
#######################################################
#                                                     #
#                        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   37 (  182),  selected   37 , name T0306TS239_2_1
# Molecule2: number of CA atoms   95 (  694),  selected   95 , name T0306.pdb
# PARAMETERS: T0306TS239_2_1.T0306.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      M       1           -
LGA    -       -      K       2           -
LGA    -       -      L       3           -
LGA    -       -      A       4           -
LGA    -       -      V       5           -
LGA    -       -      V       6           -
LGA    -       -      T       7           -
LGA    -       -      G       8           -
LGA    -       -      Q       9           -
LGA    -       -      I      10           -
LGA    -       -      V      11           -
LGA    -       -      C      12           -
LGA    K       2      T      13           #
LGA    L       3      V      14           -
LGA    A       4      R      15           -
LGA    -       -      H      16           -
LGA    V       5      H      17          5.053
LGA    -       -      G      18           -
LGA    -       -      L      19           -
LGA    V       6      A      20          2.166
LGA    T       7      H      21          1.966
LGA    G       8      D      22          3.886
LGA    Q       9      K      23          1.876
LGA    I      10      L      24          1.618
LGA    V      11      L      25          2.000
LGA    C      12      M      26          2.731
LGA    T      13      V      27          1.860
LGA    V      14      E      28          2.154
LGA    R      15      M      29          2.147
LGA    H      16      I      30          1.896
LGA    H      17      D      31          1.733
LGA    -       -      P      32           -
LGA    G      18      Q      33          3.655
LGA    L      19      G      34          3.485
LGA    A      20      N      35           -
LGA    H      21      P      36           -
LGA    -       -      D      37           -
LGA    -       -      G      38           -
LGA    -       -      Q      39           -
LGA    -       -      C      40           -
LGA    -       -      A      41           -
LGA    -       -      V      42           -
LGA    -       -      A      43           -
LGA    -       -      I      44           -
LGA    -       -      D      45           -
LGA    -       -      N      46           -
LGA    -       -      I      47           -
LGA    -       -      G      48           -
LGA    D      22      A      49           #
LGA    K      23      -       -           -
LGA    L      24      -       -           -
LGA    L      25      G      50           #
LGA    M      26      T      51          2.065
LGA    V      27      G      52          3.081
LGA    E      28      E      53          4.065
LGA    M      29      W      54          3.068
LGA    I      30      V      55           #
LGA    D      31      -       -           -
LGA    P      32      -       -           -
LGA    Q      33      L      56          1.205
LGA    G      34      L      57          4.833
LGA    -       -      V      58           -
LGA    -       -      S      59           -
LGA    -       -      G      60           -
LGA    -       -      S      61           -
LGA    -       -      S      62           -
LGA    -       -      A      63           -
LGA    -       -      R      64           -
LGA    -       -      Q      65           -
LGA    -       -      A      66           -
LGA    -       -      H      67           -
LGA    -       -      K      68           -
LGA    -       -      S      69           -
LGA    -       -      E      70           -
LGA    -       -      T      71           -
LGA    -       -      S      72           -
LGA    -       -      P      73           -
LGA    -       -      V      74           -
LGA    -       -      D      75           -
LGA    -       -      L      76           -
LGA    N      35      C      77           #
LGA    P      36      V      78          2.499
LGA    D      37      I      79          4.095
LGA    -       -      G      80           -
LGA    -       -      I      81           -
LGA    -       -      V      82           -
LGA    -       -      D      83           -
LGA    -       -      E      84           -
LGA    -       -      V      85           -
LGA    -       -      V      86           -
LGA    -       -      S      87           -
LGA    -       -      G      88           -
LGA    -       -      G      89           -
LGA    -       -      Q      90           -
LGA    -       -      V      91           -
LGA    -       -      I      92           -
LGA    -       -      F      93           -
LGA    -       -      H      94           -
LGA    -       -      K      95           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   37   95    5.0     23    2.94     4.35     16.399     0.756

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.065678 * X  +   0.172684 * Y  +   0.982785 * Z  + -85.908852
  Y_new =  -0.526942 * X  +   0.830378 * Y  +  -0.181120 * Z  +  -0.829933
  Z_new =  -0.847359 * X  +  -0.529767 * Y  +   0.036457 * Z  + 187.498672 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.502088    1.639505  [ DEG:   -86.0633     93.9367 ]
  Theta =   1.010993    2.130600  [ DEG:    57.9256    122.0744 ]
  Phi   =  -1.694797    1.446796  [ DEG:   -97.1047     82.8953 ]
 
# 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: T0306TS239_2_1                                
REMARK     2: T0306.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0306TS239_2_1.T0306.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   37   95   5.0   23   2.94    4.35  16.399
REMARK  ---------------------------------------------------------- 
MOLECULE T0306TS239_2_1
REMARK PARENT number 1
PFRMAT TS
TARGET T0306
PARENT 1qk3_A
ATOM      1  N   MET     1      15.184  17.426  64.203  1.00  9.99
ATOM      2  CA  MET     1      15.535  17.682  62.812  1.00  9.99
ATOM      3  C   MET     1      16.931  17.138  62.513  1.00  9.99
ATOM      4  O   MET     1      17.737  17.839  61.903  1.00  9.99
ATOM      5  CB  MET     1      15.494  19.196  62.535  1.00  9.99
ATOM      6  N   LYS     2      17.217  15.913  62.954  1.00  9.99
ATOM      7  CA  LYS     2      18.505  15.260  62.831  1.00  9.99
ATOM      8  C   LYS     2      18.970  14.925  61.421  1.00  9.99
ATOM      9  O   LYS     2      20.124  14.504  61.247  1.00  9.99
ATOM     10  CB  LYS     2      18.529  13.978  63.681  1.00  9.99
ATOM     11  N   LEU     3      18.097  15.020  60.417  1.00  9.99
ATOM     12  CA  LEU     3      18.510  14.762  59.045  1.00  9.99
ATOM     13  C   LEU     3      18.666  16.062  58.255  1.00  9.99
ATOM     14  O   LEU     3      19.228  16.017  57.151  1.00  9.99
ATOM     15  CB  LEU     3      17.520  13.829  58.344  1.00  9.99
ATOM     16  N   ALA     4      18.189  17.184  58.777  1.00  9.99
ATOM     17  CA  ALA     4      18.212  18.436  58.034  1.00  9.99
ATOM     18  C   ALA     4      19.093  19.538  58.563  1.00  9.99
ATOM     19  O   ALA     4      18.986  20.685  58.104  1.00  9.99
ATOM     20  CB  ALA     4      16.755  18.943  57.918  1.00  9.99
ATOM     21  N   VAL     5      19.936  19.305  59.573  1.00  9.99
ATOM     22  CA  VAL     5      20.841  20.343  60.091  1.00  9.99
ATOM     23  C   VAL     5      22.242  19.747  60.286  1.00  9.99
ATOM     24  O   VAL     5      22.322  18.587  60.732  1.00  9.99
ATOM     25  CB  VAL     5      20.321  20.947  61.401  1.00  9.99
ATOM     26  N   VAL     6      23.308  20.429  59.936  1.00  9.99
ATOM     27  CA  VAL     6      24.678  19.943  60.106  1.00  9.99
ATOM     28  C   VAL     6      25.160  19.924  61.537  1.00  9.99
ATOM     29  O   VAL     6      24.998  20.878  62.298  1.00  9.99
ATOM     30  CB  VAL     6      25.481  20.921  59.248  1.00  9.99
ATOM     31  N   THR     7      25.691  18.789  62.041  1.00  9.99
ATOM     32  CA  THR     7      26.098  18.700  63.440  1.00  9.99
ATOM     33  C   THR     7      27.261  19.650  63.722  1.00  9.99
ATOM     34  O   THR     7      28.042  19.974  62.817  1.00  9.99
ATOM     35  CB  THR     7      26.480  17.244  63.644  1.00  9.99
ATOM     36  N   GLY     8      27.419  20.117  64.956  1.00  9.99
ATOM     37  CA  GLY     8      28.469  21.063  65.318  1.00  9.99
ATOM     38  C   GLY     8      29.871  20.492  65.172  1.00  9.99
ATOM     39  O   GLY     8      30.061  19.258  65.154  1.00  9.99
ATOM     40  N   GLN     9      30.847  21.396  65.056  1.00  9.99
ATOM     41  CA  GLN     9      32.252  21.020  64.955  1.00  9.99
ATOM     42  C   GLN     9      33.005  21.506  66.203  1.00  9.99
ATOM     43  O   GLN     9      32.745  22.575  66.777  1.00  9.99
ATOM     44  CB  GLN     9      32.914  21.765  63.752  1.00  9.99
ATOM     45  N   ILE    10      33.893  20.657  66.732  1.00  9.99
ATOM     46  CA  ILE    10      34.723  20.978  67.876  1.00  9.99
ATOM     47  C   ILE    10      36.179  21.289  67.438  1.00  9.99
ATOM     48  O   ILE    10      36.717  20.520  66.611  1.00  9.99
ATOM     49  CB  ILE    10      34.847  19.823  68.901  1.00  9.99
ATOM     50  N   VAL    11      36.692  22.373  67.976  1.00  9.99
ATOM     51  CA  VAL    11      38.105  22.724  67.700  1.00  9.99
ATOM     52  C   VAL    11      38.885  22.983  68.983  1.00  9.99
ATOM     53  O   VAL    11      38.348  23.393  70.021  1.00  9.99
ATOM     54  CB  VAL    11      38.134  24.007  66.858  1.00  9.99
ATOM     55  N   CYS    12      40.207  22.680  68.923  1.00  9.99
ATOM     56  CA  CYS    12      41.091  22.805  70.088  1.00  9.99
ATOM     57  C   CYS    12      42.168  23.857  69.811  1.00  9.99
ATOM     58  O   CYS    12      42.754  23.720  68.743  1.00  9.99
ATOM     59  CB  CYS    12      41.696  21.407  70.406  1.00  9.99
ATOM     60  N   THR    13      42.205  24.919  70.578  1.00  9.99
ATOM     61  CA  THR    13      43.076  26.063  70.197  1.00  9.99
ATOM     62  C   THR    13      43.892  26.593  71.351  1.00  9.99
ATOM     63  O   THR    13      43.457  26.560  72.524  1.00  9.99
ATOM     64  CB  THR    13      42.135  27.191  69.689  1.00  9.99
ATOM     65  N   VAL    14      45.125  27.049  71.042  1.00  9.99
ATOM     66  CA  VAL    14      45.962  27.707  72.036  1.00  9.99
ATOM     67  C   VAL    14      45.636  29.218  72.053  1.00  9.99
ATOM     68  O   VAL    14      45.287  29.794  71.053  1.00  9.99
ATOM     69  CB  VAL    14      47.453  27.591  71.719  1.00  9.99
ATOM     70  N   ARG    15      45.847  29.880  73.196  1.00  9.99
ATOM     71  CA  ARG    15      45.588  31.328  73.277  1.00  9.99
ATOM     72  C   ARG    15      46.472  32.187  72.416  1.00  9.99
ATOM     73  O   ARG    15      46.128  33.240  71.858  1.00  9.99
ATOM     74  CB  ARG    15      45.766  31.732  74.754  1.00  9.99
ATOM     75  N   HIS    16      47.763  31.824  72.371  1.00  9.99
ATOM     76  CA  HIS    16      48.738  32.616  71.646  1.00  9.99
ATOM     77  C   HIS    16      49.260  31.870  70.427  1.00  9.99
ATOM     78  O   HIS    16      49.068  30.657  70.330  1.00  9.99
ATOM     79  CB  HIS    16      49.876  33.055  72.583  1.00  9.99
ATOM     80  N   HIS    17      49.935  32.613  69.562  1.00  9.99
ATOM     81  CA  HIS    17      50.475  32.015  68.351  1.00  9.99
ATOM     82  C   HIS    17      51.845  31.393  68.600  1.00  9.99
ATOM     83  O   HIS    17      52.895  32.019  68.470  1.00  9.99
ATOM     84  CB  HIS    17      50.499  32.976  67.180  1.00  9.99
ATOM     85  N   GLY    18      51.859  30.116  68.940  1.00  9.99
ATOM     86  CA  GLY    18      53.099  29.365  69.140  1.00  9.99
ATOM     87  C   GLY    18      53.416  28.554  67.883  1.00  9.99
ATOM     88  O   GLY    18      52.522  28.466  67.036  1.00  9.99
ATOM     89  N   LEU    19      54.596  27.937  67.836  1.00  9.99
ATOM     90  CA  LEU    19      54.865  27.069  66.660  1.00  9.99
ATOM     91  C   LEU    19      53.974  25.829  66.727  1.00  9.99
ATOM     92  O   LEU    19      53.892  25.312  67.841  1.00  9.99
ATOM     93  CB  LEU    19      56.350  26.756  66.605  1.00  9.99
ATOM     94  N   ALA    20      53.292  25.445  65.645  1.00  9.99
ATOM     95  CA  ALA    20      52.416  24.264  65.696  1.00  9.99
ATOM     96  C   ALA    20      53.211  23.046  66.183  1.00  9.99
ATOM     97  O   ALA    20      54.415  22.878  65.949  1.00  9.99
ATOM     98  CB  ALA    20      51.712  24.031  64.352  1.00  9.99
ATOM     99  N   HIS    21      52.586  22.215  67.009  1.00  9.99
ATOM    100  CA  HIS    21      53.116  20.958  67.512  1.00  9.99
ATOM    101  C   HIS    21      52.310  19.775  66.980  1.00  9.99
ATOM    102  O   HIS    21      52.232  18.710  67.612  1.00  9.99
ATOM    103  CB  HIS    21      53.131  20.910  69.058  1.00  9.99
ATOM    104  N   ASP    22      51.684  19.935  65.815  1.00  9.99
ATOM    105  CA  ASP    22      50.843  18.871  65.271  1.00  9.99
ATOM    106  C   ASP    22      51.650  17.759  64.599  1.00  9.99
ATOM    107  O   ASP    22      52.793  17.976  64.212  1.00  9.99
ATOM    108  CB  ASP    22      49.852  19.491  64.276  1.00  9.99
ATOM    109  N   LYS    23      51.026  16.607  64.440  1.00  9.99
ATOM    110  CA  LYS    23      51.622  15.467  63.734  1.00  9.99
ATOM    111  C   LYS    23      50.521  14.495  63.343  1.00  9.99
ATOM    112  O   LYS    23      49.417  14.513  63.955  1.00  9.99
ATOM    113  CB  LYS    23      52.769  14.834  64.498  1.00  9.99
ATOM    114  N   LEU    24      50.779  13.671  62.341  1.00  9.99
ATOM    115  CA  LEU    24      49.801  12.702  61.827  1.00  9.99
ATOM    116  C   LEU    24      49.278  11.746  62.922  1.00  9.99
ATOM    117  O   LEU    24      50.116  11.218  63.642  1.00  9.99
ATOM    118  CB  LEU    24      50.429  11.812  60.725  1.00  9.99
ATOM    119  N   LEU    25      47.775  12.643  65.651  1.00  9.99
ATOM    120  CA  LEU    25      47.641  13.310  66.938  1.00  9.99
ATOM    121  C   LEU    25      46.563  14.395  66.880  1.00  9.99
ATOM    122  O   LEU    25      46.132  14.813  65.759  1.00  9.99
ATOM    123  CB  LEU    25      48.976  13.897  67.423  1.00  9.99
ATOM    124  N   MET    26      46.121  14.867  68.041  1.00  9.99
ATOM    125  CA  MET    26      45.046  15.887  68.067  1.00  9.99
ATOM    126  C   MET    26      45.411  17.156  67.302  1.00  9.99
ATOM    127  O   MET    26      46.568  17.619  67.452  1.00  9.99
ATOM    128  CB  MET    26      44.731  16.285  69.531  1.00  9.99
ATOM    129  N   VAL    27      44.483  17.645  66.475  1.00  9.99
ATOM    130  CA  VAL    27      44.777  18.929  65.805  1.00  9.99
ATOM    131  C   VAL    27      44.586  20.053  66.819  1.00  9.99
ATOM    132  O   VAL    27      43.489  20.299  67.346  1.00  9.99
ATOM    133  CB  VAL    27      43.841  19.160  64.604  1.00  9.99
ATOM    134  N   GLU    28      45.682  20.782  67.085  1.00  9.99
ATOM    135  CA  GLU    28      45.644  21.940  67.981  1.00  9.99
ATOM    136  C   GLU    28      46.033  23.187  67.169  1.00  9.99
ATOM    137  O   GLU    28      47.165  23.246  66.706  1.00  9.99
ATOM    138  CB  GLU    28      46.587  21.825  69.181  1.00  9.99
ATOM    139  N   MET    29      45.141  24.161  67.082  1.00  9.99
ATOM    140  CA  MET    29      45.479  25.380  66.318  1.00  9.99
ATOM    141  C   MET    29      46.165  26.393  67.205  1.00  9.99
ATOM    142  O   MET    29      45.846  26.649  68.393  1.00  9.99
ATOM    143  CB  MET    29      44.192  25.974  65.707  1.00  9.99
ATOM    144  N   ILE    30      47.180  27.079  66.635  1.00  9.99
ATOM    145  CA  ILE    30      47.860  28.144  67.372  1.00  9.99
ATOM    146  C   ILE    30      48.129  29.380  66.489  1.00  9.99
ATOM    147  O   ILE    30      47.431  30.391  66.566  1.00  9.99
ATOM    148  CB  ILE    30      49.130  27.661  68.050  1.00  9.99
ATOM    149  N   ASP    31      49.065  29.224  65.575  1.00  9.99
ATOM    150  CA  ASP    31      49.498  30.257  64.658  1.00  9.99
ATOM    151  C   ASP    31      48.485  30.557  63.561  1.00  9.99
ATOM    152  O   ASP    31      48.305  31.739  63.241  1.00  9.99
ATOM    153  CB  ASP    31      50.846  29.876  64.012  1.00  9.99
ATOM    154  N   PRO    32      47.754  29.568  63.073  1.00  9.99
ATOM    155  CA  PRO    32      46.808  29.816  61.979  1.00  9.99
ATOM    156  C   PRO    32      45.354  29.587  62.346  1.00  9.99
ATOM    157  O   PRO    32      44.938  28.461  62.642  1.00  9.99
ATOM    158  CB  PRO    32      47.243  28.935  60.794  1.00  9.99
ATOM    159  N   GLN    33      44.577  30.659  62.367  1.00  9.99
ATOM    160  CA  GLN    33      43.142  30.594  62.698  1.00  9.99
ATOM    161  C   GLN    33      42.265  30.780  61.478  1.00  9.99
ATOM    162  O   GLN    33      41.030  30.945  61.520  1.00  9.99
ATOM    163  CB  GLN    33      42.890  31.690  63.742  1.00  9.99
ATOM    164  N   GLY    34      42.834  30.623  60.261  1.00  9.99
ATOM    165  CA  GLY    34      42.111  30.830  59.023  1.00  9.99
ATOM    166  C   GLY    34      40.923  29.933  58.731  1.00  9.99
ATOM    167  O   GLY    34      40.009  30.387  58.036  1.00  9.99
ATOM    168  N   ASN    35      40.833  28.722  59.305  1.00  9.99
ATOM    169  CA  ASN    35      39.641  27.889  59.105  1.00  9.99
ATOM    170  C   ASN    35      38.360  28.566  59.609  1.00  9.99
ATOM    171  O   ASN    35      37.246  28.165  59.206  1.00  9.99
ATOM    172  CB  ASN    35      39.830  26.559  59.884  1.00  9.99
ATOM    173  N   PRO    36      38.443  29.589  60.486  1.00  9.99
ATOM    174  CA  PRO    36      37.261  30.243  60.998  1.00  9.99
ATOM    175  C   PRO    36      36.702  31.370  60.119  1.00  9.99
ATOM    176  O   PRO    36      35.679  31.959  60.445  1.00  9.99
ATOM    177  CB  PRO    36      37.491  30.768  62.436  1.00  9.99
ATOM    178  N   ASP    37      37.335  31.654  58.981  1.00  9.99
ATOM    179  CA  ASP    37      36.802  32.719  58.085  1.00  9.99
ATOM    180  C   ASP    37      35.376  32.409  57.677  1.00  9.99
ATOM    181  O   ASP    37      35.107  31.269  57.288  1.00  9.99
ATOM    182  CB  ASP    37      37.725  32.871  56.873  1.00  9.99
TER
END
