
#######################################################
#                                                     #
#                        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   18 (   90),  selected   18 , name T0378TS102_4-D1
# Molecule2: number of CA atoms   89 (  716),  selected   89 , name T0378_D1.pdb
# PARAMETERS: T0378TS102_4-D1.T0378_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    L      20      M       1           #
LGA    R      21      L       2          2.502
LGA    E      22      S       3          2.972
LGA    Q      23      A       4          2.009
LGA    A      49      N       5          2.810
LGA    A      50      Q       6          2.653
LGA    M      51      I       7          0.923
LGA    L      52      K       8          0.840
LGA    F      72      F       9          1.125
LGA    K      73      L      10          1.042
LGA    R      74      R      11          0.675
LGA    I      75      S      12          0.748
LGA    S      76      L      13          2.405
LGA    T      77      R      14          2.851
LGA    Q      78      E      15          1.719
LGA    V      87      R      16          2.921
LGA    -       -      K      17           -
LGA    -       -      Y      18           -
LGA    F      88      R      19          3.140
LGA    D      89      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)   18   89    5.0     16    2.15    12.50     15.379     0.710

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.895220 * X  +  -0.279463 * Y  +   0.347104 * Z  +  33.115383
  Y_new =   0.176936 * X  +  -0.937798 * Y  +  -0.298711 * Z  +  29.816341
  Z_new =   0.408992 * X  +  -0.205997 * Y  +   0.888983 * Z  +  32.661060 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.227703    2.913889  [ DEG:   -13.0464    166.9536 ]
  Theta =  -0.421349   -2.720244  [ DEG:   -24.1415   -155.8585 ]
  Phi   =   2.946463   -0.195130  [ DEG:   168.8199    -11.1801 ]
 
# 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: T0378TS102_4-D1                               
REMARK     2: T0378_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0378TS102_4-D1.T0378_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   18   89   5.0   16   2.15   12.50  15.379
REMARK  ---------------------------------------------------------- 
MOLECULE T0378TS102_4-D1
PFRMAT TS
TARGET T0378
MODEL 4
PARENT 1v2x_A
ATOM      1  N   LEU    20       2.203  38.122  55.967  1.00  1.00
ATOM      2  CA  LEU    20       2.574  36.878  56.708  1.00  1.00
ATOM      3  C   LEU    20       3.110  35.781  55.795  1.00  1.00
ATOM      4  O   LEU    20       4.126  35.154  56.102  1.00  1.00
ATOM      5  CB  LEU    20       1.368  36.332  57.476  1.00  1.00
ATOM      6  N   ARG    21       2.425  35.534  54.681  1.00  1.00
ATOM      7  CA  ARG    21       2.880  34.498  53.766  1.00  1.00
ATOM      8  C   ARG    21       3.959  35.075  52.852  1.00  1.00
ATOM      9  O   ARG    21       4.734  34.344  52.241  1.00  1.00
ATOM     10  CB  ARG    21       1.710  33.939  52.940  1.00  1.00
ATOM     11  N   GLU    22       4.017  36.396  52.762  1.00  1.00
ATOM     12  CA  GLU    22       5.032  37.034  51.938  1.00  1.00
ATOM     13  C   GLU    22       6.354  36.837  52.691  1.00  1.00
ATOM     14  O   GLU    22       7.421  36.625  52.105  1.00  1.00
ATOM     15  CB  GLU    22       4.713  38.526  51.786  1.00  1.00
ATOM     16  N   GLN    23       6.243  36.889  54.011  1.00  1.00
ATOM     17  CA  GLN    23       7.358  36.727  54.930  1.00  1.00
ATOM     18  C   GLN    23       7.795  35.265  55.028  1.00  1.00
ATOM     19  O   GLN    23       8.982  34.956  55.153  1.00  1.00
ATOM     20  CB  GLN    23       6.928  37.252  56.312  1.00  1.00
ATOM     21  N   ALA    49       6.829  34.361  54.948  1.00  1.00
ATOM     22  CA  ALA    49       7.128  32.950  55.083  1.00  1.00
ATOM     23  C   ALA    49       7.003  32.189  53.753  1.00  1.00
ATOM     24  O   ALA    49       7.956  31.560  53.297  1.00  1.00
ATOM     25  CB  ALA    49       6.217  32.354  56.211  1.00  1.00
ATOM     26  N   ALA    50       5.844  32.280  53.115  1.00  1.00
ATOM     27  CA  ALA    50       5.613  31.579  51.856  1.00  1.00
ATOM     28  C   ALA    50       6.644  31.939  50.799  1.00  1.00
ATOM     29  O   ALA    50       6.924  31.141  49.913  1.00  1.00
ATOM     30  CB  ALA    50       4.204  31.891  51.340  1.00  1.00
ATOM     31  N   MET    51       7.226  33.125  50.895  1.00  1.00
ATOM     32  CA  MET    51       8.198  33.531  49.892  1.00  1.00
ATOM     33  C   MET    51       9.651  33.428  50.339  1.00  1.00
ATOM     34  O   MET    51      10.312  32.418  50.108  1.00  1.00
ATOM     35  CB  MET    51       7.896  34.952  49.425  1.00  1.00
ATOM     36  N   LEU    52      10.139  34.493  50.965  1.00  1.00
ATOM     37  CA  LEU    52      11.508  34.563  51.433  1.00  1.00
ATOM     38  C   LEU    52      11.911  33.262  52.116  1.00  1.00
ATOM     39  O   LEU    52      12.858  32.600  51.700  1.00  1.00
ATOM     40  CB  LEU    52      11.656  35.735  52.404  1.00  1.00
ATOM     41  N   PHE    72      11.165  32.904  53.157  1.00  1.00
ATOM     42  CA  PHE    72      11.410  31.704  53.940  1.00  1.00
ATOM     43  C   PHE    72      11.552  30.427  53.101  1.00  1.00
ATOM     44  O   PHE    72      12.549  29.720  53.214  1.00  1.00
ATOM     45  CB  PHE    72      10.288  31.543  54.973  1.00  1.00
ATOM     46  N   LYS    73      10.557  30.151  52.263  1.00  1.00
ATOM     47  CA  LYS    73      10.530  28.959  51.407  1.00  1.00
ATOM     48  C   LYS    73      11.610  28.936  50.321  1.00  1.00
ATOM     49  O   LYS    73      12.248  27.900  50.119  1.00  1.00
ATOM     50  CB  LYS    73       9.127  28.809  50.775  1.00  1.00
ATOM     51  N   ARG    74      11.827  30.048  49.620  1.00  1.00
ATOM     52  CA  ARG    74      12.853  30.049  48.580  1.00  1.00
ATOM     53  C   ARG    74      14.265  29.892  49.161  1.00  1.00
ATOM     54  O   ARG    74      15.104  29.213  48.581  1.00  1.00
ATOM     55  CB  ARG    74      12.803  31.327  47.726  1.00  1.00
ATOM     56  N   ILE    75      14.531  30.516  50.303  1.00  1.00
ATOM     57  CA  ILE    75      15.845  30.409  50.917  1.00  1.00
ATOM     58  C   ILE    75      16.158  28.968  51.363  1.00  1.00
ATOM     59  O   ILE    75      17.296  28.488  51.249  1.00  1.00
ATOM     60  CB  ILE    75      15.954  31.341  52.154  1.00  1.00
ATOM     61  N   SER    76      15.156  28.279  51.890  1.00  1.00
ATOM     62  CA  SER    76      15.403  26.929  52.361  1.00  1.00
ATOM     63  C   SER    76      15.563  26.056  51.150  1.00  1.00
ATOM     64  O   SER    76      16.374  25.140  51.159  1.00  1.00
ATOM     65  CB  SER    76      14.232  26.405  53.184  1.00  1.00
ATOM     66  N   THR    77      14.784  26.329  50.116  1.00  1.00
ATOM     67  CA  THR    77      14.883  25.530  48.898  1.00  1.00
ATOM     68  C   THR    77      16.324  25.521  48.413  1.00  1.00
ATOM     69  O   THR    77      16.865  24.476  48.050  1.00  1.00
ATOM     70  CB  THR    77      13.970  26.060  47.796  1.00  1.00
ATOM     71  N   GLN    78      16.946  26.690  48.409  1.00  1.00
ATOM     72  CA  GLN    78      18.327  26.820  47.995  1.00  1.00
ATOM     73  C   GLN    78      19.311  26.217  49.001  1.00  1.00
ATOM     74  O   GLN    78      20.319  25.603  48.624  1.00  1.00
ATOM     75  CB  GLN    78      18.661  28.307  47.787  1.00  1.00
ATOM     76  N   VAL    87      19.013  26.370  50.295  1.00  1.00
ATOM     77  CA  VAL    87      19.883  25.830  51.315  1.00  1.00
ATOM     78  C   VAL    87      19.929  24.310  51.180  1.00  1.00
ATOM     79  O   VAL    87      20.938  23.667  51.489  1.00  1.00
ATOM     80  CB  VAL    87      19.330  26.177  52.693  1.00  1.00
ATOM     81  N   PHE    88      18.822  23.755  50.714  1.00  1.00
ATOM     82  CA  PHE    88      18.702  22.303  50.545  1.00  1.00
ATOM     83  C   PHE    88      19.544  21.751  49.402  1.00  1.00
ATOM     84  O   PHE    88      19.724  20.535  49.282  1.00  1.00
ATOM     85  CB  PHE    88      17.224  21.917  50.369  1.00  1.00
ATOM     86  N   ASP    89      20.065  22.632  48.552  1.00  1.00
ATOM     87  CA  ASP    89      20.922  22.200  47.461  1.00  1.00
ATOM     88  C   ASP    89      22.397  22.526  47.783  1.00  1.00
ATOM     89  O   ASP    89      23.261  22.263  46.977  1.00  1.00
ATOM     90  CB  ASP    89      20.533  22.884  46.121  1.00  1.00
TER
END
