
#######################################################
#                                                     #
#                        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   42 (  203),  selected   42 , name T0306TS239_5_2
# Molecule2: number of CA atoms   95 (  694),  selected   95 , name T0306.pdb
# PARAMETERS: T0306TS239_5_2.T0306.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      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    -       -      T      13           -
LGA    -       -      V      14           -
LGA    -       -      R      15           -
LGA    -       -      H      16           -
LGA    -       -      H      17           -
LGA    C      40      G      18          2.050
LGA    A      41      L      19          0.866
LGA    V      42      A      20           #
LGA    -       -      H      21           -
LGA    -       -      D      22           -
LGA    -       -      K      23           -
LGA    -       -      L      24           -
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    -       -      I      44           -
LGA    A      43      D      45          3.946
LGA    I      44      N      46          2.475
LGA    I      47      I      47          0.299
LGA    G      48      G      48          4.403
LGA    -       -      A      49           -
LGA    -       -      G      50           -
LGA    -       -      T      51           -
LGA    -       -      G      52           -
LGA    -       -      E      53           -
LGA    A      49      W      54           #
LGA    G      50      V      55          3.355
LGA    T      51      L      56          2.611
LGA    G      52      -       -           -
LGA    G      60      -       -           -
LGA    S      61      L      57          2.319
LGA    S      62      -       -           -
LGA    A      63      V      58          4.467
LGA    R      64      S      59          2.903
LGA    Q      65      G      60          3.769
LGA    -       -      S      61           -
LGA    -       -      S      62           -
LGA    A      66      A      63          1.938
LGA    H      67      R      64           #
LGA    K      68      Q      65           -
LGA    S      69      A      66           -
LGA    E      70      H      67           -
LGA    -       -      K      68           -
LGA    -       -      S      69           -
LGA    -       -      E      70           -
LGA    T      71      T      71           #
LGA    -       -      S      72           -
LGA    -       -      P      73           -
LGA    -       -      V      74           -
LGA    -       -      D      75           -
LGA    S      72      L      76           #
LGA    P      73      -       -           -
LGA    I      79      -       -           -
LGA    G      80      C      77           #
LGA    I      81      V      78           #
LGA    -       -      I      79           -
LGA    V      82      G      80           #
LGA    D      83      -       -           -
LGA    E      84      -       -           -
LGA    V      85      -       -           -
LGA    V      86      -       -           -
LGA    S      87      -       -           -
LGA    G      88      I      81          5.631
LGA    G      89      V      82          2.959
LGA    Q      90      D      83          2.824
LGA    V      91      E      84          3.400
LGA    I      92      V      85          2.893
LGA    -       -      V      86           -
LGA    -       -      S      87           -
LGA    -       -      G      88           -
LGA    -       -      G      89           -
LGA    -       -      Q      90           -
LGA    -       -      V      91           -
LGA    -       -      I      92           -
LGA    F      93      F      93          2.307
LGA    H      94      H      94          4.230
LGA    K      95      K      95           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   42   95    5.0     20    3.22    25.00     12.978     0.602

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.389089 * X  +  -0.811946 * Y  +   0.435148 * Z  +  57.507927
  Y_new =   0.917235 * X  +   0.385245 * Y  +  -0.101319 * Z  + -119.020599
  Z_new =  -0.085373 * X  +   0.438555 * Y  +   0.894640 * Z  +   4.183117 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.455779   -2.685814  [ DEG:    26.1142   -153.8858 ]
  Theta =   0.085477    3.056115  [ DEG:     4.8975    175.1025 ]
  Phi   =   1.169605   -1.971987  [ DEG:    67.0135   -112.9865 ]
 
# 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_5_2                                
REMARK     2: T0306.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0306TS239_5_2.T0306.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   42   95   5.0   20   3.22   25.00  12.978
REMARK  ---------------------------------------------------------- 
MOLECULE T0306TS239_5_2
REMARK PARENT number 2
PFRMAT TS
TARGET T0306
PARENT 1b37_B
ATOM      1  N   CYS    40      22.762  28.342  64.573  1.00  9.99
ATOM      2  CA  CYS    40      23.128  27.602  63.334  1.00  9.99
ATOM      3  C   CYS    40      24.390  26.877  63.694  1.00  9.99
ATOM      4  O   CYS    40      25.163  27.373  64.522  1.00  9.99
ATOM      5  CB  CYS    40      23.485  28.670  62.293  1.00  9.99
ATOM      6  N   ALA    41      24.568  25.687  63.131  1.00  9.99
ATOM      7  CA  ALA    41      25.777  24.950  63.438  1.00  9.99
ATOM      8  C   ALA    41      26.540  25.119  62.143  1.00  9.99
ATOM      9  O   ALA    41      25.956  25.021  61.041  1.00  9.99
ATOM     10  CB  ALA    41      25.417  23.483  63.633  1.00  9.99
ATOM     11  N   VAL    42      27.841  25.333  62.323  1.00  9.99
ATOM     12  CA  VAL    42      28.729  25.517  61.182  1.00  9.99
ATOM     13  C   VAL    42      29.936  24.587  61.301  1.00  9.99
ATOM     14  O   VAL    42      30.588  24.523  62.359  1.00  9.99
ATOM     15  CB  VAL    42      29.252  26.980  61.088  1.00  9.99
ATOM     16  N   ALA    43      30.222  23.865  60.216  1.00  9.99
ATOM     17  CA  ALA    43      31.401  23.021  60.221  1.00  9.99
ATOM     18  C   ALA    43      32.449  23.777  59.419  1.00  9.99
ATOM     19  O   ALA    43      32.137  24.281  58.341  1.00  9.99
ATOM     20  CB  ALA    43      31.128  21.666  59.565  1.00  9.99
ATOM     21  N   ILE    44      33.661  23.861  59.965  1.00  9.99
ATOM     22  CA  ILE    44      34.776  24.522  59.284  1.00  9.99
ATOM     23  C   ILE    44      35.774  23.409  58.970  1.00  9.99
ATOM     24  O   ILE    44      36.246  22.670  59.851  1.00  9.99
ATOM     25  CB  ILE    44      35.491  25.528  60.205  1.00  9.99
ATOM     26  N   ILE    47      36.091  23.279  57.691  1.00  9.99
ATOM     27  CA  ILE    47      37.067  22.270  57.237  1.00  9.99
ATOM     28  C   ILE    47      38.455  22.916  57.200  1.00  9.99
ATOM     29  O   ILE    47      38.730  23.795  56.394  1.00  9.99
ATOM     30  CB  ILE    47      36.707  21.793  55.816  1.00  9.99
ATOM     31  N   GLY    48      39.348  22.434  58.044  1.00  9.99
ATOM     32  CA  GLY    48      40.718  22.918  58.112  1.00  9.99
ATOM     33  C   GLY    48      41.017  23.894  59.255  1.00  9.99
ATOM     34  O   GLY    48      40.238  24.815  59.485  1.00  9.99
ATOM     35  N   ALA    49      42.121  23.708  59.982  1.00  9.99
ATOM     36  CA  ALA    49      42.459  24.640  61.071  1.00  9.99
ATOM     37  C   ALA    49      43.766  25.376  60.842  1.00  9.99
ATOM     38  O   ALA    49      44.661  25.435  61.701  1.00  9.99
ATOM     39  CB  ALA    49      42.458  23.979  62.451  1.00  9.99
ATOM     40  N   GLY    50      43.916  25.865  59.623  1.00  9.99
ATOM     41  CA  GLY    50      45.082  26.679  59.284  1.00  9.99
ATOM     42  C   GLY    50      44.594  28.093  59.665  1.00  9.99
ATOM     43  O   GLY    50      43.550  28.322  60.289  1.00  9.99
ATOM     44  N   THR    51      45.347  29.085  59.218  1.00  9.99
ATOM     45  CA  THR    51      44.997  30.453  59.576  1.00  9.99
ATOM     46  C   THR    51      43.592  30.924  59.214  1.00  9.99
ATOM     47  O   THR    51      42.880  31.579  59.991  1.00  9.99
ATOM     48  CB  THR    51      46.072  31.405  59.004  1.00  9.99
ATOM     49  N   GLY    52      43.160  30.607  58.006  1.00  9.99
ATOM     50  CA  GLY    52      41.861  31.136  57.608  1.00  9.99
ATOM     51  C   GLY    52      40.742  30.415  58.317  1.00  9.99
ATOM     52  O   GLY    52      39.726  31.032  58.627  1.00  9.99
ATOM     53  N   GLY    60      40.896  29.105  58.519  1.00  9.99
ATOM     54  CA  GLY    60      39.786  28.411  59.191  1.00  9.99
ATOM     55  C   GLY    60      39.664  28.877  60.650  1.00  9.99
ATOM     56  O   GLY    60      38.569  29.120  61.201  1.00  9.99
ATOM     57  N   SER    61      40.679  31.605  61.750  1.00  9.99
ATOM     58  CA  SER    61      40.232  32.975  61.742  1.00  9.99
ATOM     59  C   SER    61      38.732  33.060  61.460  1.00  9.99
ATOM     60  O   SER    61      38.009  33.885  62.025  1.00  9.99
ATOM     61  CB  SER    61      41.056  33.684  60.664  1.00  9.99
ATOM     62  N   SER    62      38.229  32.211  60.572  1.00  9.99
ATOM     63  CA  SER    62      36.801  32.269  60.238  1.00  9.99
ATOM     64  C   SER    62      35.982  31.851  61.461  1.00  9.99
ATOM     65  O   SER    62      35.008  32.485  61.845  1.00  9.99
ATOM     66  CB  SER    62      36.536  31.286  59.073  1.00  9.99
ATOM     67  N   ALA    63      36.408  30.776  62.090  1.00  9.99
ATOM     68  CA  ALA    63      35.661  30.304  63.232  1.00  9.99
ATOM     69  C   ALA    63      35.684  31.379  64.301  1.00  9.99
ATOM     70  O   ALA    63      34.683  31.554  65.025  1.00  9.99
ATOM     71  CB  ALA    63      36.249  28.998  63.761  1.00  9.99
ATOM     72  N   ARG    64      36.808  32.087  64.411  1.00  9.99
ATOM     73  CA  ARG    64      36.869  33.135  65.456  1.00  9.99
ATOM     74  C   ARG    64      35.805  34.233  65.237  1.00  9.99
ATOM     75  O   ARG    64      35.077  34.681  66.141  1.00  9.99
ATOM     76  CB  ARG    64      38.267  33.764  65.532  1.00  9.99
ATOM     77  N   GLN    65      35.661  34.625  63.982  1.00  9.99
ATOM     78  CA  GLN    65      34.709  35.654  63.639  1.00  9.99
ATOM     79  C   GLN    65      33.293  35.180  63.832  1.00  9.99
ATOM     80  O   GLN    65      32.456  35.991  64.223  1.00  9.99
ATOM     81  CB  GLN    65      34.917  36.072  62.193  1.00  9.99
ATOM     82  N   ALA    66      33.015  33.913  63.518  1.00  9.99
ATOM     83  CA  ALA    66      31.651  33.406  63.699  1.00  9.99
ATOM     84  C   ALA    66      31.389  33.442  65.201  1.00  9.99
ATOM     85  O   ALA    66      30.369  33.864  65.702  1.00  9.99
ATOM     86  CB  ALA    66      31.579  31.923  63.328  1.00  9.99
ATOM     87  N   HIS    67      32.355  32.977  65.950  1.00  9.99
ATOM     88  CA  HIS    67      32.142  32.942  67.379  1.00  9.99
ATOM     89  C   HIS    67      31.806  34.343  67.796  1.00  9.99
ATOM     90  O   HIS    67      30.813  34.569  68.464  1.00  9.99
ATOM     91  CB  HIS    67      33.452  32.603  68.054  1.00  9.99
ATOM     92  N   LYS    68      32.629  35.287  67.370  1.00  9.99
ATOM     93  CA  LYS    68      32.340  36.667  67.721  1.00  9.99
ATOM     94  C   LYS    68      30.928  37.120  67.369  1.00  9.99
ATOM     95  O   LYS    68      30.383  37.968  68.065  1.00  9.99
ATOM     96  CB  LYS    68      33.367  37.629  67.127  1.00  9.99
ATOM     97  N   SER    69      30.325  36.610  66.304  1.00  9.99
ATOM     98  CA  SER    69      28.973  37.063  65.953  1.00  9.99
ATOM     99  C   SER    69      27.988  36.254  66.748  1.00  9.99
ATOM    100  O   SER    69      26.797  36.228  66.460  1.00  9.99
ATOM    101  CB  SER    69      28.696  36.834  64.488  1.00  9.99
ATOM    102  N   GLU    70      28.510  35.522  67.712  1.00  9.99
ATOM    103  CA  GLU    70      27.643  34.674  68.507  1.00  9.99
ATOM    104  C   GLU    70      27.352  33.289  67.921  1.00  9.99
ATOM    105  O   GLU    70      26.508  32.609  68.494  1.00  9.99
ATOM    106  CB  GLU    70      26.332  35.442  68.745  1.00  9.99
ATOM    107  N   THR    71      27.980  32.872  66.816  1.00  9.99
ATOM    108  CA  THR    71      27.716  31.548  66.253  1.00  9.99
ATOM    109  C   THR    71      28.793  30.691  66.902  1.00  9.99
ATOM    110  O   THR    71      29.948  30.705  66.502  1.00  9.99
ATOM    111  CB  THR    71      27.818  31.589  64.748  1.00  9.99
ATOM    112  N   SER    72      28.413  30.007  67.972  1.00  9.99
ATOM    113  CA  SER    72      29.336  29.210  68.734  1.00  9.99
ATOM    114  C   SER    72      29.134  27.707  68.582  1.00  9.99
ATOM    115  O   SER    72      29.913  26.937  69.152  1.00  9.99
ATOM    116  CB  SER    72      29.270  29.678  70.181  1.00  9.99
ATOM    117  N   PRO    73      28.103  27.313  67.835  1.00  9.99
ATOM    118  CA  PRO    73      27.854  25.878  67.606  1.00  9.99
ATOM    119  C   PRO    73      28.717  25.534  66.386  1.00  9.99
ATOM    120  O   PRO    73      28.222  25.455  65.245  1.00  9.99
ATOM    121  CB  PRO    73      26.402  25.601  67.222  1.00  9.99
ATOM    122  N   ILE    79      30.004  25.398  66.686  1.00  9.99
ATOM    123  CA  ILE    79      31.031  25.181  65.674  1.00  9.99
ATOM    124  C   ILE    79      31.698  23.822  65.738  1.00  9.99
ATOM    125  O   ILE    79      31.876  23.310  66.841  1.00  9.99
ATOM    126  CB  ILE    79      32.154  26.212  65.992  1.00  9.99
ATOM    127  N   GLY    80      32.196  23.320  64.607  1.00  9.99
ATOM    128  CA  GLY    80      32.947  22.066  64.676  1.00  9.99
ATOM    129  C   GLY    80      34.043  22.272  63.641  1.00  9.99
ATOM    130  O   GLY    80      33.743  22.440  62.457  1.00  9.99
ATOM    131  N   ILE    81      35.281  22.325  64.112  1.00  9.99
ATOM    132  CA  ILE    81      36.446  22.493  63.233  1.00  9.99
ATOM    133  C   ILE    81      37.114  21.143  63.038  1.00  9.99
ATOM    134  O   ILE    81      37.588  20.523  64.029  1.00  9.99
ATOM    135  CB  ILE    81      37.462  23.436  63.841  1.00  9.99
ATOM    136  N   VAL    82      37.098  20.712  61.769  1.00  9.99
ATOM    137  CA  VAL    82      37.689  19.420  61.371  1.00  9.99
ATOM    138  C   VAL    82      39.051  19.651  60.703  1.00  9.99
ATOM    139  O   VAL    82      39.103  20.263  59.649  1.00  9.99
ATOM    140  CB  VAL    82      36.748  18.594  60.485  1.00  9.99
ATOM    141  N   ASP    83      40.131  19.216  61.352  1.00  9.99
ATOM    142  CA  ASP    83      41.487  19.350  60.840  1.00  9.99
ATOM    143  C   ASP    83      42.076  17.987  60.476  1.00  9.99
ATOM    144  O   ASP    83      42.105  17.041  61.283  1.00  9.99
ATOM    145  CB  ASP    83      42.374  20.064  61.859  1.00  9.99
ATOM    146  N   GLU    84      42.566  17.927  59.241  1.00  9.99
ATOM    147  CA  GLU    84      43.148  16.707  58.730  1.00  9.99
ATOM    148  C   GLU    84      44.342  16.206  59.542  1.00  9.99
ATOM    149  O   GLU    84      44.414  15.006  59.836  1.00  9.99
ATOM    150  CB  GLU    84      43.556  16.943  57.278  1.00  9.99
ATOM    151  N   VAL    85      45.299  17.091  59.855  1.00  9.99
ATOM    152  CA  VAL    85      46.507  16.656  60.559  1.00  9.99
ATOM    153  C   VAL    85      46.309  16.598  62.064  1.00  9.99
ATOM    154  O   VAL    85      45.225  16.909  62.578  1.00  9.99
ATOM    155  CB  VAL    85      47.738  17.580  60.300  1.00  9.99
ATOM    156  N   VAL    86      47.408  16.230  62.720  1.00  9.99
ATOM    157  CA  VAL    86      47.409  16.148  64.155  1.00  9.99
ATOM    158  C   VAL    86      47.716  17.500  64.764  1.00  9.99
ATOM    159  O   VAL    86      48.023  17.566  65.942  1.00  9.99
ATOM    160  CB  VAL    86      48.404  15.111  64.627  1.00  9.99
ATOM    161  N   SER    87      47.646  18.584  63.994  1.00  9.99
ATOM    162  CA  SER    87      47.913  19.894  64.605  1.00  9.99
ATOM    163  C   SER    87      47.205  21.039  63.874  1.00  9.99
ATOM    164  O   SER    87      46.697  20.864  62.774  1.00  9.99
ATOM    165  CB  SER    87      49.416  20.152  64.588  1.00  9.99
ATOM    166  N   GLY    88      47.157  22.232  64.460  1.00  9.99
ATOM    167  CA  GLY    88      46.550  23.356  63.737  1.00  9.99
ATOM    168  C   GLY    88      47.671  24.216  63.129  1.00  9.99
ATOM    169  O   GLY    88      48.840  24.039  63.492  1.00  9.99
ATOM    170  N   GLY    89      47.343  25.203  62.292  1.00  9.99
ATOM    171  CA  GLY    89      48.385  26.059  61.717  1.00  9.99
ATOM    172  C   GLY    89      48.614  25.894  60.200  1.00  9.99
ATOM    173  O   GLY    89      48.983  26.857  59.511  1.00  9.99
ATOM    174  N   GLN    90      48.399  24.683  59.680  1.00  9.99
ATOM    175  CA  GLN    90      48.514  24.447  58.230  1.00  9.99
ATOM    176  C   GLN    90      49.844  24.836  57.636  1.00  9.99
ATOM    177  O   GLN    90      50.900  24.325  58.024  1.00  9.99
ATOM    178  CB  GLN    90      47.382  25.202  57.514  1.00  9.99
ATOM    179  N   VAL    91      49.765  25.747  56.676  1.00  9.99
ATOM    180  CA  VAL    91      50.988  26.191  56.010  1.00  9.99
ATOM    181  C   VAL    91      51.953  27.032  56.871  1.00  9.99
ATOM    182  O   VAL    91      53.025  27.485  56.401  1.00  9.99
ATOM    183  CB  VAL    91      50.706  26.835  54.650  1.00  9.99
ATOM    184  N   ILE    92      51.575  27.279  58.121  1.00  9.99
ATOM    185  CA  ILE    92      52.524  27.968  59.039  1.00  9.99
ATOM    186  C   ILE    92      52.913  26.764  59.895  1.00  9.99
ATOM    187  O   ILE    92      52.082  26.304  60.692  1.00  9.99
ATOM    188  CB  ILE    92      51.845  29.064  59.901  1.00  9.99
ATOM    189  N   PHE    93      54.130  26.245  59.746  1.00  9.99
ATOM    190  CA  PHE    93      54.476  25.059  60.536  1.00  9.99
ATOM    191  C   PHE    93      55.985  24.896  60.578  1.00  9.99
ATOM    192  O   PHE    93      56.691  24.941  59.529  1.00  9.99
ATOM    193  CB  PHE    93      53.895  23.824  59.851  1.00  9.99
ATOM    194  N   HIS    94      56.473  24.740  61.813  1.00  9.99
ATOM    195  CA  HIS    94      57.922  24.600  62.038  1.00  9.99
ATOM    196  C   HIS    94      58.334  23.149  62.155  1.00  9.99
ATOM    197  O   HIS    94      57.524  22.247  62.343  1.00  9.99
ATOM    198  CB  HIS    94      58.367  25.312  63.329  1.00  9.99
ATOM    199  N   LYS    95      59.633  22.939  62.102  1.00  9.99
ATOM    200  CA  LYS    95      60.122  21.602  62.269  1.00  9.99
ATOM    201  C   LYS    95      61.553  21.625  62.835  1.00  9.99
ATOM    202  O   LYS    95      62.287  22.595  62.684  1.00  9.99
ATOM    203  CB  LYS    95      60.089  20.802  60.952  1.00  9.99
TER
END
