
#######################################################
#                                                     #
#                        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 T0324TS168_5-D2
# Molecule2: number of CA atoms   65 (  494),  selected   65 , name T0324_D2.pdb
# PARAMETERS: T0324TS168_5-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    S      17      P      19          5.315
LGA    Q      18      A      20          2.316
LGA    P      19      Y      21          2.004
LGA    A      20      T      22          1.950
LGA    Y      21      T      23          2.464
LGA    T      22      V      24          2.242
LGA    T      23      M      25          2.076
LGA    V      24      R      26          2.492
LGA    M      25      E      27          2.853
LGA    R      26      V      28          2.660
LGA    E      27      L      29          2.634
LGA    V      28      A      30          3.347
LGA    L      29      T      31          4.254
LGA    A      30      Y      32          3.401
LGA    T      31      G      33          2.576
LGA    Y      32      K      34          3.694
LGA    G      33      -       -           -
LGA    K      34      -       -           -
LGA    P      35      P      35           #
LGA    F      36      F      36           #
LGA    S      37      -       -           -
LGA    P      38      -       -           -
LGA    A      39      -       -           -
LGA    Q      40      -       -           -
LGA    A      41      S      37           #
LGA    Q      42      P      38           #
LGA    K      43      A      39          4.118
LGA    T      44      Q      40          3.173
LGA    F      45      A      41          3.366
LGA    P      46      Q      42          4.243
LGA    M      47      K      43          3.768
LGA    A      48      -       -           -
LGA    A      49      T      44          3.542
LGA    E      50      F      45          2.231
LGA    Q      51      P      46          4.367
LGA    A      52      M      47          1.879
LGA    M      53      A      48          5.029
LGA    T      54      A      49          1.108
LGA    E      55      E      50          2.446
LGA    L      56      Q      51          2.939
LGA    -       -      A      52           -
LGA    -       -      M      53           -
LGA    G      57      T      54           #
LGA    I      58      E      55           -
LGA    A      59      L      56           -
LGA    -       -      G      57           -
LGA    -       -      I      58           -
LGA    -       -      A      59           -
LGA    A      60      A      60          4.320
LGA    S      61      S      61          4.372
LGA    E      62      E      62          1.972
LGA    F      63      F      63          1.103
LGA    D      64      D      64          2.170
LGA    H      65      H      65          2.083
LGA    F      66      F      66          1.095
LGA    Q      67      Q      67          1.233
LGA    A      68      A      68          1.816
LGA    Q      69      Q      69          1.601
LGA    Y      70      Y      70          0.915
LGA    E      71      E      71          1.054
LGA    D      72      D      72          1.390
LGA    V      73      V      73          1.435
LGA    M      74      M      74          0.838
LGA    A      75      A      75          1.418
LGA    S      76      S      76          3.524
LGA    H      77      H      77          3.668
LGA    Y      78      Y      78          3.930
LGA    D      79      D      79           #
LGA    Q      80      Q      80           -
LGA    I      81      I      81           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   65   65    5.0     48    2.92    41.67     48.132     1.591

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.566683 * X  +  -0.571573 * Y  +   0.593443 * Z  +  28.242035
  Y_new =  -0.195370 * X  +   0.792927 * Y  +   0.577145 * Z  +  19.380026
  Z_new =  -0.800438 * X  +   0.211118 * Y  +  -0.561007 * Z  +   0.385973 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.781666   -0.359927  [ DEG:   159.3777    -20.6223 ]
  Theta =   0.928025    2.213567  [ DEG:    53.1719    126.8281 ]
  Phi   =  -2.809593    0.331999  [ DEG:  -160.9778     19.0222 ]
 
# 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: T0324TS168_5-D2                               
REMARK     2: T0324_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0324TS168_5-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   48   2.92   41.67  48.132
REMARK  ---------------------------------------------------------- 
MOLECULE T0324TS168_5-D2
PFRMAT TS
TARGET T0324
MODEL 5
PARENT N/A
ATOM     17  CA  SER    17      29.612  16.616   4.940  1.00 25.00           C
ATOM     18  CA  GLN    18      27.783  17.703   8.163  1.00 25.00           C
ATOM     19  CA  PRO    19      24.657  17.496  10.364  1.00 25.00           C
ATOM     20  CA  ALA    20      22.571  19.127   7.597  1.00 25.00           C
ATOM     21  CA  TYR    21      23.953  16.626   5.046  1.00 25.00           C
ATOM     22  CA  THR    22      23.089  13.723   7.390  1.00 25.00           C
ATOM     23  CA  THR    23      19.538  15.091   7.816  1.00 25.00           C
ATOM     24  CA  VAL    24      19.166  15.378   4.015  1.00 25.00           C
ATOM     25  CA  MET    25      20.377  11.770   3.599  1.00 25.00           C
ATOM     26  CA  ARG    26      17.859  10.595   6.234  1.00 25.00           C
ATOM     27  CA  GLU    27      15.052  12.471   4.425  1.00 25.00           C
ATOM     28  CA  VAL    28      16.076  10.853   1.108  1.00 25.00           C
ATOM     29  CA  LEU    29      16.058   7.397   2.759  1.00 25.00           C
ATOM     30  CA  ALA    30      12.572   8.074   4.193  1.00 25.00           C
ATOM     31  CA  THR    31      11.332   9.153   0.734  1.00 25.00           C
ATOM     32  CA  TYR    32       7.909   9.562   2.363  1.00 25.00           C
ATOM     33  CA  GLY    33       5.441  11.717   0.427  1.00 25.00           C
ATOM     34  CA  LYS    34       8.392  12.270  -1.874  1.00 25.00           C
ATOM     35  CA  PRO    35       7.087  15.740  -2.792  1.00 25.00           C
ATOM     36  CA  PHE    36       6.893  17.702   0.445  1.00 25.00           C
ATOM     37  CA  SER    37       3.962  19.608   1.986  1.00 25.00           C
ATOM     38  CA  PRO    38       5.205  23.240   1.674  1.00 25.00           C
ATOM     39  CA  ALA    39       8.045  22.844  -0.865  1.00 25.00           C
ATOM     40  CA  GLN    40       9.770  25.960   0.544  1.00 25.00           C
ATOM     41  CA  ALA    41       9.435  24.570   4.096  1.00 25.00           C
ATOM     42  CA  GLN    42      10.932  21.233   2.958  1.00 25.00           C
ATOM     43  CA  LYS    43      13.851  23.079   1.303  1.00 25.00           C
ATOM     44  CA  THR    44      14.446  25.070   4.520  1.00 25.00           C
ATOM     45  CA  PHE    45      14.425  21.829   6.561  1.00 25.00           C
ATOM     46  CA  PRO    46      14.532  23.516  10.007  1.00 25.00           C
ATOM     47  CA  MET    47      11.107  24.942  10.893  1.00 25.00           C
ATOM     48  CA  ALA    48      12.508  24.683  14.463  1.00 25.00           C
ATOM     49  CA  ALA    49      16.230  24.001  14.848  1.00 25.00           C
ATOM     50  CA  GLU    50      17.923  20.569  15.004  1.00 25.00           C
ATOM     51  CA  GLN    51      17.100  20.305  18.735  1.00 25.00           C
ATOM     52  CA  ALA    52      13.450  21.216  18.019  1.00 25.00           C
ATOM     53  CA  MET    53      13.298  18.551  15.272  1.00 25.00           C
ATOM     54  CA  THR    54      14.758  15.954  17.678  1.00 25.00           C
ATOM     55  CA  GLU    55      12.161  16.908  20.325  1.00 25.00           C
ATOM     56  CA  LEU    56       9.360  16.562  17.736  1.00 25.00           C
ATOM     57  CA  GLY    57       7.103  17.773  20.559  1.00 25.00           C
ATOM     58  CA  ILE    58       8.008  15.621  23.526  1.00 25.00           C
ATOM     59  CA  ALA    59       5.600  13.069  22.163  1.00 25.00           C
ATOM     60  CA  ALA    60       4.564  10.036  20.142  1.00 25.00           C
ATOM     61  CA  SER    61       5.928   6.461  20.298  1.00 25.00           C
ATOM     62  CA  GLU    62       6.414   6.454  16.500  1.00 25.00           C
ATOM     63  CA  PHE    63       8.260   9.803  16.704  1.00 25.00           C
ATOM     64  CA  ASP    64      10.514   8.419  19.474  1.00 25.00           C
ATOM     65  CA  HIS    65      11.266   5.323  17.349  1.00 25.00           C
ATOM     66  CA  PHE    66      12.131   7.555  14.359  1.00 25.00           C
ATOM     67  CA  GLN    67      14.459   9.647  16.563  1.00 25.00           C
ATOM     68  CA  ALA    68      16.166   6.461  17.830  1.00 25.00           C
ATOM     69  CA  GLN    69      16.624   5.246  14.226  1.00 25.00           C
ATOM     70  CA  TYR    70      18.139   8.626  13.253  1.00 25.00           C
ATOM     71  CA  GLU    71      20.535   8.439  16.235  1.00 25.00           C
ATOM     72  CA  ASP    72      21.568   4.895  15.214  1.00 25.00           C
ATOM     73  CA  VAL    73      22.194   6.086  11.628  1.00 25.00           C
ATOM     74  CA  MET    74      24.324   8.988  12.936  1.00 25.00           C
ATOM     75  CA  ALA    75      26.338   6.562  15.110  1.00 25.00           C
ATOM     76  CA  SER    76      26.889   4.274  12.088  1.00 25.00           C
ATOM     77  CA  HIS    77      28.063   7.267  10.006  1.00 25.00           C
ATOM     78  CA  TYR    78      30.485   8.287  12.792  1.00 25.00           C
ATOM     79  CA  ASP    79      31.850   4.712  12.948  1.00 25.00           C
ATOM     80  CA  GLN    80      31.845   2.509   9.889  1.00 25.00           C
ATOM     81  CA  ILE    81      30.891   4.792   6.948  1.00 25.00           C
TER
END
