
#######################################################
#                                                     #
#                        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   89 (   89),  selected   89 , name T0347TS393_2-D1
# Molecule2: number of CA atoms   89 (  730),  selected   89 , name T0347_D1.pdb
# PARAMETERS: T0347TS393_2-D1.T0347_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    P       7      P       7           -
LGA    R       8      R       8           -
LGA    L       9      L       9           -
LGA    S      10      S      10           -
LGA    R      11      -       -           -
LGA    I      12      -       -           -
LGA    A      13      -       -           -
LGA    I      14      -       -           -
LGA    D      15      -       -           -
LGA    K      16      -       -           -
LGA    L      17      -       -           -
LGA    R      18      -       -           -
LGA    P      19      -       -           -
LGA    T      20      -       -           -
LGA    Q      21      -       -           -
LGA    I      22      -       -           -
LGA    A      23      -       -           -
LGA    V      24      -       -           -
LGA    G      25      -       -           -
LGA    F      26      -       -           -
LGA    R      27      -       -           -
LGA    E      28      R      11           #
LGA    V      29      I      12           -
LGA    E      30      -       -           -
LGA    L      31      -       -           -
LGA    K      32      A      13           #
LGA    R      33      I      14           #
LGA    K      34      -       -           -
LGA    E      35      -       -           -
LGA    W      36      -       -           -
LGA    R      37      -       -           -
LGA    H      51      D      15           #
LGA    -       -      K      16           -
LGA    -       -      L      17           -
LGA    -       -      R      18           -
LGA    -       -      P      19           -
LGA    -       -      T      20           -
LGA    -       -      Q      21           -
LGA    -       -      I      22           -
LGA    -       -      A      23           -
LGA    -       -      V      24           -
LGA    -       -      G      25           -
LGA    -       -      F      26           -
LGA    -       -      R      27           -
LGA    -       -      E      28           -
LGA    -       -      V      29           -
LGA    -       -      E      30           -
LGA    -       -      L      31           -
LGA    -       -      K      32           -
LGA    -       -      R      33           -
LGA    -       -      K      34           -
LGA    -       -      E      35           -
LGA    -       -      W      36           -
LGA    -       -      R      37           -
LGA    -       -      H      51           -
LGA    -       -      I      52           -
LGA    -       -      V      53           -
LGA    -       -      P      54           -
LGA    -       -      V      55           -
LGA    -       -      V      56           -
LGA    -       -      A      57           -
LGA    -       -      G      58           -
LGA    -       -      P      59           -
LGA    -       -      K      60           -
LGA    -       -      D      61           -
LGA    I      52      R      62           #
LGA    V      53      A      63          4.082
LGA    P      54      Y      64          4.939
LGA    V      55      -       -           -
LGA    V      56      -       -           -
LGA    A      57      -       -           -
LGA    G      58      -       -           -
LGA    P      59      -       -           -
LGA    K      60      -       -           -
LGA    D      61      -       -           -
LGA    R      62      -       -           -
LGA    A      63      -       -           -
LGA    Y      64      -       -           -
LGA    L      65      -       -           -
LGA    I      66      -       -           -
LGA    D      67      -       -           -
LGA    H      68      -       -           -
LGA    H      69      -       -           -
LGA    H      70      -       -           -
LGA    L      71      L      65          2.243
LGA    V      72      I      66          2.018
LGA    L      73      D      67          3.362
LGA    A      74      H      68           -
LGA    L      75      H      69           -
LGA    S      76      H      70           -
LGA    K      77      L      71           -
LGA    E      78      V      72           -
LGA    G      79      L      73           -
LGA    V      80      A      74           -
LGA    E      81      L      75           -
LGA    H      82      S      76           -
LGA    V      83      K      77           -
LGA    L      84      E      78           -
LGA    T      85      G      79           -
LGA    S      86      V      80           -
LGA    E      87      E      81           -
LGA    -       -      H      82           -
LGA    -       -      V      83           -
LGA    -       -      L      84           -
LGA    -       -      T      85           -
LGA    -       -      S      86           -
LGA    V      88      E      87          3.657
LGA    A      89      V      88           -
LGA    K      90      A      89           #
LGA    F      91      K      90          4.205
LGA    S      92      F      91          2.884
LGA    H      93      S      92          5.207
LGA    L      94      H      93          3.561
LGA    G      95      L      94          2.596
LGA    K      96      G      95          2.521
LGA    D      97      K      96          2.779
LGA    -       -      D      97           -
LGA    E      98      E      98          2.432
LGA    F      99      F      99          1.861
LGA    W     100      W     100          1.492
LGA    S     101      S     101          1.278
LGA    V     102      V     102          1.199
LGA    M     103      M     103          1.241
LGA    D     104      D     104          1.426
LGA    H     105      H     105          1.139
LGA    R     106      R     106          0.813
LGA    N     107      N     107          3.558
LGA    L     108      L     108           #

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   89   89    5.0     23    2.91    47.83     18.141     0.765

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.777795 * X  +  -0.501969 * Y  +   0.378236 * Z  +  12.116361
  Y_new =   0.045230 * X  +  -0.555528 * Y  +  -0.830267 * Z  +  34.286739
  Z_new =   0.626889 * X  +   0.662885 * Y  +  -0.409383 * Z  + -10.014513 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.124040   -1.017552  [ DEG:   121.6986    -58.3014 ]
  Theta =  -0.677554   -2.464039  [ DEG:   -38.8210   -141.1790 ]
  Phi   =   0.058086   -3.083507  [ DEG:     3.3281   -176.6719 ]
 
# 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: T0347TS393_2-D1                               
REMARK     2: T0347_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0347TS393_2-D1.T0347_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   89   89   5.0   23   2.91   47.83  18.141
REMARK  ---------------------------------------------------------- 
MOLECULE T0347TS393_2-D1
PFRMAT TS
TARGET T0347
MODEL 2
PARENT N/A
ATOM      7  CA  PRO     7      20.068  63.805 -36.089  1.00 25.00           C
ATOM      8  CA  ARG     8      19.652  60.081 -35.445  1.00 25.00           C
ATOM      9  CA  LEU     9      19.457  57.975 -32.272  1.00 25.00           C
ATOM     10  CA  SER    10      19.853  55.026 -34.615  1.00 25.00           C
ATOM     11  CA  ARG    11      16.803  53.543 -36.335  1.00 25.00           C
ATOM     12  CA  ILE    12      16.004  51.521 -33.256  1.00 25.00           C
ATOM     13  CA  ALA    13      13.038  53.056 -31.470  1.00 25.00           C
ATOM     14  CA  ILE    14      12.377  50.107 -29.207  1.00 25.00           C
ATOM     15  CA  ASP    15      12.111  48.146 -32.488  1.00 25.00           C
ATOM     16  CA  LYS    16      14.892  45.782 -31.327  1.00 25.00           C
ATOM     17  CA  LEU    17      15.522  42.137 -30.300  1.00 25.00           C
ATOM     18  CA  ARG    18      18.717  40.020 -29.855  1.00 25.00           C
ATOM     19  CA  PRO    19      20.201  38.492 -26.655  1.00 25.00           C
ATOM     20  CA  THR    20      17.889  35.515 -27.333  1.00 25.00           C
ATOM     21  CA  GLN    21      17.165  35.194 -23.586  1.00 25.00           C
ATOM     22  CA  ILE    22      16.365  38.934 -23.395  1.00 25.00           C
ATOM     23  CA  ALA    23      14.004  38.607 -26.393  1.00 25.00           C
ATOM     24  CA  VAL    24      12.261  35.631 -24.728  1.00 25.00           C
ATOM     25  CA  GLY    25      11.864  37.643 -21.493  1.00 25.00           C
ATOM     26  CA  PHE    26      10.382  40.572 -23.467  1.00 25.00           C
ATOM     27  CA  ARG    27       7.931  38.194 -25.201  1.00 25.00           C
ATOM     28  CA  GLU    28       6.901  36.743 -21.810  1.00 25.00           C
ATOM     29  CA  VAL    29       6.347  40.276 -20.439  1.00 25.00           C
ATOM     30  CA  GLU    30       4.207  41.152 -23.492  1.00 25.00           C
ATOM     31  CA  LEU    31       2.141  37.967 -22.988  1.00 25.00           C
ATOM     32  CA  LYS    32       1.636  38.847 -19.295  1.00 25.00           C
ATOM     33  CA  ARG    33       0.514  42.378 -20.267  1.00 25.00           C
ATOM     34  CA  LYS    34      -1.954  40.922 -22.807  1.00 25.00           C
ATOM     35  CA  GLU    35      -3.338  38.548 -20.139  1.00 25.00           C
ATOM     36  CA  TRP    36      -3.752  41.480 -17.710  1.00 25.00           C
ATOM     37  CA  ARG    37      -5.587  43.487 -20.408  1.00 25.00           C
ATOM     51  CA  HIS    51       0.382  37.088  -5.634  1.00 25.00           C
ATOM     52  CA  ILE    52       2.718  34.192  -6.407  1.00 25.00           C
ATOM     53  CA  VAL    53       4.392  34.341  -3.047  1.00 25.00           C
ATOM     54  CA  PRO    54       7.306  32.776  -4.849  1.00 25.00           C
ATOM     55  CA  VAL    55      10.634  31.836  -3.259  1.00 25.00           C
ATOM     56  CA  VAL    56      11.850  29.914  -0.208  1.00 25.00           C
ATOM     57  CA  ALA    57      12.655  27.790   2.783  1.00 25.00           C
ATOM     58  CA  GLY    58      14.938  26.478   5.588  1.00 25.00           C
ATOM     59  CA  PRO    59      17.315  23.961   7.226  1.00 25.00           C
ATOM     60  CA  LYS    60      17.964  25.733  10.580  1.00 25.00           C
ATOM     61  CA  ASP    61      19.621  28.472   8.578  1.00 25.00           C
ATOM     62  CA  ARG    62      19.169  30.873   5.589  1.00 25.00           C
ATOM     63  CA  ALA    63      15.735  31.739   4.119  1.00 25.00           C
ATOM     64  CA  TYR    64      16.157  32.543   0.483  1.00 25.00           C
ATOM     65  CA  LEU    65      15.211  33.906  -2.988  1.00 25.00           C
ATOM     66  CA  ILE    66      12.991  35.746  -5.467  1.00 25.00           C
ATOM     67  CA  ASP    67      11.425  33.132  -7.745  1.00 25.00           C
ATOM     68  CA  HIS    68      10.088  36.333  -9.161  1.00 25.00           C
ATOM     69  CA  HIS    69      11.479  39.619  -7.774  1.00 25.00           C
ATOM     70  CA  HIS    70       7.937  41.063  -7.576  1.00 25.00           C
ATOM     71  CA  LEU    71       6.736  37.928  -5.733  1.00 25.00           C
ATOM     72  CA  VAL    72       9.654  38.228  -3.271  1.00 25.00           C
ATOM     73  CA  LEU    73       8.801  41.912  -2.669  1.00 25.00           C
ATOM     74  CA  ALA    74       5.138  40.987  -2.041  1.00 25.00           C
ATOM     75  CA  LEU    75       6.222  38.277   0.439  1.00 25.00           C
ATOM     76  CA  SER    76       8.468  40.796   2.248  1.00 25.00           C
ATOM     77  CA  LYS    77       5.563  43.285   2.440  1.00 25.00           C
ATOM     78  CA  GLU    78       6.413  46.974   2.374  1.00 25.00           C
ATOM     79  CA  GLY    79       9.950  45.641   2.990  1.00 25.00           C
ATOM     80  CA  VAL    80      13.029  43.419   2.554  1.00 25.00           C
ATOM     81  CA  GLU    81      12.379  41.778   5.988  1.00 25.00           C
ATOM     82  CA  HIS    82      15.967  40.485   6.002  1.00 25.00           C
ATOM     83  CA  VAL    83      15.854  37.203   4.079  1.00 25.00           C
ATOM     84  CA  LEU    84      15.836  37.880   0.358  1.00 25.00           C
ATOM     85  CA  THR    85      12.409  36.202   0.478  1.00 25.00           C
ATOM     86  CA  SER    86       9.220  34.155   0.427  1.00 25.00           C
ATOM     87  CA  GLU    87       6.583  31.408   0.110  1.00 25.00           C
ATOM     88  CA  VAL    88       7.069  28.401  -2.248  1.00 25.00           C
ATOM     89  CA  ALA    89       4.069  28.594  -4.634  1.00 25.00           C
ATOM     90  CA  LYS    90       2.268  26.347  -2.134  1.00 25.00           C
ATOM     91  CA  PHE    91       2.725  27.390   1.536  1.00 25.00           C
ATOM     92  CA  SER    92       2.124  23.960   3.066  1.00 25.00           C
ATOM     93  CA  HIS    93       2.671  24.451   6.806  1.00 25.00           C
ATOM     94  CA  LEU    94      -0.629  23.424   8.323  1.00 25.00           C
ATOM     95  CA  GLY    95      -3.104  24.891   5.897  1.00 25.00           C
ATOM     96  CA  LYS    96      -3.144  28.668   5.585  1.00 25.00           C
ATOM     97  CA  ASP    97      -3.094  30.184   9.102  1.00 25.00           C
ATOM     98  CA  GLU    98       0.328  28.597   9.765  1.00 25.00           C
ATOM     99  CA  PHE    99       1.651  30.008   6.460  1.00 25.00           C
ATOM    100  CA  TRP   100       0.331  33.482   7.386  1.00 25.00           C
ATOM    101  CA  SER   101       2.026  33.240  10.812  1.00 25.00           C
ATOM    102  CA  VAL   102       5.318  32.226   9.137  1.00 25.00           C
ATOM    103  CA  MET   103       5.040  35.196   6.735  1.00 25.00           C
ATOM    104  CA  ASP   104       4.406  37.554   9.685  1.00 25.00           C
ATOM    105  CA  HIS   105       7.465  36.142  11.504  1.00 25.00           C
ATOM    106  CA  ARG   106      10.037  33.922   9.868  1.00 25.00           C
ATOM    107  CA  ASN   107      11.531  34.930   6.472  1.00 25.00           C
ATOM    108  CA  LEU   108      10.218  31.566   5.173  1.00 25.00           C
TER
END
