
#######################################################
#                                                     #
#                        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   65 (   65),  selected   65 , name T0324TS393_1-D2
# Molecule2: number of CA atoms   65 (  494),  selected   65 , name T0324_D2.pdb
# PARAMETERS: T0324TS393_1-D2.T0324_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    S      17      -       -           -
LGA    Q      18      -       -           -
LGA    P      19      S      17          2.519
LGA    A      20      Q      18          3.163
LGA    Y      21      P      19          1.910
LGA    T      22      A      20          0.675
LGA    T      23      Y      21          2.235
LGA    V      24      T      22          1.438
LGA    M      25      T      23          1.183
LGA    R      26      V      24          2.382
LGA    E      27      M      25          2.372
LGA    V      28      R      26          1.762
LGA    L      29      E      27          3.727
LGA    A      30      V      28          4.569
LGA    T      31      L      29          4.223
LGA    Y      32      A      30          2.887
LGA    -       -      T      31           -
LGA    -       -      Y      32           -
LGA    G      33      G      33          2.163
LGA    K      34      K      34          2.467
LGA    P      35      P      35          3.292
LGA    F      36      F      36           #
LGA    S      37      -       -           -
LGA    P      38      -       -           -
LGA    A      39      -       -           -
LGA    Q      40      -       -           -
LGA    A      41      -       -           -
LGA    Q      42      S      37          3.338
LGA    K      43      P      38          6.077
LGA    T      44      A      39          2.380
LGA    F      45      Q      40          2.548
LGA    P      46      A      41          2.613
LGA    M      47      Q      42           #
LGA    A      48      K      43          1.177
LGA    A      49      T      44          2.394
LGA    -       -      F      45           -
LGA    E      50      P      46          3.020
LGA    Q      51      M      47          3.247
LGA    A      52      A      48          4.592
LGA    M      53      A      49          3.249
LGA    T      54      E      50          4.701
LGA    E      55      Q      51          2.904
LGA    -       -      A      52           -
LGA    L      56      M      53           #
LGA    G      57      T      54           -
LGA    I      58      E      55           -
LGA    -       -      L      56           -
LGA    -       -      G      57           -
LGA    -       -      I      58           -
LGA    -       -      A      59           -
LGA    A      59      A      60          4.795
LGA    A      60      S      61          2.335
LGA    S      61      -       -           -
LGA    E      62      E      62          1.498
LGA    F      63      F      63          1.153
LGA    D      64      D      64          0.500
LGA    H      65      H      65          0.607
LGA    F      66      F      66          0.689
LGA    Q      67      Q      67          0.324
LGA    A      68      A      68          0.972
LGA    Q      69      Q      69          1.086
LGA    Y      70      Y      70          0.696
LGA    E      71      E      71          1.197
LGA    D      72      D      72          1.638
LGA    V      73      V      73          1.742
LGA    M      74      M      74          2.018
LGA    A      75      A      75          2.145
LGA    S      76      S      76          2.564
LGA    H      77      H      77          2.218
LGA    Y      78      Y      78          3.055
LGA    D      79      -       -           -
LGA    Q      80      -       -           -
LGA    I      81      D      79          2.674
LGA    -       -      Q      80           -
LGA    -       -      I      81           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   65   65    5.0     50    2.69    44.00     50.254     1.793

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.005192 * X  +  -0.992762 * Y  +   0.119990 * Z  +  29.723038
  Y_new =  -0.884113 * X  +   0.060624 * Y  +   0.463325 * Z  +  22.068041
  Z_new =  -0.467245 * X  +  -0.103679 * Y  +  -0.878028 * Z  +   3.083281 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -3.024055    0.117537  [ DEG:  -173.2656      6.7344 ]
  Theta =   0.486172    2.655420  [ DEG:    27.8556    152.1444 ]
  Phi   =  -1.576669    1.564923  [ DEG:   -90.3365     89.6635 ]
 
# 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: T0324TS393_1-D2                               
REMARK     2: T0324_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0324TS393_1-D2.T0324_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   65   65   5.0   50   2.69   44.00  50.254
REMARK  ---------------------------------------------------------- 
MOLECULE T0324TS393_1-D2
PFRMAT TS
TARGET T0324
MODEL 1
PARENT N/A
ATOM     17  CA  SER    17      31.083  21.591   8.320  1.00 25.00           C
ATOM     18  CA  GLN    18      29.226  20.468  11.442  1.00 25.00           C
ATOM     19  CA  PRO    19      27.841  17.299  13.088  1.00 25.00           C
ATOM     20  CA  ALA    20      24.272  18.636  12.715  1.00 25.00           C
ATOM     21  CA  TYR    21      24.919  19.405   9.019  1.00 25.00           C
ATOM     22  CA  THR    22      26.287  15.866   8.499  1.00 25.00           C
ATOM     23  CA  THR    23      23.188  14.391  10.197  1.00 25.00           C
ATOM     24  CA  VAL    24      20.920  16.507   7.950  1.00 25.00           C
ATOM     25  CA  MET    25      22.830  15.312   4.854  1.00 25.00           C
ATOM     26  CA  ARG    26      22.457  11.676   5.998  1.00 25.00           C
ATOM     27  CA  GLU    27      18.700  12.198   6.519  1.00 25.00           C
ATOM     28  CA  VAL    28      18.401  13.717   3.016  1.00 25.00           C
ATOM     29  CA  LEU    29      20.285  10.732   1.533  1.00 25.00           C
ATOM     30  CA  ALA    30      17.953   8.314   3.374  1.00 25.00           C
ATOM     31  CA  THR    31      14.902  10.204   2.039  1.00 25.00           C
ATOM     32  CA  TYR    32      11.478  10.075   3.717  1.00 25.00           C
ATOM     33  CA  GLY    33       9.175  10.740   0.785  1.00 25.00           C
ATOM     34  CA  LYS    34      10.899  14.129   0.874  1.00 25.00           C
ATOM     35  CA  PRO    35      12.800  15.275  -2.172  1.00 25.00           C
ATOM     36  CA  PHE    36      11.257  18.701  -2.645  1.00 25.00           C
ATOM     37  CA  SER    37       7.924  17.192  -1.716  1.00 25.00           C
ATOM     38  CA  PRO    38       6.941  20.325   0.271  1.00 25.00           C
ATOM     39  CA  ALA    39       8.358  23.586  -1.152  1.00 25.00           C
ATOM     40  CA  GLN    40       8.252  25.181   2.329  1.00 25.00           C
ATOM     41  CA  ALA    41      10.066  22.146   3.801  1.00 25.00           C
ATOM     42  CA  GLN    42      12.737  22.385   1.066  1.00 25.00           C
ATOM     43  CA  LYS    43      13.190  26.117   1.801  1.00 25.00           C
ATOM     44  CA  THR    44      13.557  25.362   5.538  1.00 25.00           C
ATOM     45  CA  PHE    45      16.171  22.673   4.763  1.00 25.00           C
ATOM     46  CA  PRO    46      15.508  20.003   7.470  1.00 25.00           C
ATOM     47  CA  MET    47      13.248  21.189  10.343  1.00 25.00           C
ATOM     48  CA  ALA    48      14.687  24.607  11.309  1.00 25.00           C
ATOM     49  CA  ALA    49      16.533  22.593  13.925  1.00 25.00           C
ATOM     50  CA  GLU    50      15.351  23.867  17.338  1.00 25.00           C
ATOM     51  CA  GLN    51      11.825  22.545  16.637  1.00 25.00           C
ATOM     52  CA  ALA    52      13.271  19.140  15.649  1.00 25.00           C
ATOM     53  CA  MET    53      15.333  19.052  18.876  1.00 25.00           C
ATOM     54  CA  THR    54      12.210  19.897  20.924  1.00 25.00           C
ATOM     55  CA  GLU    55      10.271  17.101  19.169  1.00 25.00           C
ATOM     56  CA  LEU    56      13.106  14.635  19.911  1.00 25.00           C
ATOM     57  CA  GLY    57      11.961  13.104  23.206  1.00 25.00           C
ATOM     58  CA  ILE    58       8.834  12.674  21.039  1.00 25.00           C
ATOM     59  CA  ALA    59       5.536  10.922  20.337  1.00 25.00           C
ATOM     60  CA  ALA    60       4.899   7.739  18.284  1.00 25.00           C
ATOM     61  CA  SER    61       6.663   4.354  17.968  1.00 25.00           C
ATOM     62  CA  GLU    62       7.738   5.221  14.396  1.00 25.00           C
ATOM     63  CA  PHE    63       9.091   8.597  15.594  1.00 25.00           C
ATOM     64  CA  ASP    64      11.037   6.850  18.393  1.00 25.00           C
ATOM     65  CA  HIS    65      12.498   4.373  15.864  1.00 25.00           C
ATOM     66  CA  PHE    66      13.535   7.272  13.587  1.00 25.00           C
ATOM     67  CA  GLN    67      15.205   9.034  16.549  1.00 25.00           C
ATOM     68  CA  ALA    68      17.078   5.815  17.440  1.00 25.00           C
ATOM     69  CA  GLN    69      18.248   5.463  13.810  1.00 25.00           C
ATOM     70  CA  TYR    70      19.459   9.096  13.822  1.00 25.00           C
ATOM     71  CA  GLU    71      21.358   8.479  17.090  1.00 25.00           C
ATOM     72  CA  ASP    72      22.979   5.352  15.586  1.00 25.00           C
ATOM     73  CA  VAL    73      24.007   7.347  12.482  1.00 25.00           C
ATOM     74  CA  MET    74      25.520  10.074  14.707  1.00 25.00           C
ATOM     75  CA  ALA    75      27.457   7.423  16.679  1.00 25.00           C
ATOM     76  CA  SER    76      28.762   5.909  13.412  1.00 25.00           C
ATOM     77  CA  HIS    77      29.863   9.377  12.217  1.00 25.00           C
ATOM     78  CA  TYR    78      31.666   9.979  15.542  1.00 25.00           C
ATOM     79  CA  ASP    79      33.430   6.594  15.224  1.00 25.00           C
ATOM     80  CA  GLN    80      36.220   8.505  13.453  1.00 25.00           C
ATOM     81  CA  ILE    81      35.191  10.195  10.207  1.00 25.00           C
TER
END
