
#######################################################
#                                                     #
#                        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_1-D1
# Molecule2: number of CA atoms   89 (  730),  selected   89 , name T0347_D1.pdb
# PARAMETERS: T0347TS393_1-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      -       -           -
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      -       -           -
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      S      10           #
LGA    -       -      R      11           -
LGA    -       -      I      12           -
LGA    I      52      A      13          3.276
LGA    V      53      I      14          2.047
LGA    P      54      D      15           #
LGA    -       -      K      16           -
LGA    V      55      L      17          3.911
LGA    V      56      R      18          5.144
LGA    A      57      P      19          2.792
LGA    G      58      T      20          3.281
LGA    P      59      Q      21          3.419
LGA    K      60      I      22          3.142
LGA    D      61      A      23           #
LGA    R      62      V      24           #
LGA    A      63      G      25           #
LGA    -       -      F      26           -
LGA    -       -      R      27           -
LGA    Y      64      E      28           #
LGA    -       -      V      29           -
LGA    -       -      E      30           -
LGA    -       -      L      31           -
LGA    L      65      K      32           #
LGA    I      66      R      33           -
LGA    D      67      K      34           -
LGA    -       -      E      35           -
LGA    -       -      W      36           -
LGA    -       -      R      37           -
LGA    H      68      H      51          4.257
LGA    H      69      -       -           -
LGA    H      70      -       -           -
LGA    L      71      I      52          4.113
LGA    V      72      V      53          4.715
LGA    L      73      -       -           -
LGA    A      74      P      54           #
LGA    L      75      V      55          1.253
LGA    S      76      V      56          3.316
LGA    K      77      A      57          2.561
LGA    E      78      G      58          5.074
LGA    G      79      P      59          5.090
LGA    -       -      K      60           -
LGA    -       -      D      61           -
LGA    V      80      R      62          2.579
LGA    E      81      A      63           #
LGA    H      82      Y      64          3.914
LGA    V      83      L      65          3.680
LGA    L      84      I      66          4.111
LGA    T      85      D      67          1.807
LGA    S      86      H      68           #
LGA    -       -      H      69           -
LGA    -       -      H      70           -
LGA    -       -      L      71           -
LGA    -       -      V      72           -
LGA    -       -      L      73           -
LGA    -       -      A      74           -
LGA    -       -      L      75           -
LGA    -       -      S      76           -
LGA    -       -      K      77           -
LGA    -       -      E      78           -
LGA    -       -      G      79           -
LGA    -       -      V      80           -
LGA    -       -      E      81           -
LGA    -       -      H      82           -
LGA    -       -      V      83           -
LGA    -       -      L      84           -
LGA    E      87      T      85           #
LGA    V      88      S      86          3.265
LGA    A      89      E      87           -
LGA    K      90      -       -           -
LGA    F      91      -       -           -
LGA    S      92      -       -           -
LGA    H      93      -       -           -
LGA    L      94      -       -           -
LGA    G      95      V      88           #
LGA    K      96      A      89          4.884
LGA    D      97      K      90          4.304
LGA    E      98      -       -           -
LGA    F      99      -       -           -
LGA    W     100      -       -           -
LGA    S     101      F      91          3.980
LGA    V     102      S      92           -
LGA    M     103      H      93           -
LGA    -       -      L      94           -
LGA    -       -      G      95           -
LGA    -       -      K      96           -
LGA    -       -      D      97           -
LGA    -       -      E      98           -
LGA    -       -      F      99           -
LGA    -       -      W     100           -
LGA    -       -      S     101           -
LGA    D     104      V     102           #
LGA    H     105      M     103          0.681
LGA    R     106      D     104          4.848
LGA    N     107      H     105           -
LGA    -       -      R     106           -
LGA    -       -      N     107           -
LGA    L     108      L     108          4.415

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   89   89    5.0     28    3.75    10.71     18.244     0.728

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.186553 * X  +   0.224198 * Y  +   0.956521 * Z  +   8.906140
  Y_new =  -0.861228 * X  +  -0.431172 * Y  +   0.269030 * Z  +  36.872765
  Z_new =   0.472741 * X  +  -0.873971 * Y  +   0.112649 * Z  + -13.648983 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.442609    1.698983  [ DEG:   -82.6554     97.3446 ]
  Theta =  -0.492399   -2.649194  [ DEG:   -28.2124   -151.7876 ]
  Phi   =  -1.357479    1.784113  [ DEG:   -77.7778    102.2222 ]
 
# 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_1-D1                               
REMARK     2: T0347_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0347TS393_1-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   28   3.75   10.71  18.244
REMARK  ---------------------------------------------------------- 
MOLECULE T0347TS393_1-D1
PFRMAT TS
TARGET T0347
MODEL 1
PARENT N/A
ATOM      7  CA  PRO     7      -8.297  50.580 -41.440  1.00 25.00           C
ATOM      8  CA  ARG     8      -6.412  52.995 -39.272  1.00 25.00           C
ATOM      9  CA  LEU     9      -4.309  50.419 -37.460  1.00 25.00           C
ATOM     10  CA  SER    10      -0.821  50.521 -38.967  1.00 25.00           C
ATOM     11  CA  ARG    11      -0.486  48.402 -42.121  1.00 25.00           C
ATOM     12  CA  ILE    12      -0.339  45.193 -40.116  1.00 25.00           C
ATOM     13  CA  ALA    13      -0.139  42.992 -37.020  1.00 25.00           C
ATOM     14  CA  ILE    14       2.493  40.543 -35.890  1.00 25.00           C
ATOM     15  CA  ASP    15       4.898  42.516 -38.124  1.00 25.00           C
ATOM     16  CA  LYS    16       7.893  40.882 -36.384  1.00 25.00           C
ATOM     17  CA  LEU    17       9.295  44.044 -34.843  1.00 25.00           C
ATOM     18  CA  ARG    18       7.067  45.339 -32.084  1.00 25.00           C
ATOM     19  CA  PRO    19       6.753  42.495 -29.522  1.00 25.00           C
ATOM     20  CA  THR    20       9.944  40.806 -30.798  1.00 25.00           C
ATOM     21  CA  GLN    21      10.991  40.012 -27.201  1.00 25.00           C
ATOM     22  CA  ILE    22       7.533  38.523 -26.498  1.00 25.00           C
ATOM     23  CA  ALA    23       7.785  36.381 -29.661  1.00 25.00           C
ATOM     24  CA  VAL    24      11.252  35.159 -28.589  1.00 25.00           C
ATOM     25  CA  GLY    25       9.893  34.272 -25.120  1.00 25.00           C
ATOM     26  CA  PHE    26       6.994  32.348 -26.720  1.00 25.00           C
ATOM     27  CA  ARG    27       9.456  30.450 -28.956  1.00 25.00           C
ATOM     28  CA  GLU    28      11.597  29.579 -25.902  1.00 25.00           C
ATOM     29  CA  VAL    29       8.488  28.326 -24.049  1.00 25.00           C
ATOM     30  CA  GLU    30       7.524  26.178 -27.070  1.00 25.00           C
ATOM     31  CA  LEU    31      11.065  24.723 -27.197  1.00 25.00           C
ATOM     32  CA  LYS    32      10.895  23.923 -23.455  1.00 25.00           C
ATOM     33  CA  ARG    33       7.511  22.202 -23.950  1.00 25.00           C
ATOM     34  CA  LYS    34       8.951  20.146 -26.842  1.00 25.00           C
ATOM     35  CA  GLU    35      11.933  19.127 -24.665  1.00 25.00           C
ATOM     36  CA  TRP    36       9.553  18.083 -21.852  1.00 25.00           C
ATOM     37  CA  ARG    37       7.494  16.010 -24.329  1.00 25.00           C
ATOM     51  CA  HIS    51       1.033  28.180 -11.705  1.00 25.00           C
ATOM     52  CA  ILE    52       1.404  31.931 -12.441  1.00 25.00           C
ATOM     53  CA  VAL    53       1.403  35.704 -13.025  1.00 25.00           C
ATOM     54  CA  PRO    54       1.944  35.214  -9.296  1.00 25.00           C
ATOM     55  CA  VAL    55       3.932  38.233  -8.274  1.00 25.00           C
ATOM     56  CA  VAL    56       4.661  39.201  -4.708  1.00 25.00           C
ATOM     57  CA  ALA    57       3.887  42.343  -2.705  1.00 25.00           C
ATOM     58  CA  GLY    58       3.053  43.407   0.852  1.00 25.00           C
ATOM     59  CA  PRO    59       2.640  46.344   3.155  1.00 25.00           C
ATOM     60  CA  LYS    60      -1.046  46.359   2.056  1.00 25.00           C
ATOM     61  CA  ASP    61      -0.559  48.083  -1.330  1.00 25.00           C
ATOM     62  CA  ARG    62       0.075  46.917  -4.941  1.00 25.00           C
ATOM     63  CA  ALA    63       3.850  46.831  -4.972  1.00 25.00           C
ATOM     64  CA  TYR    64       6.272  44.072  -6.164  1.00 25.00           C
ATOM     65  CA  LEU    65       9.765  43.569  -7.666  1.00 25.00           C
ATOM     66  CA  ILE    66       8.971  39.926  -8.045  1.00 25.00           C
ATOM     67  CA  ASP    67      10.217  37.346 -10.613  1.00 25.00           C
ATOM     68  CA  HIS    68       9.337  35.750 -13.949  1.00 25.00           C
ATOM     69  CA  HIS    69       5.829  34.250 -13.612  1.00 25.00           C
ATOM     70  CA  HIS    70       7.341  30.765 -13.122  1.00 25.00           C
ATOM     71  CA  LEU    71       9.697  32.139 -10.433  1.00 25.00           C
ATOM     72  CA  VAL    72       6.741  33.808  -8.662  1.00 25.00           C
ATOM     73  CA  LEU    73       4.785  30.518  -8.770  1.00 25.00           C
ATOM     74  CA  ALA    74       7.794  28.653  -7.308  1.00 25.00           C
ATOM     75  CA  LEU    75       8.079  31.253  -4.511  1.00 25.00           C
ATOM     76  CA  SER    76       4.344  30.877  -3.748  1.00 25.00           C
ATOM     77  CA  LYS    77       4.730  27.070  -3.614  1.00 25.00           C
ATOM     78  CA  GLU    78       0.950  26.646  -3.601  1.00 25.00           C
ATOM     79  CA  GLY    79      -1.834  29.124  -3.217  1.00 25.00           C
ATOM     80  CA  VAL    80      -0.564  32.399  -4.630  1.00 25.00           C
ATOM     81  CA  GLU    81      -0.973  35.507  -2.428  1.00 25.00           C
ATOM     82  CA  HIS    82       1.732  37.416  -0.520  1.00 25.00           C
ATOM     83  CA  VAL    83       5.549  36.841  -0.408  1.00 25.00           C
ATOM     84  CA  LEU    84       7.064  40.321  -0.060  1.00 25.00           C
ATOM     85  CA  THR    85       9.674  39.039  -2.516  1.00 25.00           C
ATOM     86  CA  SER    86      10.519  35.729  -4.141  1.00 25.00           C
ATOM     87  CA  GLU    87      12.184  33.401  -6.669  1.00 25.00           C
ATOM     88  CA  VAL    88      13.970  30.482  -8.298  1.00 25.00           C
ATOM     89  CA  ALA    89      17.019  28.341  -9.145  1.00 25.00           C
ATOM     90  CA  LYS    90      17.687  27.742  -5.400  1.00 25.00           C
ATOM     91  CA  PHE    91      19.192  28.817  -2.036  1.00 25.00           C
ATOM     92  CA  SER    92      18.294  29.173   1.653  1.00 25.00           C
ATOM     93  CA  HIS    93      15.195  27.077   2.531  1.00 25.00           C
ATOM     94  CA  LEU    94      15.866  23.363   3.010  1.00 25.00           C
ATOM     95  CA  GLY    95      12.609  22.111   1.475  1.00 25.00           C
ATOM     96  CA  LYS    96       8.856  22.206   1.084  1.00 25.00           C
ATOM     97  CA  ASP    97       7.006  22.527   4.422  1.00 25.00           C
ATOM     98  CA  GLU    98       9.632  25.024   5.665  1.00 25.00           C
ATOM     99  CA  PHE    99       9.260  27.058   2.440  1.00 25.00           C
ATOM    100  CA  TRP   100       5.453  27.077   2.863  1.00 25.00           C
ATOM    101  CA  SER   101       5.837  28.259   6.485  1.00 25.00           C
ATOM    102  CA  VAL   102       8.200  31.051   5.350  1.00 25.00           C
ATOM    103  CA  MET   103       5.685  32.122   2.668  1.00 25.00           C
ATOM    104  CA  ASP   104       2.886  32.180   5.280  1.00 25.00           C
ATOM    105  CA  HIS   105       5.063  34.312   7.602  1.00 25.00           C
ATOM    106  CA  ARG   106       6.915  36.365   5.049  1.00 25.00           C
ATOM    107  CA  ASN   107       9.980  38.330   3.995  1.00 25.00           C
ATOM    108  CA  LEU   108      12.926  36.066   3.346  1.00 25.00           C
TER
END
