
#######################################################
#                                                     #
#                        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   36 (  180),  selected   36 , name T0372TS239_5_2-D1
# Molecule2: number of CA atoms  126 ( 1027),  selected  126 , name T0372_D1.pdb
# PARAMETERS: T0372TS239_5_2-D1.T0372_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      M       1           -
LGA    -       -      I       2           -
LGA    -       -      P       3           -
LGA    -       -      F       4           -
LGA    -       -      K       5           -
LGA    -       -      D       6           -
LGA    -       -      I       7           -
LGA    -       -      T       8           -
LGA    -       -      L       9           -
LGA    -       -      A      10           -
LGA    -       -      D      11           -
LGA    -       -      R      12           -
LGA    -       -      D      13           -
LGA    -       -      T      14           -
LGA    -       -      I      15           -
LGA    -       -      T      16           -
LGA    -       -      A      17           -
LGA    -       -      F      18           -
LGA    -       -      T      19           -
LGA    -       -      M      20           -
LGA    -       -      K      21           -
LGA    -       -      S      22           -
LGA    -       -      D      23           -
LGA    -       -      R      24           -
LGA    -       -      R      25           -
LGA    -       -      N      26           -
LGA    -       -      C      27           -
LGA    -       -      D      28           -
LGA    -       -      L      29           -
LGA    -       -      S      30           -
LGA    -       -      F      31           -
LGA    -       -      S      32           -
LGA    -       -      N      33           -
LGA    -       -      L      34           -
LGA    -       -      C      35           -
LGA    -       -      S      36           -
LGA    -       -      W      37           -
LGA    -       -      R      38           -
LGA    -       -      F      39           -
LGA    -       -      L      40           -
LGA    -       -      Y      41           -
LGA    -       -      D      42           -
LGA    -       -      T      43           -
LGA    -       -      Q      44           -
LGA    -       -      F      45           -
LGA    -       -      A      46           -
LGA    -       -      V      47           -
LGA    -       -      I      48           -
LGA    -       -      D      49           -
LGA    -       -      D      50           -
LGA    -       -      F      51           -
LGA    -       -      L      52           -
LGA    -       -      V      53           -
LGA    -       -      F      54           -
LGA    -       -      K      55           -
LGA    -       -      F      56           -
LGA    -       -      W      57           -
LGA    -       -      A      58           -
LGA    -       -      G      59           -
LGA    -       -      E      60           -
LGA    -       -      Q      61           -
LGA    -       -      L      62           -
LGA    -       -      A      63           -
LGA    -       -      Y      64           -
LGA    -       -      M      65           -
LGA    -       -      M      66           -
LGA    -       -      P      67           -
LGA    -       -      V      68           -
LGA    -       -      G      69           -
LGA    -       -      N      70           -
LGA    -       -      G      71           -
LGA    -       -      D      72           -
LGA    -       -      L      73           -
LGA    -       -      K      74           -
LGA    -       -      A      75           -
LGA    -       -      V      76           -
LGA    -       -      L      77           -
LGA    -       -      R      78           -
LGA    M       1      K      79          3.699
LGA    I       2      L      80          2.271
LGA    P       3      I      81          2.067
LGA    T       8      E      82          0.691
LGA    L       9      D      83          2.116
LGA    A      10      A      84          3.504
LGA    D      11      D      85          3.308
LGA    R      12      K      86          3.063
LGA    -       -      E      87           -
LGA    D      13      K      88          2.215
LGA    T      14      H      89          2.345
LGA    I      15      N      90          2.594
LGA    T      16      F      91          2.853
LGA    A      17      C      92          2.471
LGA    F      18      M      93          0.451
LGA    T      19      L      94          2.887
LGA    -       -      G      95           -
LGA    M      20      V      96          2.438
LGA    K      21      C      97          2.841
LGA    -       -      S      98           -
LGA    -       -      N      99           -
LGA    -       -      M     100           -
LGA    S      22      R     101          1.331
LGA    D      23      A     102          4.636
LGA    -       -      D     103           -
LGA    R      24      L     104          4.987
LGA    R      25      E     105          2.909
LGA    N      26      A     106          3.522
LGA    C      27      I     107          3.210
LGA    D      28      L     108          4.345
LGA    L      29      P     109          2.920
LGA    S      30      E     110           #
LGA    F      31      R     111          4.863
LGA    S      32      F     112          1.648
LGA    N      33      I     113           -
LGA    L      34      F     114           -
LGA    C      35      T     115           -
LGA    S      36      E     116           -
LGA    W      37      D     117           -
LGA    -       -      K     290           -
LGA    -       -      Y     291           -
LGA    -       -      M     292           -
LGA    R      38      A     293          3.937
LGA    F      39      C     294          3.711
LGA    L      40      L     295           -
LGA    -       -      K     296           -
LGA    -       -      D     297           -
LGA    -       -      H     298           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   36  126    5.0     29    3.09     6.90     14.247     0.909

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.750009 * X  +  -0.630335 * Y  +   0.200410 * Z  +  67.464806
  Y_new =   0.638498 * X  +   0.769063 * Y  +   0.029378 * Z  +   8.967187
  Z_new =  -0.172646 * X  +   0.105927 * Y  +   0.979272 * Z  + -37.277790 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.107751   -3.033842  [ DEG:     6.1737   -173.8264 ]
  Theta =   0.173515    2.968078  [ DEG:     9.9417    170.0583 ]
  Phi   =   0.705260   -2.436333  [ DEG:    40.4084   -139.5916 ]
 
# 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: T0372TS239_5_2-D1                             
REMARK     2: T0372_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0372TS239_5_2-D1.T0372_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   36  126   5.0   29   3.09    6.90  14.247
REMARK  ---------------------------------------------------------- 
MOLECULE T0372TS239_5_2-D1
REMARK PARENT number 2
PFRMAT TS
TARGET T0372
PARENT 1k6i_A
ATOM      1  N   MET     1      37.472  56.813  -5.893  1.00  9.99
ATOM      2  CA  MET     1      38.097  55.524  -6.208  1.00  9.99
ATOM      3  C   MET     1      37.121  54.591  -6.921  1.00  9.99
ATOM      4  O   MET     1      37.475  53.974  -7.921  1.00  9.99
ATOM      5  CB  MET     1      38.602  54.838  -4.923  1.00  9.99
ATOM      6  N   ILE     2      35.898  54.494  -6.395  1.00  9.99
ATOM      7  CA  ILE     2      34.869  53.615  -6.952  1.00  9.99
ATOM      8  C   ILE     2      34.609  53.863  -8.439  1.00  9.99
ATOM      9  O   ILE     2      34.623  52.914  -9.236  1.00  9.99
ATOM     10  CB  ILE     2      33.540  53.726  -6.127  1.00  9.99
ATOM     11  N   PRO     3      34.395  55.130  -8.805  1.00  9.99
ATOM     12  CA  PRO     3      34.138  55.507 -10.201  1.00  9.99
ATOM     13  C   PRO     3      35.236  55.055 -11.144  1.00  9.99
ATOM     14  O   PRO     3      34.942  54.378 -12.131  1.00  9.99
ATOM     15  CB  PRO     3      33.944  57.028 -10.357  1.00  9.99
ATOM     16  N   THR     8      36.495  55.412 -10.860  1.00  9.99
ATOM     17  CA  THR     8      37.586  55.014 -11.756  1.00  9.99
ATOM     18  C   THR     8      37.887  53.524 -11.732  1.00  9.99
ATOM     19  O   THR     8      38.159  52.921 -12.776  1.00  9.99
ATOM     20  CB  THR     8      38.921  55.794 -11.498  1.00  9.99
ATOM     21  N   LEU     9      37.838  52.925 -10.545  1.00  9.99
ATOM     22  CA  LEU     9      38.108  51.501 -10.417  1.00  9.99
ATOM     23  C   LEU     9      37.121  50.709 -11.265  1.00  9.99
ATOM     24  O   LEU     9      37.513  49.810 -11.999  1.00  9.99
ATOM     25  CB  LEU     9      38.005  51.078  -8.961  1.00  9.99
ATOM     26  N   ALA    10      35.840  51.050 -11.161  1.00  9.99
ATOM     27  CA  ALA    10      34.824  50.346 -11.940  1.00  9.99
ATOM     28  C   ALA    10      35.017  50.573 -13.462  1.00  9.99
ATOM     29  O   ALA    10      34.870  49.653 -14.261  1.00  9.99
ATOM     30  CB  ALA    10      33.427  50.795 -11.501  1.00  9.99
ATOM     31  N   ASP    11      35.359  51.793 -13.859  1.00  9.99
ATOM     32  CA  ASP    11      35.567  52.079 -15.275  1.00  9.99
ATOM     33  C   ASP    11      36.721  51.260 -15.891  1.00  9.99
ATOM     34  O   ASP    11      36.700  50.961 -17.086  1.00  9.99
ATOM     35  CB  ASP    11      35.802  53.572 -15.462  1.00  9.99
ATOM     36  N   ARG    12      37.720  50.882 -15.089  1.00  9.99
ATOM     37  CA  ARG    12      38.828  50.098 -15.614  1.00  9.99
ATOM     38  C   ARG    12      38.656  48.602 -15.392  1.00  9.99
ATOM     39  O   ARG    12      39.574  47.821 -15.654  1.00  9.99
ATOM     40  CB  ARG    12      40.222  50.580 -15.064  1.00  9.99
ATOM     41  N   ASP    13      37.483  48.194 -14.911  1.00  9.99
ATOM     42  CA  ASP    13      37.247  46.771 -14.743  1.00  9.99
ATOM     43  C   ASP    13      37.276  46.158 -13.357  1.00  9.99
ATOM     44  O   ASP    13      37.131  44.943 -13.208  1.00  9.99
ATOM     45  CB  ASP    13      38.271  46.046 -15.633  1.00  9.99
ATOM     46  N   THR    14      37.478  46.964 -12.329  1.00  9.99
ATOM     47  CA  THR    14      37.481  46.390 -10.992  1.00  9.99
ATOM     48  C   THR    14      36.043  46.170 -10.562  1.00  9.99
ATOM     49  O   THR    14      35.168  46.976 -10.886  1.00  9.99
ATOM     50  CB  THR    14      38.093  47.350  -9.959  1.00  9.99
ATOM     51  N   ILE    15      35.802  45.077  -9.841  1.00  9.99
ATOM     52  CA  ILE    15      34.488  44.856  -9.254  1.00  9.99
ATOM     53  C   ILE    15      34.698  45.511  -7.889  1.00  9.99
ATOM     54  O   ILE    15      35.795  45.448  -7.320  1.00  9.99
ATOM     55  CB  ILE    15      34.189  43.369  -9.104  1.00  9.99
ATOM     56  N   THR    16      33.665  46.178  -7.393  1.00  9.99
ATOM     57  CA  THR    16      33.757  46.865  -6.115  1.00  9.99
ATOM     58  C   THR    16      32.639  46.441  -5.157  1.00  9.99
ATOM     59  O   THR    16      31.473  46.314  -5.557  1.00  9.99
ATOM     60  CB  THR    16      33.667  48.413  -6.322  1.00  9.99
ATOM     61  N   ALA    17      33.016  46.204  -3.911  1.00  9.99
ATOM     62  CA  ALA    17      32.065  45.868  -2.847  1.00  9.99
ATOM     63  C   ALA    17      32.161  47.088  -1.918  1.00  9.99
ATOM     64  O   ALA    17      33.213  47.328  -1.308  1.00  9.99
ATOM     65  CB  ALA    17      32.496  44.583  -2.132  1.00  9.99
ATOM     66  N   PHE    18      31.080  47.860  -1.830  1.00  9.99
ATOM     67  CA  PHE    18      31.094  49.076  -1.030  1.00  9.99
ATOM     68  C   PHE    18      29.980  49.206   0.014  1.00  9.99
ATOM     69  O   PHE    18      28.799  49.017  -0.272  1.00  9.99
ATOM     70  CB  PHE    18      31.072  50.318  -1.977  1.00  9.99
ATOM     71  N   THR    19      30.365  49.542   1.234  1.00  9.99
ATOM     72  CA  THR    19      29.380  49.739   2.284  1.00  9.99
ATOM     73  C   THR    19      28.866  51.188   2.252  1.00  9.99
ATOM     74  O   THR    19      29.635  52.106   1.976  1.00  9.99
ATOM     75  CB  THR    19      30.027  49.446   3.636  1.00  9.99
ATOM     76  N   MET    20      27.570  51.386   2.491  1.00  9.99
ATOM     77  CA  MET    20      26.976  52.729   2.572  1.00  9.99
ATOM     78  C   MET    20      26.027  52.698   3.765  1.00  9.99
ATOM     79  O   MET    20      25.424  51.660   4.046  1.00  9.99
ATOM     80  CB  MET    20      26.138  53.138   1.316  1.00  9.99
ATOM     81  N   LYS    21      25.884  53.813   4.476  1.00  9.99
ATOM     82  CA  LYS    21      24.969  53.795   5.611  1.00  9.99
ATOM     83  C   LYS    21      23.515  53.642   5.156  1.00  9.99
ATOM     84  O   LYS    21      22.695  53.063   5.870  1.00  9.99
ATOM     85  CB  LYS    21      25.198  55.013   6.505  1.00  9.99
ATOM     86  N   SER    22      23.206  54.140   3.962  1.00  9.99
ATOM     87  CA  SER    22      21.877  53.974   3.365  1.00  9.99
ATOM     88  C   SER    22      21.967  54.106   1.834  1.00  9.99
ATOM     89  O   SER    22      22.825  54.824   1.292  1.00  9.99
ATOM     90  CB  SER    22      20.859  54.968   3.938  1.00  9.99
ATOM     91  N   ASP    23      21.087  53.400   1.136  1.00  9.99
ATOM     92  CA  ASP    23      21.098  53.417  -0.318  1.00  9.99
ATOM     93  C   ASP    23      20.496  54.679  -0.938  1.00  9.99
ATOM     94  O   ASP    23      20.669  54.931  -2.138  1.00  9.99
ATOM     95  CB  ASP    23      20.374  52.177  -0.866  1.00  9.99
ATOM     96  N   ARG    24      19.775  55.465  -0.145  1.00  9.99
ATOM     97  CA  ARG    24      19.177  56.689  -0.682  1.00  9.99
ATOM     98  C   ARG    24      20.285  57.743  -0.819  1.00  9.99
ATOM     99  O   ARG    24      21.299  57.709  -0.112  1.00  9.99
ATOM    100  CB  ARG    24      18.098  57.239   0.256  1.00  9.99
ATOM    101  N   ARG    25      20.078  58.690  -1.720  1.00  9.99
ATOM    102  CA  ARG    25      21.072  59.724  -1.903  1.00  9.99
ATOM    103  C   ARG    25      21.550  59.747  -3.328  1.00  9.99
ATOM    104  O   ARG    25      21.700  58.699  -3.959  1.00  9.99
ATOM    105  CB  ARG    25      22.239  59.495  -0.928  1.00  9.99
ATOM    106  N   ASN    26      21.784  60.953  -3.827  1.00  9.99
ATOM    107  CA  ASN    26      22.241  61.172  -5.190  1.00  9.99
ATOM    108  C   ASN    26      23.443  60.273  -5.497  1.00  9.99
ATOM    109  O   ASN    26      23.461  59.545  -6.498  1.00  9.99
ATOM    110  CB  ASN    26      22.628  62.652  -5.350  1.00  9.99
ATOM    111  N   CYS    27      24.447  60.301  -4.628  1.00  9.99
ATOM    112  CA  CYS    27      25.646  59.498  -4.871  1.00  9.99
ATOM    113  C   CYS    27      25.451  58.002  -4.709  1.00  9.99
ATOM    114  O   CYS    27      25.918  57.228  -5.556  1.00  9.99
ATOM    115  CB  CYS    27      26.823  59.969  -3.998  1.00  9.99
ATOM    116  N   ASP    28      24.772  57.575  -3.646  1.00  9.99
ATOM    117  CA  ASP    28      24.542  56.141  -3.474  1.00  9.99
ATOM    118  C   ASP    28      23.794  55.609  -4.704  1.00  9.99
ATOM    119  O   ASP    28      24.175  54.583  -5.283  1.00  9.99
ATOM    120  CB  ASP    28      23.735  55.864  -2.201  1.00  9.99
ATOM    121  N   LEU    29      22.730  56.308  -5.094  1.00  9.99
ATOM    122  CA  LEU    29      21.947  55.909  -6.259  1.00  9.99
ATOM    123  C   LEU    29      22.829  55.899  -7.508  1.00  9.99
ATOM    124  O   LEU    29      22.736  54.995  -8.339  1.00  9.99
ATOM    125  CB  LEU    29      20.766  56.858  -6.416  1.00  9.99
ATOM    126  N   SER    30      23.702  56.897  -7.625  1.00  9.99
ATOM    127  CA  SER    30      24.624  56.974  -8.755  1.00  9.99
ATOM    128  C   SER    30      25.567  55.757  -8.726  1.00  9.99
ATOM    129  O   SER    30      25.794  55.096  -9.748  1.00  9.99
ATOM    130  CB  SER    30      25.463  58.255  -8.670  1.00  9.99
ATOM    131  N   PHE    31      26.113  55.461  -7.549  1.00  9.99
ATOM    132  CA  PHE    31      27.043  54.343  -7.429  1.00  9.99
ATOM    133  C   PHE    31      26.417  52.981  -7.642  1.00  9.99
ATOM    134  O   PHE    31      27.051  52.109  -8.233  1.00  9.99
ATOM    135  CB  PHE    31      27.755  54.375  -6.076  1.00  9.99
ATOM    136  N   SER    32      25.185  52.765  -7.183  1.00  9.99
ATOM    137  CA  SER    32      24.605  51.438  -7.397  1.00  9.99
ATOM    138  C   SER    32      24.234  51.170  -8.862  1.00  9.99
ATOM    139  O   SER    32      24.110  50.014  -9.266  1.00  9.99
ATOM    140  CB  SER    32      23.411  51.174  -6.462  1.00  9.99
ATOM    141  N   ASN    33      24.092  52.229  -9.657  1.00  9.99
ATOM    142  CA  ASN    33      23.783  52.101 -11.085  1.00  9.99
ATOM    143  C   ASN    33      25.036  51.703 -11.927  1.00  9.99
ATOM    144  O   ASN    33      24.941  51.474 -13.144  1.00  9.99
ATOM    145  CB  ASN    33      23.157  53.442 -11.617  1.00  9.99
ATOM    146  N   LEU    34      26.203  51.628 -11.283  1.00  9.99
ATOM    147  CA  LEU    34      27.437  51.233 -11.974  1.00  9.99
ATOM    148  C   LEU    34      27.462  49.707 -11.853  1.00  9.99
ATOM    149  O   LEU    34      27.530  49.161 -10.752  1.00  9.99
ATOM    150  CB  LEU    34      28.709  51.819 -11.295  1.00  9.99
ATOM    151  N   CYS    35      27.399  48.994 -12.984  1.00  9.99
ATOM    152  CA  CYS    35      27.403  47.521 -12.956  1.00  9.99
ATOM    153  C   CYS    35      28.458  46.800 -12.093  1.00  9.99
ATOM    154  O   CYS    35      28.115  45.892 -11.342  1.00  9.99
ATOM    155  CB  CYS    35      27.498  47.152 -14.437  1.00  9.99
ATOM    156  N   SER    36      29.726  47.193 -12.205  1.00  9.99
ATOM    157  CA  SER    36      30.809  46.557 -11.433  1.00  9.99
ATOM    158  C   SER    36      30.729  46.819  -9.928  1.00  9.99
ATOM    159  O   SER    36      31.524  46.281  -9.160  1.00  9.99
ATOM    160  CB  SER    36      32.190  47.058 -11.899  1.00  9.99
ATOM    161  N   TRP    37      29.795  47.655  -9.507  1.00  9.99
ATOM    162  CA  TRP    37      29.679  47.979  -8.085  1.00  9.99
ATOM    163  C   TRP    37      28.500  47.309  -7.381  1.00  9.99
ATOM    164  O   TRP    37      27.420  47.166  -7.945  1.00  9.99
ATOM    165  CB  TRP    37      29.552  49.516  -7.876  1.00  9.99
ATOM    166  N   ARG    38      28.735  46.864  -6.155  1.00  9.99
ATOM    167  CA  ARG    38      27.678  46.277  -5.347  1.00  9.99
ATOM    168  C   ARG    38      27.714  47.022  -4.015  1.00  9.99
ATOM    169  O   ARG    38      28.771  47.159  -3.400  1.00  9.99
ATOM    170  CB  ARG    38      27.896  44.782  -5.092  1.00  9.99
ATOM    171  N   PHE    39      26.566  47.532  -3.596  1.00  9.99
ATOM    172  CA  PHE    39      26.463  48.261  -2.330  1.00  9.99
ATOM    173  C   PHE    39      25.901  47.331  -1.269  1.00  9.99
ATOM    174  O   PHE    39      25.107  46.447  -1.565  1.00  9.99
ATOM    175  CB  PHE    39      25.549  49.482  -2.498  1.00  9.99
ATOM    176  N   LEU    40      26.343  47.528  -0.033  1.00  9.99
ATOM    177  CA  LEU    40      25.879  46.747   1.110  1.00  9.99
ATOM    178  C   LEU    40      25.530  47.813   2.140  1.00  9.99
ATOM    179  O   LEU    40      26.422  48.425   2.736  1.00  9.99
ATOM    180  CB  LEU    40      27.002  45.839   1.630  1.00  9.99
TER
END
