
#######################################################
#                                                     #
#                        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   43 (  208),  selected   43 , name T0306TS239_4_1
# Molecule2: number of CA atoms   95 (  694),  selected   95 , name T0306.pdb
# PARAMETERS: T0306TS239_4_1.T0306.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    Q      39      M       1           -
LGA    C      40      -       -           -
LGA    A      41      -       -           -
LGA    V      42      -       -           -
LGA    A      43      -       -           -
LGA    I      44      -       -           -
LGA    I      47      K       2           #
LGA    G      48      L       3           #
LGA    A      49      A       4           #
LGA    G      50      V       5          3.664
LGA    T      51      V       6          1.547
LGA    G      52      T       7          3.445
LGA    G      60      -       -           -
LGA    S      61      G       8          2.836
LGA    S      62      Q       9          3.317
LGA    A      63      -       -           -
LGA    R      64      -       -           -
LGA    Q      65      -       -           -
LGA    A      66      I      10          1.878
LGA    H      67      V      11          3.084
LGA    K      68      C      12          1.922
LGA    S      69      T      13          2.178
LGA    E      70      V      14          2.411
LGA    T      71      R      15          2.595
LGA    C      77      H      16          5.021
LGA    -       -      H      17           -
LGA    -       -      G      18           -
LGA    V      78      L      19          3.156
LGA    -       -      A      20           -
LGA    -       -      H      21           -
LGA    -       -      D      22           -
LGA    -       -      K      23           -
LGA    I      79      L      24          4.505
LGA    -       -      L      25           -
LGA    -       -      M      26           -
LGA    -       -      V      27           -
LGA    -       -      E      28           -
LGA    -       -      M      29           -
LGA    -       -      I      30           -
LGA    -       -      D      31           -
LGA    -       -      P      32           -
LGA    -       -      Q      33           -
LGA    -       -      G      34           -
LGA    -       -      N      35           -
LGA    -       -      P      36           -
LGA    -       -      D      37           -
LGA    -       -      G      38           -
LGA    -       -      Q      39           -
LGA    -       -      C      40           -
LGA    -       -      A      41           -
LGA    -       -      V      42           -
LGA    -       -      A      43           -
LGA    G      80      I      44          2.447
LGA    I      81      D      45          3.174
LGA    -       -      N      46           -
LGA    -       -      I      47           -
LGA    -       -      G      48           -
LGA    -       -      A      49           -
LGA    -       -      G      50           -
LGA    -       -      T      51           -
LGA    -       -      G      52           -
LGA    -       -      E      53           -
LGA    -       -      W      54           -
LGA    -       -      V      55           -
LGA    -       -      L      56           -
LGA    -       -      L      57           -
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    V      82      C      77          1.798
LGA    D      83      V      78          2.136
LGA    E      84      I      79          3.123
LGA    V      85      G      80          2.721
LGA    V      86      I      81          2.256
LGA    S      87      -       -           -
LGA    G      88      -       -           -
LGA    G      89      -       -           -
LGA    Q      90      V      82          3.735
LGA    V      91      -       -           -
LGA    I      92      D      83           #
LGA    F      93      E      84          4.591
LGA    H      94      V      85          4.484
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    K      95      H      94          3.534
LGA    -       -      K      95           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   43   95    5.0     25    3.16     0.00     15.976     0.766

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.000774 * X  +   0.789105 * Y  +  -0.614258 * Z  +  14.954723
  Y_new =   0.099980 * X  +   0.611119 * Y  +   0.785199 * Z  + -18.920860
  Z_new =   0.994989 * X  +  -0.062021 * Y  +  -0.078422 * Z  +  75.478882 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.472448    0.669144  [ DEG:  -141.6608     38.3392 ]
  Theta =  -1.470646   -1.670947  [ DEG:   -84.2618    -95.7382 ]
  Phi   =   1.563058   -1.578534  [ DEG:    89.5566    -90.4434 ]
 
# 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_4_1                                
REMARK     2: T0306.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0306TS239_4_1.T0306.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   43   95   5.0   25   3.16    0.00  15.976
REMARK  ---------------------------------------------------------- 
MOLECULE T0306TS239_4_1
REMARK PARENT number 1
PFRMAT TS
TARGET T0306
PARENT 1xdi_A
ATOM      1  N   GLN    39      19.037  25.151  71.407  1.00  9.99
ATOM      2  CA  GLN    39      20.374  24.577  71.079  1.00  9.99
ATOM      3  C   GLN    39      21.484  25.582  71.380  1.00  9.99
ATOM      4  O   GLN    39      21.370  26.789  71.075  1.00  9.99
ATOM      5  CB  GLN    39      20.495  24.153  69.567  1.00  9.99
ATOM      6  N   CYS    40      22.571  25.090  71.970  1.00  9.99
ATOM      7  CA  CYS    40      23.650  25.976  72.277  1.00  9.99
ATOM      8  C   CYS    40      24.612  26.095  71.051  1.00  9.99
ATOM      9  O   CYS    40      25.042  25.097  70.429  1.00  9.99
ATOM     10  CB  CYS    40      24.279  25.565  73.678  1.00  9.99
ATOM     11  N   ALA    41      24.868  27.342  70.662  1.00  9.99
ATOM     12  CA  ALA    41      25.745  27.674  69.520  1.00  9.99
ATOM     13  C   ALA    41      27.220  27.848  69.849  1.00  9.99
ATOM     14  O   ALA    41      27.575  28.840  70.477  1.00  9.99
ATOM     15  CB  ALA    41      25.329  28.990  68.863  1.00  9.99
ATOM     16  N   VAL    42      28.071  26.923  69.420  1.00  9.99
ATOM     17  CA  VAL    42      29.494  27.079  69.678  1.00  9.99
ATOM     18  C   VAL    42      30.246  27.600  68.429  1.00  9.99
ATOM     19  O   VAL    42      30.150  26.999  67.348  1.00  9.99
ATOM     20  CB  VAL    42      30.134  25.741  70.095  1.00  9.99
ATOM     21  N   ALA    43      30.951  28.727  68.568  1.00  9.99
ATOM     22  CA  ALA    43      31.771  29.244  67.476  1.00  9.99
ATOM     23  C   ALA    43      33.231  29.327  67.990  1.00  9.99
ATOM     24  O   ALA    43      33.536  29.935  69.019  1.00  9.99
ATOM     25  CB  ALA    43      31.295  30.615  66.956  1.00  9.99
ATOM     26  N   ILE    44      34.106  28.655  67.260  1.00  9.99
ATOM     27  CA  ILE    44      35.531  28.540  67.530  1.00  9.99
ATOM     28  C   ILE    44      36.347  29.355  66.486  1.00  9.99
ATOM     29  O   ILE    44      36.222  29.163  65.270  1.00  9.99
ATOM     30  CB  ILE    44      35.933  27.027  67.437  1.00  9.99
ATOM     31  N   ILE    47      37.151  30.299  66.965  1.00  9.99
ATOM     32  CA  ILE    47      37.986  31.068  66.065  1.00  9.99
ATOM     33  C   ILE    47      39.287  30.315  66.069  1.00  9.99
ATOM     34  O   ILE    47      39.917  30.153  67.125  1.00  9.99
ATOM     35  CB  ILE    47      38.203  32.471  66.566  1.00  9.99
ATOM     36  N   GLY    48      39.659  29.793  64.901  1.00  9.99
ATOM     37  CA  GLY    48      40.914  29.076  64.775  1.00  9.99
ATOM     38  C   GLY    48      40.789  27.584  64.771  1.00  9.99
ATOM     39  O   GLY    48      40.133  27.042  65.638  1.00  9.99
ATOM     40  N   ALA    49      41.458  26.905  63.848  1.00  9.99
ATOM     41  CA  ALA    49      41.315  25.468  63.803  1.00  9.99
ATOM     42  C   ALA    49      42.496  24.563  64.067  1.00  9.99
ATOM     43  O   ALA    49      42.554  23.467  63.459  1.00  9.99
ATOM     44  CB  ALA    49      40.735  25.136  62.418  1.00  9.99
ATOM     45  N   GLY    50      43.428  24.949  64.940  1.00  9.99
ATOM     46  CA  GLY    50      44.540  24.052  65.206  1.00  9.99
ATOM     47  C   GLY    50      44.166  23.177  66.384  1.00  9.99
ATOM     48  O   GLY    50      42.999  23.178  66.763  1.00  9.99
ATOM     49  N   THR    51      45.113  22.436  67.015  1.00  9.99
ATOM     50  CA  THR    51      44.756  21.586  68.159  1.00  9.99
ATOM     51  C   THR    51      43.810  22.291  69.131  1.00  9.99
ATOM     52  O   THR    51      42.777  21.735  69.489  1.00  9.99
ATOM     53  CB  THR    51      46.099  21.281  68.807  1.00  9.99
ATOM     54  N   GLY    52      44.123  23.501  69.573  1.00  9.99
ATOM     55  CA  GLY    52      43.176  24.119  70.490  1.00  9.99
ATOM     56  C   GLY    52      41.738  24.029  69.934  1.00  9.99
ATOM     57  O   GLY    52      40.865  23.398  70.530  1.00  9.99
ATOM     58  N   GLY    60      41.514  24.585  68.751  1.00  9.99
ATOM     59  CA  GLY    60      40.174  24.632  68.218  1.00  9.99
ATOM     60  C   GLY    60      39.529  23.371  67.711  1.00  9.99
ATOM     61  O   GLY    60      38.390  23.010  68.075  1.00  9.99
ATOM     62  N   SER    61      39.970  20.547  68.389  1.00  9.99
ATOM     63  CA  SER    61      39.856  19.400  69.161  1.00  9.99
ATOM     64  C   SER    61      39.139  19.679  70.348  1.00  9.99
ATOM     65  O   SER    61      39.046  18.941  71.331  1.00  9.99
ATOM     66  CB  SER    61      41.203  18.875  69.474  1.00  9.99
ATOM     67  N   SER    62      38.471  20.845  70.263  1.00  9.99
ATOM     68  CA  SER    62      37.568  21.390  71.268  1.00  9.99
ATOM     69  C   SER    62      36.228  21.148  70.571  1.00  9.99
ATOM     70  O   SER    62      35.211  20.828  71.197  1.00  9.99
ATOM     71  CB  SER    62      37.790  22.889  71.467  1.00  9.99
ATOM     72  N   ALA    63      36.253  21.288  69.245  1.00  9.99
ATOM     73  CA  ALA    63      35.075  21.079  68.416  1.00  9.99
ATOM     74  C   ALA    63      34.759  19.603  68.421  1.00  9.99
ATOM     75  O   ALA    63      33.614  19.191  68.545  1.00  9.99
ATOM     76  CB  ALA    63      35.341  21.550  66.990  1.00  9.99
ATOM     77  N   ARG    64      35.809  18.811  68.284  1.00  9.99
ATOM     78  CA  ARG    64      35.677  17.367  68.250  1.00  9.99
ATOM     79  C   ARG    64      34.948  16.894  69.476  1.00  9.99
ATOM     80  O   ARG    64      34.007  16.144  69.357  1.00  9.99
ATOM     81  CB  ARG    64      37.053  16.712  68.193  1.00  9.99
ATOM     82  N   GLN    65      35.401  17.348  70.651  1.00  9.99
ATOM     83  CA  GLN    65      34.815  16.982  71.948  1.00  9.99
ATOM     84  C   GLN    65      33.420  17.495  72.014  1.00  9.99
ATOM     85  O   GLN    65      32.560  16.818  72.530  1.00  9.99
ATOM     86  CB  GLN    65      35.638  17.571  73.194  1.00  9.99
ATOM     87  N   ALA    66      33.209  18.696  71.486  1.00  9.99
ATOM     88  CA  ALA    66      31.893  19.339  71.484  1.00  9.99
ATOM     89  C   ALA    66      30.851  18.552  70.758  1.00  9.99
ATOM     90  O   ALA    66      29.864  18.141  71.339  1.00  9.99
ATOM     91  CB  ALA    66      31.985  20.706  70.863  1.00  9.99
ATOM     92  N   HIS    67      30.414  14.497  71.988  1.00  9.99
ATOM     93  CA  HIS    67      29.665  14.199  73.192  1.00  9.99
ATOM     94  C   HIS    67      28.292  14.844  73.306  1.00  9.99
ATOM     95  O   HIS    67      27.512  14.476  74.188  1.00  9.99
ATOM     96  CB  HIS    67      30.489  14.557  74.428  1.00  9.99
ATOM     97  N   LYS    68      27.979  15.796  72.431  1.00  9.99
ATOM     98  CA  LYS    68      26.682  16.468  72.497  1.00  9.99
ATOM     99  C   LYS    68      26.075  16.714  71.145  1.00  9.99
ATOM    100  O   LYS    68      25.590  17.814  70.883  1.00  9.99
ATOM    101  CB  LYS    68      26.819  17.791  73.256  1.00  9.99
ATOM    102  N   SER    69      26.060  15.681  70.277  1.00  9.99
ATOM    103  CA  SER    69      25.516  15.754  68.917  1.00  9.99
ATOM    104  C   SER    69      24.183  16.489  68.763  1.00  9.99
ATOM    105  O   SER    69      24.014  17.277  67.827  1.00  9.99
ATOM    106  CB  SER    69      25.420  14.288  68.509  1.00  9.99
ATOM    107  N   GLU    70      23.238  16.271  69.673  1.00  9.99
ATOM    108  CA  GLU    70      21.950  16.942  69.503  1.00  9.99
ATOM    109  C   GLU    70      21.605  18.213  70.266  1.00  9.99
ATOM    110  O   GLU    70      20.540  18.815  70.035  1.00  9.99
ATOM    111  CB  GLU    70      20.817  15.921  69.659  1.00  9.99
ATOM    112  N   THR    71      22.492  18.649  71.151  1.00  9.99
ATOM    113  CA  THR    71      22.199  19.849  71.914  1.00  9.99
ATOM    114  C   THR    71      23.084  20.990  71.435  1.00  9.99
ATOM    115  O   THR    71      22.900  22.128  71.841  1.00  9.99
ATOM    116  CB  THR    71      22.346  19.575  73.437  1.00  9.99
ATOM    117  N   CYS    77      24.008  20.699  70.518  1.00  9.99
ATOM    118  CA  CYS    77      24.902  21.746  69.996  1.00  9.99
ATOM    119  C   CYS    77      25.012  21.961  68.486  1.00  9.99
ATOM    120  O   CYS    77      24.690  21.110  67.664  1.00  9.99
ATOM    121  CB  CYS    77      26.366  21.528  70.410  1.00  9.99
ATOM    122  N   VAL    78      25.529  23.127  68.136  1.00  9.99
ATOM    123  CA  VAL    78      25.798  23.441  66.741  1.00  9.99
ATOM    124  C   VAL    78      27.211  24.060  66.742  1.00  9.99
ATOM    125  O   VAL    78      27.417  25.225  67.114  1.00  9.99
ATOM    126  CB  VAL    78      24.773  24.419  66.177  1.00  9.99
ATOM    127  N   ILE    79      28.189  23.276  66.322  1.00  9.99
ATOM    128  CA  ILE    79      29.574  23.740  66.335  1.00  9.99
ATOM    129  C   ILE    79      30.062  24.308  64.991  1.00  9.99
ATOM    130  O   ILE    79      30.063  23.653  63.967  1.00  9.99
ATOM    131  CB  ILE    79      30.525  22.552  66.771  1.00  9.99
ATOM    132  N   GLY    80      30.517  25.535  65.020  1.00  9.99
ATOM    133  CA  GLY    80      31.072  26.174  63.832  1.00  9.99
ATOM    134  C   GLY    80      32.537  26.478  64.093  1.00  9.99
ATOM    135  O   GLY    80      32.831  27.055  65.113  1.00  9.99
ATOM    136  N   ILE    81      33.453  26.070  63.212  1.00  9.99
ATOM    137  CA  ILE    81      34.909  26.364  63.356  1.00  9.99
ATOM    138  C   ILE    81      35.234  27.322  62.219  1.00  9.99
ATOM    139  O   ILE    81      35.055  26.962  61.076  1.00  9.99
ATOM    140  CB  ILE    81      35.827  25.102  63.154  1.00  9.99
ATOM    141  N   VAL    82      35.668  28.539  62.526  1.00  9.99
ATOM    142  CA  VAL    82      36.057  29.562  61.527  1.00  9.99
ATOM    143  C   VAL    82      37.580  29.620  61.645  1.00  9.99
ATOM    144  O   VAL    82      38.122  30.109  62.642  1.00  9.99
ATOM    145  CB  VAL    82      35.530  30.943  61.904  1.00  9.99
ATOM    146  N   ASP    83      38.257  29.069  60.646  1.00  9.99
ATOM    147  CA  ASP    83      39.713  29.006  60.591  1.00  9.99
ATOM    148  C   ASP    83      40.158  29.542  59.235  1.00  9.99
ATOM    149  O   ASP    83      39.532  29.260  58.202  1.00  9.99
ATOM    150  CB  ASP    83      40.160  27.551  60.775  1.00  9.99
ATOM    151  N   GLU    84      41.241  30.303  59.211  1.00  9.99
ATOM    152  CA  GLU    84      41.646  30.863  57.932  1.00  9.99
ATOM    153  C   GLU    84      42.669  30.036  57.194  1.00  9.99
ATOM    154  O   GLU    84      42.599  29.928  55.982  1.00  9.99
ATOM    155  CB  GLU    84      42.131  32.316  58.081  1.00  9.99
ATOM    156  N   VAL    85      43.579  29.375  57.883  1.00  9.99
ATOM    157  CA  VAL    85      44.561  28.639  57.097  1.00  9.99
ATOM    158  C   VAL    85      44.302  27.177  56.818  1.00  9.99
ATOM    159  O   VAL    85      44.980  26.577  56.002  1.00  9.99
ATOM    160  CB  VAL    85      45.969  28.811  57.697  1.00  9.99
ATOM    161  N   VAL    86      43.329  26.586  57.481  1.00  9.99
ATOM    162  CA  VAL    86      43.089  25.184  57.218  1.00  9.99
ATOM    163  C   VAL    86      43.308  24.367  58.458  1.00  9.99
ATOM    164  O   VAL    86      44.359  24.492  59.129  1.00  9.99
ATOM    165  CB  VAL    86      44.003  24.712  56.074  1.00  9.99
ATOM    166  N   SER    87      42.283  23.544  58.732  1.00  9.99
ATOM    167  CA  SER    87      42.178  22.632  59.865  1.00  9.99
ATOM    168  C   SER    87      43.454  21.878  60.196  1.00  9.99
ATOM    169  O   SER    87      43.986  21.119  59.369  1.00  9.99
ATOM    170  CB  SER    87      41.066  21.628  59.652  1.00  9.99
ATOM    171  N   GLY    88      43.920  22.088  61.428  1.00  9.99
ATOM    172  CA  GLY    88      45.136  21.472  61.891  1.00  9.99
ATOM    173  C   GLY    88      45.986  22.635  62.303  1.00  9.99
ATOM    174  O   GLY    88      46.959  22.493  63.066  1.00  9.99
ATOM    175  N   GLY    89      45.609  23.801  61.783  1.00  9.99
ATOM    176  CA  GLY    89      46.339  25.026  62.064  1.00  9.99
ATOM    177  C   GLY    89      47.833  24.954  61.810  1.00  9.99
ATOM    178  O   GLY    89      48.325  24.029  61.196  1.00  9.99
ATOM    179  N   GLN    90      48.558  25.941  62.303  1.00  9.99
ATOM    180  CA  GLN    90      50.008  25.999  62.129  1.00  9.99
ATOM    181  C   GLN    90      50.741  24.830  62.703  1.00  9.99
ATOM    182  O   GLN    90      51.764  24.480  62.183  1.00  9.99
ATOM    183  CB  GLN    90      50.584  27.303  62.717  1.00  9.99
ATOM    184  N   VAL    91      50.230  24.262  63.786  1.00  9.99
ATOM    185  CA  VAL    91      50.860  23.093  64.409  1.00  9.99
ATOM    186  C   VAL    91      51.051  21.972  63.390  1.00  9.99
ATOM    187  O   VAL    91      52.110  21.304  63.357  1.00  9.99
ATOM    188  CB  VAL    91      50.011  22.559  65.553  1.00  9.99
ATOM    189  N   ILE    92      50.012  21.759  62.581  1.00  9.99
ATOM    190  CA  ILE    92      49.989  20.716  61.567  1.00  9.99
ATOM    191  C   ILE    92      50.502  21.134  60.187  1.00  9.99
ATOM    192  O   ILE    92      51.177  20.374  59.493  1.00  9.99
ATOM    193  CB  ILE    92      48.545  20.213  61.408  1.00  9.99
ATOM    194  N   PHE    93      50.146  22.336  59.775  1.00  9.99
ATOM    195  CA  PHE    93      50.538  22.836  58.459  1.00  9.99
ATOM    196  C   PHE    93      51.878  23.598  58.386  1.00  9.99
ATOM    197  O   PHE    93      52.490  23.716  57.315  1.00  9.99
ATOM    198  CB  PHE    93      49.426  23.756  57.911  1.00  9.99
ATOM    199  N   HIS    94      52.359  24.063  59.534  1.00  9.99
ATOM    200  CA  HIS    94      53.523  24.904  59.516  1.00  9.99
ATOM    201  C   HIS    94      54.716  24.593  60.372  1.00  9.99
ATOM    202  O   HIS    94      55.854  24.470  59.887  1.00  9.99
ATOM    203  CB  HIS    94      53.060  26.308  59.858  1.00  9.99
ATOM    204  N   LYS    95      54.440  24.526  61.665  1.00  9.99
ATOM    205  CA  LYS    95      55.467  24.319  62.634  1.00  9.99
ATOM    206  C   LYS    95      55.735  22.874  63.081  1.00  9.99
ATOM    207  O   LYS    95      56.718  22.217  62.673  1.00  9.99
ATOM    208  CB  LYS    95      55.135  25.170  63.846  1.00  9.99
TER
END
