          4.842
LGA    V      28      V      24          5.186
LGA    L      29      M      25          2.728
LGA    A      30      R      26          1.304
LGA    T      31      E      27          2.966
LGA    -       -      V      28           -
LGA    Y      32      L      29          1.298
LGA    G      33      A      30          3.332
LGA    K      34      T      31           -
LGA    -       -      Y      32           -
LGA    -       -      G      33           -
LGA    -       -      K      34           -
LGA    -       -      P      35           -
LGA    P      35      F      36          1.702
LGA    F      36      S      37          1.673
LGA    S      37      P      38           #
LGA    -       -      A      39           -
LGA    P      38      Q      40          1.290
LGA    Q      51      A      41           -
LGA    -       -      Q      42           -
LGA    -       -      K      43           -
LGA    -       -      T      44           -
LGA    -       -      F      45           -
LGA    A      52      P      46           #
LGA    M      53      -       -           -
LGA    T      54      -       -           -
LGA    E      55      M      47          6.082
LGA    -       -      A      48           -
LGA    -       -      A      49           -
LGA    -       -      E      50           -
LGA    L      56      Q      51          4.716
LGA    G      57      -       -           -
LGA    I      58      -       -           -
LGA    A      59      A      52          3.622
LGA    A      60      M      53          2.905
LGA    -       -      T      54           -
LGA    S      61      E      55          1.534
LGA    E      62      L      56          0.923
LGA    F      63      G      57           #
LGA    D      64      I      58          2.680
LGA    H      65      A      59           #
LGA    -       -      A      60           -
LGA    -       -      S      61           -
LGA    -       -      E      62           -
LGA    F      66      F      63          2.579
LGA    Q      67      D      64          1.735
LGA    A      68      H      65          1.772
LGA    Q      69      F      66          2.330
LGA    Y      70      Q      67          1.868
LGA    E      71      A      68          1.405
LGA    D      72      Q      69          1.841
LGA    V      73      Y      70          2.269
LGA    M      74      E      71          2.000
LGA    A      75      D      72          2.142
LGA    S      76      V      73          3.076
LGA    H      77      -       -           -
LGA    Q      80      M      74          2.744
LGA    I      81      A      75          4.350
LGA    -       -      S      76           -
LGA    -       -      H      77           -
LGA    -       -      Y      78           -
LGA    -       -      D      79           -
LGA    -       -      Q      80           -
LGA    -       -      I      81           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   46   65    5.0     33    2.93    15.15     34.205     1.089

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.178326 * X  +  -0.751001 * Y  +  -0.635765 * Z  +  58.251991
  Y_new =  -0.413272 * X  +  -0.643534 * Y  +   0.644260 * Z  +  39.397175
  Z_new =  -0.892976 * X  +   0.147855 * Y  +  -0.425127 * Z  +  34.517647 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.806886   -0.334706  [ DEG:   160.8228    -19.1772 ]
  Theta =   1.103914    2.037678  [ DEG:    63.2496    116.7504 ]
  Phi   =  -1.163435    1.978158  [ DEG:   -66.6599    113.3401 ]
 
# 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: T0324AL333_3-D2                               
REMARK     2: T0324_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0324AL333_3-D2.T0324_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   46   65   5.0   33   2.93   15.15  34.205
REMARK  ---------------------------------------------------------- 
MOLECULE T0324AL333_3-D2
REMARK Aligment from pdb entry: 1nnl_A
ATOM     61  N   SER    17      28.986  17.317  12.163  1.00  0.00              
ATOM     62  CA  SER    17      27.631  17.544  11.671  1.00  0.00              
ATOM     63  C   SER    17      26.679  18.210  12.649  1.00  0.00              
ATOM     64  O   SER    17      27.077  18.697  13.708  1.00  0.00              
ATOM     65  N   GLN    18      25.411  18.227  12.251  1.00  0.00              
ATOM     66  CA  GLN    18      24.318  18.783  13.038  1.00  0.00              
ATOM     67  C   GLN    18      23.299  17.659  13.190  1.00  0.00              
ATOM     68  O   GLN    18      22.695  17.228  12.206  1.00  0.00              
ATOM     69  N   VAL    24      23.118  17.186  14.418  1.00  0.00              
ATOM     70  CA  VAL    24      22.185  16.103  14.678  1.00  0.00              
ATOM     71  C   VAL    24      20.850  16.159  13.957  1.00  0.00              
ATOM     72  O   VAL    24      20.503  15.240  13.211  1.00  0.00              
ATOM     73  N   MET    25      20.097  17.233  14.179  1.00  0.00              
ATOM     74  CA  MET    25      18.783  17.392  13.561  1.00  0.00              
ATOM     75  C   MET    25      18.850  17.333  12.036  1.00  0.00              
ATOM     76  O   MET    25      17.909  16.877  11.386  1.00  0.00              
ATOM     77  N   ARG    26      19.964  17.790  11.472  1.00  0.00              
ATOM     78  CA  ARG    26      20.149  17.768  10.024  1.00  0.00              
ATOM     79  C   ARG    26      20.213  16.316   9.553  1.00  0.00              
ATOM     80  O   ARG    26      19.569  15.938   8.571  1.00  0.00              
ATOM     81  N   GLU    27      20.992  15.506  10.263  1.00  0.00              
ATOM     82  CA  GLU    27      21.141  14.095   9.923  1.00  0.00              
ATOM     83  C   GLU    27      19.812  13.354  10.047  1.00  0.00              
ATOM     84  O   GLU    27      19.479  12.508   9.216  1.00  0.00              
ATOM     85  N   VAL    28      19.054  13.677  11.090  1.00  0.00              
ATOM     86  CA  VAL    28      17.763  13.038  11.310  1.00  0.00              
ATOM     87  C   VAL    28      16.813  13.380  10.171  1.00  0.00              
ATOM     88  O   VAL    28      16.003  12.553   9.750  1.00  0.00              
ATOM     89  N   LEU    29      16.918  14.607   9.675  1.00  0.00              
ATOM     90  CA  LEU    29      16.070  15.059   8.581  1.00  0.00              
ATOM     91  C   LEU    29      16.367  14.247   7.326  1.00  0.00              
ATOM     92  O   LEU    29      15.462  13.907   6.566  1.00  0.00              
ATOM     93  N   ALA    30      17.642  13.938   7.119  1.00  0.00              
ATOM     94  CA  ALA    30      18.065  13.173   5.955  1.00  0.00              
ATOM     95  C   ALA    30      17.557  11.735   6.006  1.00  0.00              
ATOM     96  O   ALA    30      17.011  11.226   5.025  1.00  0.00              
ATOM     97  N   THR    31      17.733  11.084   7.152  1.00  0.00              
ATOM     98  CA  THR    31      17.292   9.704   7.312  1.00  0.00              
ATOM     99  C   THR    31      15.779   9.587   7.127  1.00  0.00              
ATOM    100  O   THR    31      15.276   8.545   6.707  1.00  0.00              
ATOM    101  N   TYR    32      15.059  10.662   7.435  1.00  0.00              
ATOM    102  CA  TYR    32      13.604  10.674   7.296  1.00  0.00              
ATOM    103  C   TYR    32      13.178  11.175   5.919  1.00  0.00              
ATOM    104  O   TYR    32      11.991  11.179   5.591  1.00  0.00              
ATOM    105  N   GLY    33      14.153  11.602   5.122  1.00  0.00              
ATOM    106  CA  GLY    33      13.868  12.085   3.782  1.00  0.00              
ATOM    107  C   GLY    33      13.135  13.411   3.697  1.00  0.00              
ATOM    108  O   GLY    33      12.153  13.533   2.966  1.00  0.00              
ATOM    109  N   LYS    34      13.608  14.410   4.434  1.00  0.00              
ATOM    110  CA  LYS    34      12.982  15.727   4.420  1.00  0.00              
ATOM    111  C   LYS    34      14.023  16.844   4.435  1.00  0.00              
ATOM    112  O   LYS    34      13.733  17.972   4.837  1.00  0.00              
ATOM    113  N   PRO    35      15.235  16.523   3.993  1.00  0.00              
ATOM    114  CA  PRO    35      16.318  17.498   3.953  1.00  0.00              
ATOM    115  C   PRO    35      15.956  18.654   3.026  1.00  0.00              
ATOM    116  O   PRO    35      16.127  19.823   3.380  1.00  0.00              
ATOM    117  N   PHE    36      15.454  18.320   1.842  1.00  0.00              
ATOM    118  CA  PHE    36      15.066  19.329   0.861  1.00  0.00              
ATOM    119  C   PHE    36      13.963  20.227   1.413  1.00  0.00              
ATOM    120  O   PHE    36      14.013  21.449   1.267  1.00  0.00              
ATOM    121  N   SER    37      12.968  19.615   2.049  1.00  0.00              
ATOM    122  CA  SER    37      11.852  20.358   2.623  1.00  0.00              
ATOM    123  C   SER    37      12.279  21.106   3.882  1.00  0.00              
ATOM    124  O   SER    37      11.572  21.997   4.355  1.00  0.00              
ATOM    125  N   PRO    38      13.439  20.740   4.420  1.00  0.00              
ATOM    126  CA  PRO    38      13.936  21.390   5.619  1.00  0.00              
ATOM    127  C   PRO    38      14.488  22.775   5.345  1.00  0.00              
ATOM    128  O   PRO    38      15.672  22.935   5.048  1.00  0.00              
ATOM    129  N   GLN    51      11.622  32.499  17.791  1.00  0.00              
ATOM    130  CA  GLN    51      11.887  31.743  19.019  1.00  0.00              
ATOM    131  C   GLN    51      12.465  30.364  18.730  1.00  0.00              
ATOM    132  O   GLN    51      12.144  29.747  17.714  1.00  0.00              
ATOM    133  N   ALA    52      13.317  29.881  19.630  1.00  0.00              
ATOM    134  CA  ALA    52      13.939  28.574  19.463  1.00  0.00              
ATOM    135  C   ALA    52      12.914  27.452  19.554  1.00  0.00              
ATOM    136  O   ALA    52      12.892  26.550  18.716  1.00  0.00              
ATOM    137  N   MET    53      12.069  27.512  20.579  1.00  0.00              
ATOM    138  CA  MET    53      11.048  26.495  20.799  1.00  0.00              
ATOM    139  C   MET    53      10.104  26.362  19.606  1.00  0.00              
ATOM    140  O   MET    53       9.790  25.252  19.171  1.00  0.00              
ATOM    141  N   THR    54       9.655  27.498  19.084  1.00  0.00              
ATOM    142  CA  THR    54       8.751  27.510  17.943  1.00  0.00              
ATOM    143  C   THR    54       9.436  26.923  16.712  1.00  0.00              
ATOM    144  O   THR    54       8.822  26.180  15.947  1.00  0.00              
ATOM    145  N   GLU    55      10.708  27.260  16.528  1.00  0.00              
ATOM    146  CA  GLU    55      11.472  26.761  15.392  1.00  0.00              
ATOM    147  C   GLU    55      11.625  25.249  15.501  1.00  0.00              
ATOM    148  O   GLU    55      11.426  24.520  14.528  1.00  0.00              
ATOM    149  N   LEU    56      11.975  24.784  16.696  1.00  0.00              
ATOM    150  CA  LEU    56      12.156  23.360  16.941  1.00  0.00              
ATOM    151  C   LEU    56      10.890  22.572  16.611  1.00  0.00              
ATOM    152  O   LEU    56      10.947  21.541  15.938  1.00  0.00              
ATOM    153  N   GLY    57       9.748  23.061  17.085  1.00  0.00              
ATOM    154  CA  GLY    57       8.473  22.398  16.831  1.00  0.00              
ATOM    155  C   GLY    57       8.213  22.301  15.332  1.00  0.00              
ATOM    156  O   GLY    57       7.808  21.250  14.830  1.00  0.00              
ATOM    157  N   ILE    58       8.449  23.401  14.625  1.00  0.00              
ATOM    158  CA  ILE    58       8.241  23.448  13.182  1.00  0.00              
ATOM    159  C   ILE    58       9.080  22.405  12.456  1.00  0.00              
ATOM    160  O   ILE    58       8.565  21.637  11.644  1.00  0.00              
ATOM    161  N   ALA    59      10.378  22.389  12.748  1.00  0.00              
ATOM    162  CA  ALA    59      11.293  21.445  12.120  1.00  0.00              
ATOM    163  C   ALA    59      10.891  19.997  12.373  1.00  0.00              
ATOM    164  O   ALA    59      10.871  19.182  11.450  1.00  0.00              
ATOM    165  N   ALA    60      10.572  19.677  13.623  1.00  0.00              
ATOM    166  CA  ALA    60      10.171  18.321  13.975  1.00  0.00              
ATOM    167  C   ALA    60       8.804  17.978  13.391  1.00  0.00              
ATOM    168  O   ALA    60       8.502  16.810  13.151  1.00  0.00              
ATOM    169  N   SER    61       7.985  19.000  13.161  1.00  0.00              
ATOM    170  CA  SER    61       6.651  18.803  12.601  1.00  0.00              
ATOM    171  C   SER    61       6.750  18.243  11.188  1.00  0.00              
ATOM    172  O   SER    61       5.905  17.456  10.759  1.00  0.00              
ATOM    173  N   GLU    62       7.789  18.656  10.471  1.00  0.00              
ATOM    174  CA  GLU    62       8.012  18.198   9.107  1.00  0.00              
ATOM    175  C   GLU    62       8.725  16.851   9.108  1.00  0.00              
ATOM    176  O   GLU    62       8.434  15.977   8.291  1.00  0.00              
ATOM    177  N   PHE    63       9.659  16.687  10.040  1.00  0.00              
ATOM    178  CA  PHE    63      10.424  15.453  10.151  1.00  0.00              
ATOM    179  C   PHE    63       9.600  14.309  10.737  1.00  0.00              
ATOM    180  O   PHE    63       9.565  13.214  10.177  1.00  0.00              
ATOM    181  N   ASP    64       8.938  14.571  11.862  1.00  0.00              
ATOM    182  CA  ASP    64       8.128  13.560  12.540  1.00  0.00              
ATOM    183  C   ASP    64       8.880  12.236  12.607  1.00  0.00              
ATOM    184  O   ASP    64       8.413  11.213  12.110  1.00  0.00              
ATOM    185  N   HIS    65      10.062  12.242  13.240  1.00  0.00              
ATOM    186  CA  HIS    65      10.888  11.041  13.370  1.00  0.00              
ATOM    187  C   HIS    65      10.302   9.981  14.294  1.00  0.00              
ATOM    188  O   HIS    65       9.881  10.281  15.411  1.00  0.00              
ATOM    189  N   PHE    66      10.277   8.741  13.821  1.00  0.00              
ATOM    190  CA  PHE    66       9.771   7.632  14.619  1.00  0.00              
ATOM    191  C   PHE    66      10.952   7.102  15.425  1.00  0.00              
ATOM    192  O   PHE    66      12.108   7.395  15.109  1.00  0.00              
ATOM    193  N   GLN    67      10.672   6.325  16.466  1.00  0.00              
ATOM    194  CA  GLN    67      11.749   5.785  17.278  1.00  0.00              
ATOM    195  C   GLN    67      12.667   4.911  16.428  1.00  0.00              
ATOM    196  O   GLN    67      13.885   4.919  16.601  1.00  0.00              
ATOM    197  N   ALA    68      12.076   4.164  15.501  1.00  0.00              
ATOM    198  CA  ALA    68      12.843   3.287  14.628  1.00  0.00              
ATOM    199  C   ALA    68      13.810   4.094  13.761  1.00  0.00              
ATOM    200  O   ALA    68      14.949   3.684  13.538  1.00  0.00              
ATOM    201  N   GLN    69      13.349   5.242  13.277  1.00  0.00              
ATOM    202  CA  GLN    69      14.172   6.107  12.441  1.00  0.00              
ATOM    203  C   GLN    69      15.335   6.702  13.237  1.00  0.00              
ATOM    204  O   GLN    69      16.452   6.812  12.729  1.00  0.00              
ATOM    205  N   TYR    70      15.079   7.074  14.489  1.00  0.00              
ATOM    206  CA  TYR    70      16.142   7.618  15.327  1.00  0.00              
ATOM    207  C   TYR    70      17.144   6.498  15.594  1.00  0.00              
ATOM    208  O   TYR    70      18.359   6.715  15.594  1.00  0.00              
ATOM    209  N   GLU    71      16.629   5.292  15.811  1.00  0.00              
ATOM    210  CA  GLU    71      17.480   4.139  16.063  1.00  0.00              
ATOM    211  C   GLU    71      18.358   3.903  14.834  1.00  0.00              
ATOM    212  O   GLU    71      19.540   3.586  14.959  1.00  0.00              
ATOM    213  N   ASP    72      17.772   4.076  13.650  1.00  0.00              
ATOM    214  CA  ASP    72      18.493   3.901  12.391  1.00  0.00              
ATOM    215  C   ASP    72      19.641   4.895  12.291  1.00  0.00              
ATOM    216  O   ASP    72      20.769   4.529  11.967  1.00  0.00              
ATOM    217  N   VAL    73      19.338   6.160  12.557  1.00  0.00              
ATOM    218  CA  VAL    73      20.346   7.213  12.499  1.00  0.00              
ATOM    219  C   VAL    73      21.544   6.842  13.363  1.00  0.00              
ATOM    220  O   VAL    73      22.686   6.864  12.911  1.00  0.00              
ATOM    221  N   MET    74      21.268   6.494  14.612  1.00  0.00              
ATOM    222  CA  MET    74      22.310   6.127  15.558  1.00  0.00              
ATOM    223  C   MET    74      23.173   4.960  15.081  1.00  0.00              
ATOM    224  O   MET    74      24.402   5.016  15.159  1.00  0.00              
ATOM    225  N   ALA    75      22.531   3.911  14.578  1.00  0.00              
ATOM    226  CA  ALA    75      23.252   2.731  14.115  1.00  0.00              
ATOM    227  C   ALA    75      23.882   2.878  12.732  1.00  0.00              
ATOM    228  O   ALA    75      25.006   2.430  12.511  1.00  0.00              
ATOM    229  N   SER    76      23.165   3.510  11.810  1.00  0.00              
ATOM    230  CA  SER    76      23.646   3.674  10.440  1.00  0.00              
ATOM    231  C   SER    76      24.512   4.896  10.163  1.00  0.00              
ATOM    232  O   SER    76      25.467   4.820   9.389  1.00  0.00              
ATOM    233  N   HIS    77      24.182   6.022  10.787  1.00  0.00              
ATOM    234  CA  HIS    77      24.915   7.258  10.541  1.00  0.00              
ATOM    235  C   HIS    77      25.462   7.961  11.777  1.00  0.00              
ATOM    236  O   HIS    77      25.095   9.105  12.059  1.00  0.00              
ATOM    237  N   GLN    80      26.357   7.301  12.527  1.00  0.00              
ATOM    238  CA  GLN    80      26.897   7.967  13.717  1.00  0.00              
ATOM    239  C   GLN    80      27.656   9.230  13.319  1.00  0.00              
ATOM    240  O   GLN    80      28.241   9.303  12.241  1.00  0.00              
ATOM    241  N   ILE    81      27.638  10.253  14.182  1.00  0.00              
ATOM    242  CA  ILE    81      28.339  11.500  13.872  1.00  0.00              
ATOM    243  C   ILE    81      29.849  11.333  13.933  1.00  0.00              
ATOM    244  O   ILE    81      30.360  10.408  14.565  1.00  0.00              
END
