
#######################################################
#                                                     #
#                        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   27 (  108),  selected   27 , name T0363TS383_4-D1
# Molecule2: number of CA atoms   46 (  372),  selected   46 , name T0363_D1.pdb
# PARAMETERS: T0363TS383_4-D1.T0363_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      N      11           -
LGA    -       -      Q      12           -
LGA    -       -      I      13           -
LGA    -       -      N      14           -
LGA    -       -      I      15           -
LGA    -       -      E      16           -
LGA    -       -      I      17           -
LGA    -       -      A      18           -
LGA    -       -      Y      19           -
LGA    -       -      A      20           -
LGA    -       -      F      21           -
LGA    -       -      P      22           -
LGA    -       -      E      23           -
LGA    -       -      R      24           -
LGA    -       -      Y      25           -
LGA    L      27      Y      26          4.057
LGA    K      28      L      27          2.185
LGA    S      29      K      28          2.547
LGA    F      30      S      29          2.108
LGA    Q      31      F      30          0.994
LGA    V      32      Q      31          4.738
LGA    E      34      V      32          2.583
LGA    G      35      D      33          5.214
LGA    -       -      E      34           -
LGA    -       -      G      35           -
LGA    I      36      I      36          0.974
LGA    T      37      T      37          0.792
LGA    V      38      V      38          0.819
LGA    Q      39      Q      39          1.122
LGA    T      40      T      40          0.998
LGA    A      41      A      41          0.356
LGA    I      42      I      42          0.582
LGA    T      43      T      43          0.841
LGA    Q      44      Q      44          1.132
LGA    I      47      S      45          1.692
LGA    L      48      G      46          2.163
LGA    S      49      -       -           -
LGA    Q      50      I      47           #
LGA    F      51      L      48           #
LGA    P      52      S      49          1.567
LGA    E      53      Q      50          1.065
LGA    I      54      F      51          2.338
LGA    D      55      P      52          3.562
LGA    L      56      E      53          2.777
LGA    -       -      I      54           -
LGA    -       -      D      55           -
LGA    -       -      L      56           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   27   46    5.0     24    2.36    37.50     40.540     0.977

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.612568 * X  +   0.707710 * Y  +   0.352004 * Z  +  16.375711
  Y_new =  -0.638796 * X  +   0.180980 * Y  +   0.747788 * Z  +   7.723031
  Z_new =   0.465511 * X  +  -0.682930 * Y  +   0.562945 * Z  +  23.930973 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.881408    2.260185  [ DEG:   -50.5010    129.4990 ]
  Theta =  -0.484212   -2.657381  [ DEG:   -27.7433   -152.2567 ]
  Phi   =  -0.806354    2.335238  [ DEG:   -46.2007    133.7993 ]
 
# 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: T0363TS383_4-D1                               
REMARK     2: T0363_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0363TS383_4-D1.T0363_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   27   46   5.0   24   2.36   37.50  40.540
REMARK  ---------------------------------------------------------- 
MOLECULE T0363TS383_4-D1
PFRMAT TS
TARGET T0363
MODEL 4
PARENT 1v8cA
ATOM      1  N   LEU    27      26.198  17.623  -5.707  1.00  0.00
ATOM      2  CA  LEU    27      25.082  17.049  -4.966  1.00  0.00
ATOM      3  C   LEU    27      24.552  17.961  -3.871  1.00  0.00
ATOM      4  O   LEU    27      25.321  18.637  -3.198  1.00  0.00
ATOM      5  N   LYS    28      23.232  17.976  -3.699  1.00  0.00
ATOM      6  CA  LYS    28      22.602  18.782  -2.658  1.00  0.00
ATOM      7  C   LYS    28      22.218  17.889  -1.481  1.00  0.00
ATOM      8  O   LYS    28      22.267  18.318  -0.330  1.00  0.00
ATOM      9  N   SER    29      21.814  16.654  -1.766  1.00  0.00
ATOM     10  CA  SER    29      21.448  15.736  -0.692  1.00  0.00
ATOM     11  C   SER    29      21.883  14.313  -0.989  1.00  0.00
ATOM     12  O   SER    29      21.871  13.868  -2.139  1.00  0.00
ATOM     13  N   PHE    30      22.277  13.607   0.064  1.00  0.00
ATOM     14  CA  PHE    30      22.729  12.231  -0.051  1.00  0.00
ATOM     15  C   PHE    30      22.181  11.432   1.119  1.00  0.00
ATOM     16  O   PHE    30      21.896  11.988   2.174  1.00  0.00
ATOM     17  N   GLN    31      22.013  10.133   0.910  1.00  0.00
ATOM     18  CA  GLN    31      21.555   9.231   1.956  1.00  0.00
ATOM     19  C   GLN    31      22.775   8.357   2.243  1.00  0.00
ATOM     20  O   GLN    31      23.279   7.675   1.346  1.00  0.00
ATOM     21  N   VAL    32      23.256   8.387   3.484  1.00  0.00
ATOM     22  CA  VAL    32      24.436   7.613   3.868  1.00  0.00
ATOM     23  C   VAL    32      24.201   6.892   5.178  1.00  0.00
ATOM     24  O   VAL    32      23.538   7.418   6.066  1.00  0.00
ATOM     25  N   GLU    34      24.748   5.675   5.322  1.00  0.00
ATOM     26  CA  GLU    34      24.561   4.918   6.564  1.00  0.00
ATOM     27  C   GLU    34      25.413   5.444   7.719  1.00  0.00
ATOM     28  O   GLU    34      26.394   6.162   7.512  1.00  0.00
ATOM     29  N   GLY    35      25.015   5.096   8.938  1.00  0.00
ATOM     30  CA  GLY    35      25.765   5.524  10.107  1.00  0.00
ATOM     31  C   GLY    35      24.862   5.754  11.298  1.00  0.00
ATOM     32  O   GLY    35      23.784   6.331  11.148  1.00  0.00
ATOM     33  N   ILE    36      25.311   5.305  12.472  1.00  0.00
ATOM     34  CA  ILE    36      24.553   5.435  13.713  1.00  0.00
ATOM     35  C   ILE    36      24.995   6.621  14.573  1.00  0.00
ATOM     36  O   ILE    36      24.408   6.879  15.627  1.00  0.00
ATOM     37  N   THR    37      26.042   7.317  14.133  1.00  0.00
ATOM     38  CA  THR    37      26.529   8.516  14.822  1.00  0.00
ATOM     39  C   THR    37      26.911   9.513  13.744  1.00  0.00
ATOM     40  O   THR    37      27.118   9.140  12.578  1.00  0.00
ATOM     41  N   VAL    38      27.002  10.778  14.125  1.00  0.00
ATOM     42  CA  VAL    38      27.370  11.814  13.172  1.00  0.00
ATOM     43  C   VAL    38      28.715  11.466  12.527  1.00  0.00
ATOM     44  O   VAL    38      28.883  11.592  11.312  1.00  0.00
ATOM     45  N   GLN    39      29.661  11.006  13.341  1.00  0.00
ATOM     46  CA  GLN    39      30.972  10.639  12.831  1.00  0.00
ATOM     47  C   GLN    39      30.918   9.543  11.782  1.00  0.00
ATOM     48  O   GLN    39      31.583   9.645  10.754  1.00  0.00
ATOM     49  N   THR    40      30.139   8.494  12.042  1.00  0.00
ATOM     50  CA  THR    40      30.029   7.386  11.093  1.00  0.00
ATOM     51  C   THR    40      29.480   7.898   9.765  1.00  0.00
ATOM     52  O   THR    40      29.975   7.531   8.695  1.00  0.00
ATOM     53  N   ALA    41      28.470   8.757   9.832  1.00  0.00
ATOM     54  CA  ALA    41      27.884   9.302   8.613  1.00  0.00
ATOM     55  C   ALA    41      28.897  10.143   7.840  1.00  0.00
ATOM     56  O   ALA    41      29.015  10.009   6.619  1.00  0.00
ATOM     57  N   ILE    42      29.631  11.002   8.542  1.00  0.00
ATOM     58  CA  ILE    42      30.619  11.846   7.889  1.00  0.00
ATOM     59  C   ILE    42      31.788  11.047   7.320  1.00  0.00
ATOM     60  O   ILE    42      32.325  11.409   6.280  1.00  0.00
ATOM     61  N   THR    43      32.178   9.959   7.987  1.00  0.00
ATOM     62  CA  THR    43      33.263   9.135   7.468  1.00  0.00
ATOM     63  C   THR    43      32.770   8.516   6.166  1.00  0.00
ATOM     64  O   THR    43      33.520   8.416   5.190  1.00  0.00
ATOM     65  N   GLN    44      31.503   8.106   6.131  1.00  0.00
ATOM     66  CA  GLN    44      30.981   7.532   4.896  1.00  0.00
ATOM     67  C   GLN    44      30.860   8.584   3.804  1.00  0.00
ATOM     68  O   GLN    44      31.057   8.287   2.623  1.00  0.00
ATOM     69  N   ILE    47      30.565   9.819   4.192  1.00  0.00
ATOM     70  CA  ILE    47      30.446  10.896   3.216  1.00  0.00
ATOM     71  C   ILE    47      31.755  11.074   2.445  1.00  0.00
ATOM     72  O   ILE    47      31.744  11.219   1.217  1.00  0.00
ATOM     73  N   LEU    48      32.883  11.047   3.155  1.00  0.00
ATOM     74  CA  LEU    48      34.168  11.228   2.490  1.00  0.00
ATOM     75  C   LEU    48      34.631   9.968   1.759  1.00  0.00
ATOM     76  O   LEU    48      35.499  10.034   0.891  1.00  0.00
ATOM     77  N   SER    49      34.057   8.822   2.109  1.00  0.00
ATOM     78  CA  SER    49      34.386   7.584   1.409  1.00  0.00
ATOM     79  C   SER    49      33.646   7.650   0.071  1.00  0.00
ATOM     80  O   SER    49      34.099   7.089  -0.931  1.00  0.00
ATOM     81  N   GLN    50      32.515   8.354   0.064  1.00  0.00
ATOM     82  CA  GLN    50      31.704   8.504  -1.151  1.00  0.00
ATOM     83  C   GLN    50      32.183   9.666  -2.025  1.00  0.00
ATOM     84  O   GLN    50      32.185   9.567  -3.257  1.00  0.00
ATOM     85  N   PHE    51      32.579  10.760  -1.383  1.00  0.00
ATOM     86  CA  PHE    51      33.053  11.957  -2.071  1.00  0.00
ATOM     87  C   PHE    51      34.310  12.459  -1.380  1.00  0.00
ATOM     88  O   PHE    51      34.276  13.420  -0.613  1.00  0.00
ATOM     89  N   PRO    52      35.450  11.815  -1.667  1.00  0.00
ATOM     90  CA  PRO    52      36.730  12.192  -1.064  1.00  0.00
ATOM     91  C   PRO    52      37.173  13.638  -1.274  1.00  0.00
ATOM     92  O   PRO    52      38.031  14.132  -0.543  1.00  0.00
ATOM     93  N   GLU    53      36.584  14.320  -2.255  1.00  0.00
ATOM     94  CA  GLU    53      36.916  15.712  -2.524  1.00  0.00
ATOM     95  C   GLU    53      36.573  16.582  -1.315  1.00  0.00
ATOM     96  O   GLU    53      37.120  17.667  -1.143  1.00  0.00
ATOM     97  N   ILE    54      35.673  16.089  -0.469  1.00  0.00
ATOM     98  CA  ILE    54      35.257  16.820   0.726  1.00  0.00
ATOM     99  C   ILE    54      36.136  16.573   1.948  1.00  0.00
ATOM    100  O   ILE    54      36.021  17.278   2.950  1.00  0.00
ATOM    101  N   ASP    55      37.016  15.581   1.873  1.00  0.00
ATOM    102  CA  ASP    55      37.860  15.249   3.018  1.00  0.00
ATOM    103  C   ASP    55      38.691  16.416   3.541  1.00  0.00
ATOM    104  O   ASP    55      38.725  16.673   4.748  1.00  0.00
ATOM    105  N   LEU    56      39.354  17.110   2.623  1.00  0.00
ATOM    106  CA  LEU    56      40.213  18.244   2.945  1.00  0.00
ATOM    107  C   LEU    56      39.487  19.376   3.660  1.00  0.00
ATOM    108  O   LEU    56      40.070  20.057   4.500  1.00  0.00
TER
END
