
#######################################################
#                                                     #
#                        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   50 (  200),  selected   50 , name T0381AL333_4-D1
# Molecule2: number of CA atoms   61 (  477),  selected   61 , name T0381_D1.pdb
# PARAMETERS: T0381AL333_4-D1.T0381_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      V      17           -
LGA    -       -      Q      18           -
LGA    -       -      S      19           -
LGA    -       -      L      20           -
LGA    -       -      A      21           -
LGA    -       -      R      22           -
LGA    -       -      G      23           -
LGA    L      24      L      24          1.788
LGA    A      25      A      25          1.114
LGA    V      26      V      26          0.825
LGA    I      27      I      27          0.835
LGA    R      28      R      28          1.377
LGA    C      29      C      29          1.436
LGA    F      30      F      30          2.220
LGA    D      31      D      31          3.520
LGA    H      32      H      32          3.823
LGA    -       -      R      33           -
LGA    R      33      N      34          1.379
LGA    Q      35      Q      35          1.555
LGA    R      36      R      36          1.201
LGA    R      37      R      37          1.222
LGA    T      38      T      38          1.439
LGA    L      39      L      39          1.061
LGA    S      40      S      40          1.503
LGA    D      41      D      41          1.224
LGA    V      42      V      42          0.430
LGA    A      43      A      43          1.050
LGA    R      44      R      44          1.677
LGA    A      45      A      45          1.422
LGA    T      46      T      46          1.510
LGA    D      47      D      47          5.048
LGA    L      48      L      48          3.123
LGA    T      49      T      49          3.056
LGA    R      50      R      50          2.338
LGA    A      51      A      51          1.434
LGA    T      52      T      52          1.411
LGA    A      53      A      53          1.135
LGA    R      54      R      54          0.914
LGA    R      55      R      55          0.553
LGA    F      56      F      56          0.771
LGA    L      57      L      57          0.415
LGA    L      58      L      58          0.711
LGA    T      59      T      59          0.672
LGA    L      60      L      60          0.647
LGA    V      61      V      61          0.647
LGA    E      62      E      62          0.576
LGA    L      63      L      63          0.790
LGA    G      64      G      64          0.718
LGA    Y      65      Y      65          0.395
LGA    V      66      V      66          0.931
LGA    A      67      A      67          0.656
LGA    T      68      T      68          1.656
LGA    D      69      D      69          6.641
LGA    G      70      -       -           -
LGA    S      71      -       -           -
LGA    A      72      G      70          4.966
LGA    F      73      S      71          1.962
LGA    W      74      A      72          1.412
LGA    -       -      F      73           -
LGA    -       -      W      74           -
LGA    -       -      L      75           -
LGA    -       -      T      76           -
LGA    -       -      P      77           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   50   61    5.0     48    2.06    91.67     71.123     2.222

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.281907 * X  +   0.839591 * Y  +   0.464345 * Z  + -36.073471
  Y_new =  -0.143525 * X  +  -0.441625 * Y  +   0.885646 * Z  +  35.259754
  Z_new =   0.948646 * X  +  -0.316315 * Y  +  -0.003995 * Z  +  29.822189 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.583427    1.558166  [ DEG:   -90.7237     89.2763 ]
  Theta =  -1.248927   -1.892665  [ DEG:   -71.5583   -108.4417 ]
  Phi   =  -0.470917    2.670676  [ DEG:   -26.9815    153.0185 ]
 
# 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: T0381AL333_4-D1                               
REMARK     2: T0381_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0381AL333_4-D1.T0381_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   50   61   5.0   48   2.06   91.67  71.123
REMARK  ---------------------------------------------------------- 
MOLECULE T0381AL333_4-D1
REMARK Aligment from pdb entry: 1okr_A
ATOM     37  N   LEU    24      10.283  52.376  24.638  1.00  0.00              
ATOM     38  CA  LEU    24      10.066  51.087  24.000  1.00  0.00              
ATOM     39  C   LEU    24       8.886  51.188  23.036  1.00  0.00              
ATOM     40  O   LEU    24       8.848  50.537  22.041  1.00  0.00              
ATOM     41  N   ALA    25       7.914  52.008  23.372  1.00  0.00              
ATOM     42  CA  ALA    25       6.729  52.096  22.579  1.00  0.00              
ATOM     43  C   ALA    25       6.919  52.792  21.272  1.00  0.00              
ATOM     44  O   ALA    25       6.320  52.425  20.248  1.00  0.00              
ATOM     45  N   VAL    26       7.695  53.863  21.330  1.00  0.00              
ATOM     46  CA  VAL    26       8.094  54.566  20.139  1.00  0.00              
ATOM     47  C   VAL    26       8.972  53.636  19.341  1.00  0.00              
ATOM     48  O   VAL    26       8.715  53.452  18.171  1.00  0.00              
ATOM     49  N   ILE    27       9.969  52.987  19.954  1.00  0.00              
ATOM     50  CA  ILE    27      10.836  52.128  19.158  1.00  0.00              
ATOM     51  C   ILE    27      10.083  51.003  18.460  1.00  0.00              
ATOM     52  O   ILE    27      10.323  50.711  17.291  1.00  0.00              
ATOM     53  N   ARG    28       9.121  50.424  19.152  1.00  0.00              
ATOM     54  CA  ARG    28       8.351  49.336  18.590  1.00  0.00              
ATOM     55  C   ARG    28       7.566  49.767  17.381  1.00  0.00              
ATOM     56  O   ARG    28       7.368  48.978  16.498  1.00  0.00              
ATOM     57  N   CYS    29       7.148  51.021  17.344  1.00  0.00              
ATOM     58  CA  CYS    29       6.347  51.496  16.227  1.00  0.00              
ATOM     59  C   CYS    29       7.262  51.667  15.033  1.00  0.00              
ATOM     60  O   CYS    29       6.940  51.246  13.931  1.00  0.00              
ATOM     61  N   PHE    30       8.405  52.282  15.278  1.00  0.00              
ATOM     62  CA  PHE    30       9.426  52.448  14.271  1.00  0.00              
ATOM     63  C   PHE    30       9.919  51.125  13.641  1.00  0.00              
ATOM     64  O   PHE    30       9.978  51.021  12.430  1.00  0.00              
ATOM     65  N   ASP    31      10.253  50.116  14.442  1.00  0.00              
ATOM     66  CA  ASP    31      10.742  48.843  13.875  1.00  0.00              
ATOM     67  C   ASP    31       9.705  48.139  13.049  1.00  0.00              
ATOM     68  O   ASP    31      10.042  47.442  12.090  1.00  0.00              
ATOM     69  N   HIS    32       8.447  48.285  13.445  1.00  0.00              
ATOM     70  CA  HIS    32       7.344  47.665  12.710  1.00  0.00              
ATOM     71  C   HIS    32       7.042  48.443  11.415  1.00  0.00              
ATOM     72  O   HIS    32       6.835  47.847  10.380  1.00  0.00              
ATOM     73  N   ARG    33       7.090  49.769  11.458  1.00  0.00              
ATOM     74  CA  ARG    33       6.758  50.552  10.280  1.00  0.00              
ATOM     75  C   ARG    33       7.986  50.839   9.410  1.00  0.00              
ATOM     76  O   ARG    33       7.815  51.276   8.275  1.00  0.00              
ATOM     77  N   GLN    35       9.203  50.586   9.921  1.00  0.00              
ATOM     78  CA  GLN    35      10.477  50.910   9.215  1.00  0.00              
ATOM     79  C   GLN    35      10.835  52.408   9.064  1.00  0.00              
ATOM     80  O   GLN    35      11.950  52.804   9.429  1.00  0.00              
ATOM     81  N   ARG    36       9.940  53.210   8.464  1.00  0.00              
ATOM     82  CA  ARG    36      10.054  54.680   8.467  1.00  0.00              
ATOM     83  C   ARG    36       8.750  55.267   9.011  1.00  0.00              
ATOM     84  O   ARG    36       7.675  54.847   8.605  1.00  0.00              
ATOM     85  N   ARG    37       8.827  56.218   9.934  1.00  0.00              
ATOM     86  CA  ARG    37       7.626  56.855  10.424  1.00  0.00              
ATOM     87  C   ARG    37       7.871  58.297  10.824  1.00  0.00              
ATOM     88  O   ARG    37       8.857  58.574  11.512  1.00  0.00              
ATOM     89  N   THR    38       6.957  59.194  10.426  1.00  0.00              
ATOM     90  CA  THR    38       6.984  60.580  10.876  1.00  0.00              
ATOM     91  C   THR    38       6.597  60.766  12.339  1.00  0.00              
ATOM     92  O   THR    38       6.151  59.849  13.035  1.00  0.00              
ATOM     93  N   LEU    39       6.792  61.986  12.809  1.00  0.00              
ATOM     94  CA  LEU    39       6.349  62.353  14.118  1.00  0.00              
ATOM     95  C   LEU    39       4.843  62.092  14.225  1.00  0.00              
ATOM     96  O   LEU    39       4.383  61.384  15.142  1.00  0.00              
ATOM     97  N   SER    40       4.083  62.666  13.292  1.00  0.00              
ATOM     98  CA  SER    40       2.617  62.596  13.354  1.00  0.00              
ATOM     99  C   SER    40       2.081  61.172  13.294  1.00  0.00              
ATOM    100  O   SER    40       1.086  60.841  13.938  1.00  0.00              
ATOM    101  N   ASP    41       2.793  60.298  12.600  1.00  0.00              
ATOM    102  CA  ASP    41       2.458  58.871  12.614  1.00  0.00              
ATOM    103  C   ASP    41       2.630  58.363  14.024  1.00  0.00              
ATOM    104  O   ASP    41       1.702  57.776  14.567  1.00  0.00              
ATOM    105  N   VAL    42       3.802  58.614  14.621  1.00  0.00              
ATOM    106  CA  VAL    42       4.097  58.049  15.930  1.00  0.00              
ATOM    107  C   VAL    42       3.078  58.532  16.949  1.00  0.00              
ATOM    108  O   VAL    42       2.634  57.760  17.778  1.00  0.00              
ATOM    109  N   ALA    43       2.688  59.799  16.839  1.00  0.00              
ATOM    110  CA  ALA    43       1.723  60.407  17.739  1.00  0.00              
ATOM    111  C   ALA    43       0.430  59.668  17.566  1.00  0.00              
ATOM    112  O   ALA    43      -0.195  59.319  18.552  1.00  0.00              
ATOM    113  N   ARG    44       0.015  59.440  16.311  1.00  0.00              
ATOM    114  CA  ARG    44      -1.246  58.756  16.054  1.00  0.00              
ATOM    115  C   ARG    44      -1.339  57.365  16.713  1.00  0.00              
ATOM    116  O   ARG    44      -2.325  57.076  17.423  1.00  0.00              
ATOM    117  N   ALA    45      -0.332  56.513  16.486  1.00  0.00              
ATOM    118  CA  ALA    45      -0.336  55.143  16.985  1.00  0.00              
ATOM    119  C   ALA    45      -0.232  55.119  18.489  1.00  0.00              
ATOM    120  O   ALA    45      -0.964  54.399  19.177  1.00  0.00              
ATOM    121  N   THR    46       0.718  55.879  19.019  1.00  0.00              
ATOM    122  CA  THR    46       0.855  55.978  20.465  1.00  0.00              
ATOM    123  C   THR    46      -0.477  56.337  21.082  1.00  0.00              
ATOM    124  O   THR    46      -0.856  55.758  22.117  1.00  0.00              
ATOM    125  N   ASP    47      -2.931  58.234  26.567  1.00  0.00              
ATOM    126  CA  ASP    47      -3.424  59.579  26.690  1.00  0.00              
ATOM    127  C   ASP    47      -2.240  60.525  26.871  1.00  0.00              
ATOM    128  O   ASP    47      -2.219  61.345  27.777  1.00  0.00              
ATOM    129  N   LEU    48      -1.269  60.417  25.978  1.00  0.00              
ATOM    130  CA  LEU    48      -0.124  61.292  26.007  1.00  0.00              
ATOM    131  C   LEU    48      -0.343  62.410  25.009  1.00  0.00              
ATOM    132  O   LEU    48      -0.887  62.200  23.929  1.00  0.00              
ATOM    133  N   THR    49       0.074  63.603  25.396  1.00  0.00              
ATOM    134  CA  THR    49      -0.061  64.780  24.555  1.00  0.00              
ATOM    135  C   THR    49       1.007  64.698  23.458  1.00  0.00              
ATOM    136  O   THR    49       1.968  63.924  23.599  1.00  0.00              
ATOM    137  N   ARG    50       0.846  65.466  22.381  1.00  0.00              
ATOM    138  CA  ARG    50       1.843  65.528  21.305  1.00  0.00              
ATOM    139  C   ARG    50       3.236  65.937  21.795  1.00  0.00              
ATOM    140  O   ARG    50       4.226  65.365  21.332  1.00  0.00              
ATOM    141  N   ALA    51       3.308  66.901  22.714  1.00  0.00              
ATOM    142  CA  ALA    51       4.607  67.362  23.231  1.00  0.00              
ATOM    143  C   ALA    51       5.361  66.266  23.991  1.00  0.00              
ATOM    144  O   ALA    51       6.507  66.040  23.722  1.00  0.00              
ATOM    145  N   THR    52       4.700  65.583  24.915  1.00  0.00              
ATOM    146  CA  THR    52       5.253  64.385  25.559  1.00  0.00              
ATOM    147  C   THR    52       5.732  63.389  24.483  1.00  0.00              
ATOM    148  O   THR    52       6.740  62.762  24.662  1.00  0.00              
ATOM    149  N   ALA    53       5.033  63.234  23.356  1.00  0.00              
ATOM    150  CA  ALA    53       5.498  62.213  22.416  1.00  0.00              
ATOM    151  C   ALA    53       6.710  62.704  21.660  1.00  0.00              
ATOM    152  O   ALA    53       7.708  61.967  21.472  1.00  0.00              
ATOM    153  N   ARG    54       6.638  63.976  21.258  1.00  0.00              
ATOM    154  CA  ARG    54       7.639  64.585  20.413  1.00  0.00              
ATOM    155  C   ARG    54       8.947  64.626  21.162  1.00  0.00              
ATOM    156  O   ARG    54       9.987  64.594  20.569  1.00  0.00              
ATOM    157  N   ARG    55       8.885  64.698  22.473  1.00  0.00              
ATOM    158  CA  ARG    55      10.055  64.708  23.346  1.00  0.00              
ATOM    159  C   ARG    55      10.661  63.311  23.468  1.00  0.00              
ATOM    160  O   ARG    55      11.876  63.180  23.622  1.00  0.00              
ATOM    161  N   PHE    56       9.831  62.270  23.463  1.00  0.00              
ATOM    162  CA  PHE    56      10.368  60.934  23.338  1.00  0.00              
ATOM    163  C   PHE    56      11.156  60.758  22.013  1.00  0.00              
ATOM    164  O   PHE    56      12.237  60.180  22.036  1.00  0.00              
ATOM    165  N   LEU    57      10.623  61.266  20.884  1.00  0.00              
ATOM    166  CA  LEU    57      11.313  61.125  19.601  1.00  0.00              
ATOM    167  C   LEU    57      12.641  61.862  19.674  1.00  0.00              
ATOM    168  O   LEU    57      13.632  61.327  19.260  1.00  0.00              
ATOM    169  N   LEU    58      12.640  63.057  20.261  1.00  0.00              
ATOM    170  CA  LEU    58      13.782  63.951  20.335  1.00  0.00              
ATOM    171  C   LEU    58      14.936  63.313  21.119  1.00  0.00              
ATOM    172  O   LEU    58      16.078  63.269  20.637  1.00  0.00              
ATOM    173  N   THR    59      14.644  62.797  22.308  1.00  0.00              
ATOM    174  CA  THR    59      15.642  62.096  23.125  1.00  0.00              
ATOM    175  C   THR    59      16.211  60.868  22.375  1.00  0.00              
ATOM    176  O   THR    59      17.415  60.688  22.326  1.00  0.00              
ATOM    177  N   LEU    60      15.358  60.035  21.786  1.00  0.00              
ATOM    178  CA  LEU    60      15.852  58.848  21.113  1.00  0.00              
ATOM    179  C   LEU    60      16.712  59.199  19.893  1.00  0.00              
ATOM    180  O   LEU    60      17.664  58.507  19.550  1.00  0.00              
ATOM    181  N   VAL    61      16.354  60.270  19.228  1.00  0.00              
ATOM    182  CA  VAL    61      17.200  60.806  18.181  1.00  0.00              
ATOM    183  C   VAL    61      18.590  61.280  18.744  1.00  0.00              
ATOM    184  O   VAL    61      19.640  60.863  18.273  1.00  0.00              
ATOM    185  N   GLU    62      18.569  62.094  19.799  1.00  0.00              
ATOM    186  CA  GLU    62      19.809  62.570  20.454  1.00  0.00              
ATOM    187  C   GLU    62      20.665  61.441  21.058  1.00  0.00              
ATOM    188  O   GLU    62      21.889  61.520  21.050  1.00  0.00              
ATOM    189  N   LEU    63      20.018  60.409  21.580  1.00  0.00              
ATOM    190  CA  LEU    63      20.709  59.337  22.291  1.00  0.00              
ATOM    191  C   LEU    63      21.354  58.423  21.219  1.00  0.00              
ATOM    192  O   LEU    63      22.204  57.594  21.559  1.00  0.00              
ATOM    193  N   GLY    64      20.931  58.568  19.954  1.00  0.00              
ATOM    194  CA  GLY    64      21.511  57.847  18.816  1.00  0.00              
ATOM    195  C   GLY    64      20.721  56.632  18.390  1.00  0.00              
ATOM    196  O   GLY    64      21.179  55.839  17.573  1.00  0.00              
ATOM    197  N   TYR    65      19.538  56.451  18.979  1.00  0.00              
ATOM    198  CA  TYR    65      18.746  55.244  18.780  1.00  0.00              
ATOM    199  C   TYR    65      18.032  55.192  17.434  1.00  0.00              
ATOM    200  O   TYR    65      17.770  54.094  16.888  1.00  0.00              
ATOM    201  N   VAL    66      17.685  56.375  16.939  1.00  0.00              
ATOM    202  CA  VAL    66      16.970  56.530  15.677  1.00  0.00              
ATOM    203  C   VAL    66      17.567  57.730  14.891  1.00  0.00              
ATOM    204  O   VAL    66      18.272  58.584  15.467  1.00  0.00              
ATOM    205  N   ALA    67      17.304  57.779  13.586  1.00  0.00              
ATOM    206  CA  ALA    67      17.757  58.883  12.738  1.00  0.00              
ATOM    207  C   ALA    67      16.587  59.261  11.807  1.00  0.00              
ATOM    208  O   ALA    67      15.466  58.825  12.037  1.00  0.00              
ATOM    209  N   THR    68      16.824  60.040  10.755  1.00  0.00              
ATOM    210  CA  THR    68      15.724  60.571   9.950  1.00  0.00              
ATOM    211  C   THR    68      16.155  61.158   8.616  1.00  0.00              
ATOM    212  O   THR    68      17.185  61.816   8.538  1.00  0.00              
ATOM    213  N   ASP    69      11.707  63.235   3.600  1.00  0.00              
ATOM    214  CA  ASP    69      10.816  62.956   2.480  1.00  0.00              
ATOM    215  C   ASP    69       9.612  63.915   2.543  1.00  0.00              
ATOM    216  O   ASP    69       8.891  63.934   3.561  1.00  0.00              
ATOM    217  N   GLY    70       9.389  64.660   1.443  1.00  0.00              
ATOM    218  CA  GLY    70       8.536  65.864   1.424  1.00  0.00              
ATOM    219  C   GLY    70       9.341  67.045   2.006  1.00  0.00              
ATOM    220  O   GLY    70      10.504  67.247   1.622  1.00  0.00              
ATOM    221  N   SER    71       8.741  67.836   2.893  1.00  0.00              
ATOM    222  CA  SER    71       9.530  68.538   3.917  1.00  0.00              
ATOM    223  C   SER    71       9.335  67.819   5.257  1.00  0.00              
ATOM    224  O   SER    71       9.530  68.399   6.336  1.00  0.00              
ATOM    225  N   ALA    72       8.995  66.534   5.188  1.00  0.00              
ATOM    226  CA  ALA    72       8.551  65.811   6.374  1.00  0.00              
ATOM    227  C   ALA    72       9.586  64.796   6.825  1.00  0.00              
ATOM    228  O   ALA    72       9.947  63.896   6.090  1.00  0.00              
ATOM    229  N   PHE    73      10.062  64.945   8.048  1.00  0.00              
ATOM    230  CA  PHE    73      11.067  64.029   8.584  1.00  0.00              
ATOM    231  C   PHE    73      10.441  62.648   8.813  1.00  0.00              
ATOM    232  O   PHE    73       9.331  62.569   9.361  1.00  0.00              
ATOM    233  N   TRP    74      11.157  61.591   8.386  1.00  0.00              
ATOM    234  CA  TRP    74      10.780  60.192   8.611  1.00  0.00              
ATOM    235  C   TRP    74      11.882  59.441   9.397  1.00  0.00              
ATOM    236  O   TRP    74      13.017  59.321   8.926  1.00  0.00              
END
