
#######################################################
#                                                     #
#                        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   16 (  137),  selected   16 , name T0378TS389_4-D1
# Molecule2: number of CA atoms   89 (  716),  selected   89 , name T0378_D1.pdb
# PARAMETERS: T0378TS389_4-D1.T0378_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      M       1           -
LGA    -       -      L       2           -
LGA    I       7      S       3          2.052
LGA    K       8      A       4          0.654
LGA    F       9      N       5          0.532
LGA    L      10      Q       6          0.736
LGA    F      70      I       7          0.854
LGA    D      71      K       8          0.745
LGA    F      72      F       9          0.985
LGA    K      73      L      10          0.951
LGA    R      74      R      11          0.487
LGA    I      75      S      12          0.778
LGA    S      76      L      13          1.275
LGA    T      77      -       -           -
LGA    Q      78      R      14          1.653
LGA    T      79      E      15          2.040
LGA    T      80      R      16          2.583
LGA    P      81      K      17           -
LGA    -       -      Y      18           -
LGA    -       -      R      19           -
LGA    -       -      L      20           -
LGA    -       -      R      21           -
LGA    -       -      E      22           -
LGA    -       -      Q      23           -
LGA    -       -      A      24           -
LGA    -       -      F      25           -
LGA    -       -      A      26           -
LGA    -       -      V      27           -
LGA    -       -      E      28           -
LGA    -       -      G      29           -
LGA    -       -      P      30           -
LGA    -       -      K      31           -
LGA    -       -      L      32           -
LGA    -       -      V      33           -
LGA    -       -      G      34           -
LGA    -       -      E      35           -
LGA    -       -      M      36           -
LGA    -       -      L      37           -
LGA    -       -      P      38           -
LGA    -       -      F      39           -
LGA    -       -      Y      40           -
LGA    -       -      R      41           -
LGA    -       -      C      42           -
LGA    -       -      R      43           -
LGA    -       -      M      44           -
LGA    -       -      L      45           -
LGA    -       -      V      46           -
LGA    -       -      G      47           -
LGA    -       -      T      48           -
LGA    -       -      A      49           -
LGA    -       -      A      50           -
LGA    -       -      M      51           -
LGA    -       -      L      52           -
LGA    -       -      R      53           -
LGA    -       -      A      54           -
LGA    -       -      V      55           -
LGA    -       -      S      56           -
LGA    -       -      T      57           -
LGA    -       -      P      58           -
LGA    -       -      H      59           -
LGA    -       -      D      60           -
LGA    -       -      A      61           -
LGA    -       -      E      62           -
LGA    -       -      V      63           -
LGA    -       -      V      64           -
LGA    -       -      E      65           -
LGA    -       -      L      66           -
LGA    -       -      P      67           -
LGA    -       -      E      68           -
LGA    -       -      S      69           -
LGA    -       -      F      70           -
LGA    -       -      D      71           -
LGA    -       -      F      72           -
LGA    -       -      K      73           -
LGA    -       -      R      74           -
LGA    -       -      I      75           -
LGA    -       -      S      76           -
LGA    -       -      T      77           -
LGA    -       -      Q      78           -
LGA    -       -      T      79           -
LGA    -       -      T      80           -
LGA    -       -      P      81           -
LGA    -       -      Q      82           -
LGA    -       -      P      83           -
LGA    -       -      L      84           -
LGA    -       -      M      85           -
LGA    -       -      A      86           -
LGA    -       -      V      87           -
LGA    -       -      F      88           -
LGA    -       -      D      89           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   16   89    5.0     14    1.33    14.29     15.144     0.981

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.142118 * X  +   0.187745 * Y  +  -0.971882 * Z  +  24.546015
  Y_new =  -0.399668 * X  +  -0.909139 * Y  +  -0.117181 * Z  +  29.230257
  Z_new =  -0.905576 * X  +   0.371777 * Y  +   0.204241 * Z  +  54.207184 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.068442   -2.073151  [ DEG:    61.2172   -118.7828 ]
  Theta =   1.132736    2.008857  [ DEG:    64.9010    115.0990 ]
  Phi   =  -1.912443    1.229150  [ DEG:  -109.5749     70.4251 ]
 
# 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: T0378TS389_4-D1                               
REMARK     2: T0378_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0378TS389_4-D1.T0378_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   16   89   5.0   14   1.33   14.29  15.144
REMARK  ---------------------------------------------------------- 
MOLECULE T0378TS389_4-D1
PFRMAT TS
TARGET T0378
MODEL  4
PARENT N/A
ATOM      2  N   ILE     7       2.487  35.986  53.411  1.00  0.00
ATOM      3  CA  ILE     7       3.048  36.641  52.234  1.00  0.00
ATOM      4  CB  ILE     7       2.287  37.935  51.893  1.00  0.00
ATOM      5  CG1 ILE     7       0.873  37.610  51.408  1.00  0.00
ATOM      6  CG2 ILE     7       3.008  38.702  50.794  1.00  0.00
ATOM      7  CD1 ILE     7      -0.029  38.821  51.299  1.00  0.00
ATOM      8  O   ILE     7       5.255  37.104  51.466  1.00  0.00
ATOM      9  C   ILE     7       4.505  37.022  52.429  1.00  0.00
ATOM     10  N   LYS     8       4.919  37.236  53.670  1.00  0.00
ATOM     11  CA  LYS     8       6.298  37.632  53.910  1.00  0.00
ATOM     12  CB  LYS     8       6.362  38.745  54.956  1.00  0.00
ATOM     13  CG  LYS     8       5.737  40.057  54.507  1.00  0.00
ATOM     14  CD  LYS     8       5.833  41.115  55.593  1.00  0.00
ATOM     15  CE  LYS     8       5.213  42.427  55.143  1.00  0.00
ATOM     16  NZ  LYS     8       5.353  43.491  56.174  1.00  0.00
ATOM     17  O   LYS     8       7.866  35.836  53.641  1.00  0.00
ATOM     18  C   LYS     8       7.199  36.515  54.420  1.00  0.00
ATOM     19  N   PHE     9       7.220  36.348  55.737  1.00  0.00
ATOM     20  CA  PHE     9       8.043  35.344  56.382  1.00  0.00
ATOM     21  CB  PHE     9       7.579  35.119  57.823  1.00  0.00
ATOM     22  CG  PHE     9       8.427  34.140  58.585  1.00  0.00
ATOM     23  CD1 PHE     9       9.635  34.530  59.137  1.00  0.00
ATOM     24  CD2 PHE     9       8.015  32.829  58.751  1.00  0.00
ATOM     25  CE1 PHE     9      10.414  33.631  59.839  1.00  0.00
ATOM     26  CE2 PHE     9       8.794  31.928  59.453  1.00  0.00
ATOM     27  CZ  PHE     9       9.988  32.324  59.995  1.00  0.00
ATOM     28  O   PHE     9       8.965  33.492  55.172  1.00  0.00
ATOM     29  C   PHE     9       7.957  34.018  55.638  1.00  0.00
ATOM     30  N   LEU    10       6.738  33.501  55.521  1.00  0.00
ATOM     31  CA  LEU    10       6.466  32.236  54.859  1.00  0.00
ATOM     32  CB  LEU    10       4.959  32.030  54.697  1.00  0.00
ATOM     33  CG  LEU    10       4.523  30.738  54.004  1.00  0.00
ATOM     34  CD1 LEU    10       4.952  29.522  54.813  1.00  0.00
ATOM     35  CD2 LEU    10       3.010  30.696  53.847  1.00  0.00
ATOM     36  O   LEU    10       7.810  31.176  53.176  1.00  0.00
ATOM     37  C   LEU    10       7.077  32.122  53.456  1.00  0.00
ATOM     38  N   PHE    70       6.776  33.088  52.594  1.00  0.00
ATOM     39  CA  PHE    70       7.262  33.115  51.209  1.00  0.00
ATOM     40  CB  PHE    70       6.614  34.265  50.435  1.00  0.00
ATOM     41  CG  PHE    70       7.047  34.352  49.001  1.00  0.00
ATOM     42  CD1 PHE    70       6.526  33.486  48.052  1.00  0.00
ATOM     43  CD2 PHE    70       7.975  35.295  48.599  1.00  0.00
ATOM     44  CE1 PHE    70       6.926  33.566  46.730  1.00  0.00
ATOM     45  CE2 PHE    70       8.374  35.374  47.278  1.00  0.00
ATOM     46  CZ  PHE    70       7.853  34.515  46.345  1.00  0.00
ATOM     47  O   PHE    70       9.406  32.602  50.276  1.00  0.00
ATOM     48  C   PHE    70       8.775  33.301  51.073  1.00  0.00
ATOM     49  N   ASP    71       9.369  34.226  51.827  1.00  0.00
ATOM     50  CA  ASP    71      10.812  34.421  51.714  1.00  0.00
ATOM     51  CB  ASP    71      11.256  35.634  52.536  1.00  0.00
ATOM     52  CG  ASP    71      10.842  36.946  51.904  1.00  0.00
ATOM     53  OD1 ASP    71      10.436  36.938  50.723  1.00  0.00
ATOM     54  OD2 ASP    71      10.924  37.987  52.591  1.00  0.00
ATOM     55  O   ASP    71      12.619  32.840  51.642  1.00  0.00
ATOM     56  C   ASP    71      11.601  33.205  52.219  1.00  0.00
ATOM     57  N   PHE    72      11.137  32.574  53.292  1.00  0.00
ATOM     58  CA  PHE    72      11.827  31.411  53.825  1.00  0.00
ATOM     59  CB  PHE    72      11.164  30.942  55.122  1.00  0.00
ATOM     60  CG  PHE    72      11.816  29.735  55.735  1.00  0.00
ATOM     61  CD1 PHE    72      12.985  29.857  56.465  1.00  0.00
ATOM     62  CD2 PHE    72      11.261  28.477  55.578  1.00  0.00
ATOM     63  CE1 PHE    72      13.585  28.747  57.028  1.00  0.00
ATOM     64  CE2 PHE    72      11.860  27.367  56.143  1.00  0.00
ATOM     65  CZ  PHE    72      13.017  27.498  56.864  1.00  0.00
ATOM     66  O   PHE    72      12.791  29.481  52.707  1.00  0.00
ATOM     67  C   PHE    72      11.811  30.228  52.839  1.00  0.00
ATOM     68  N   LYS    73      10.689  30.041  52.156  1.00  0.00
ATOM     69  CA  LYS    73      10.605  28.919  51.239  1.00  0.00
ATOM     70  CB  LYS    73       9.155  28.690  50.804  1.00  0.00
ATOM     71  CG  LYS    73       8.257  28.147  51.903  1.00  0.00
ATOM     72  CD  LYS    73       6.837  27.939  51.404  1.00  0.00
ATOM     73  CE  LYS    73       5.931  27.430  52.513  1.00  0.00
ATOM     74  NZ  LYS    73       4.530  27.244  52.044  1.00  0.00
ATOM     75  O   LYS    73      12.097  28.376  49.487  1.00  0.00
ATOM     76  C   LYS    73      11.452  29.253  50.046  1.00  0.00
ATOM     77  N   ARG    74      11.442  30.515  49.646  1.00  0.00
ATOM     78  CA  ARG    74      12.247  30.922  48.497  1.00  0.00
ATOM     79  CB  ARG    74      12.185  32.440  48.313  1.00  0.00
ATOM     80  CG  ARG    74      12.910  32.943  47.074  1.00  0.00
ATOM     81  CD  ARG    74      12.921  34.462  47.021  1.00  0.00
ATOM     82  NE  ARG    74      13.720  35.042  48.099  1.00  0.00
ATOM     83  CZ  ARG    74      15.047  35.101  48.097  1.00  0.00
ATOM     84  NH1 ARG    74      15.689  35.646  49.122  1.00  0.00
ATOM     85  NH2 ARG    74      15.729  34.615  47.069  1.00  0.00
ATOM     86  O   ARG    74      14.340  29.968  47.819  1.00  0.00
ATOM     87  C   ARG    74      13.693  30.508  48.716  1.00  0.00
ATOM     88  N   ILE    75      14.196  30.764  49.913  1.00  0.00
ATOM     89  CA  ILE    75      15.553  30.399  50.265  1.00  0.00
ATOM     90  CB  ILE    75      15.981  31.041  51.598  1.00  0.00
ATOM     91  CG1 ILE    75      16.089  32.560  51.450  1.00  0.00
ATOM     92  CG2 ILE    75      17.335  30.504  52.038  1.00  0.00
ATOM     93  CD1 ILE    75      16.247  33.293  52.764  1.00  0.00
ATOM     94  O   ILE    75      16.776  28.327  50.035  1.00  0.00
ATOM     95  C   ILE    75      15.744  28.890  50.427  1.00  0.00
ATOM     96  N   SER    76      14.734  28.215  50.986  1.00  0.00
ATOM     97  CA  SER    76      14.825  26.785  51.172  1.00  0.00
ATOM     98  CB  SER    76      13.581  26.259  51.891  1.00  0.00
ATOM     99  OG  SER    76      12.424  26.417  51.089  1.00  0.00
ATOM    100  O   SER    76      15.566  25.051  49.666  1.00  0.00
ATOM    101  C   SER    76      14.939  26.108  49.809  1.00  0.00
ATOM    102  N   THR    77      14.326  26.735  48.819  1.00  0.00
ATOM    103  CA  THR    77      14.328  26.200  47.452  1.00  0.00
ATOM    104  CB  THR    77      13.335  26.957  46.550  1.00  0.00
ATOM    105  CG2 THR    77      11.920  26.835  47.094  1.00  0.00
ATOM    106  OG1 THR    77      13.694  28.344  46.498  1.00  0.00
ATOM    107  O   THR    77      15.897  25.684  45.710  1.00  0.00
ATOM    108  C   THR    77      15.684  26.291  46.764  1.00  0.00
ATOM    109  N   GLN    78      16.609  27.050  47.347  1.00  0.00
ATOM    110  CA  GLN    78      17.947  27.155  46.788  1.00  0.00
ATOM    111  CB  GLN    78      18.411  28.612  46.781  1.00  0.00
ATOM    112  CG  GLN    78      17.528  29.541  45.965  1.00  0.00
ATOM    113  CD  GLN    78      17.463  29.148  44.503  1.00  0.00
ATOM    114  OE1 GLN    78      18.490  28.912  43.866  1.00  0.00
ATOM    115  NE2 GLN    78      16.249  29.073  43.966  1.00  0.00
ATOM    116  O   GLN    78      20.116  26.309  47.333  1.00  0.00
ATOM    117  C   GLN    78      18.942  26.323  47.629  1.00  0.00
ATOM    118  N   THR    79      18.487  25.636  48.669  1.00  0.00
ATOM    119  CA  THR    79      19.421  24.854  49.479  1.00  0.00
ATOM    120  CB  THR    79      18.740  24.289  50.739  1.00  0.00
ATOM    121  CG2 THR    79      19.732  23.486  51.565  1.00  0.00
ATOM    122  OG1 THR    79      18.236  25.367  51.537  1.00  0.00
ATOM    123  O   THR    79      19.266  22.965  48.024  1.00  0.00
ATOM    124  C   THR    79      20.001  23.665  48.719  1.00  0.00
ATOM    125  N   THR    80      21.312  23.447  48.853  1.00  0.00
ATOM    126  CA  THR    80      22.025  22.382  48.140  1.00  0.00
ATOM    127  CB  THR    80      23.337  22.899  47.519  1.00  0.00
ATOM    128  CG2 THR    80      24.064  21.774  46.799  1.00  0.00
ATOM    129  OG1 THR    80      23.046  23.941  46.578  1.00  0.00
ATOM    130  O   THR    80      23.170  21.470  50.049  1.00  0.00
ATOM    131  C   THR    80      22.348  21.270  49.143  1.00  0.00
ATOM    132  N   PRO    81      21.700  20.106  49.026  1.00  0.00
ATOM    133  CA  PRO    81      21.994  19.039  49.984  1.00  0.00
ATOM    134  CB  PRO    81      20.820  18.070  49.830  1.00  0.00
ATOM    135  CG  PRO    81      20.388  18.229  48.410  1.00  0.00
ATOM    136  CD  PRO    81      20.588  19.680  48.073  1.00  0.00
ATOM    137  O   PRO    81      23.860  17.624  50.522  1.00  0.00
ATOM    138  C   PRO    81      23.325  18.343  49.677  1.00  0.00
TER
END
