
#######################################################
#                                                     #
#                        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   20 (   99),  selected   20 , name T0322TS239_4_2
# Molecule2: number of CA atoms  142 ( 1089),  selected  142 , name T0322.pdb
# PARAMETERS: T0322TS239_4_2.T0322.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

# WARNING! The change of the parameter DIST cutoff may give you better result.

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      A      12           -
LGA    -       -      I      13           -
LGA    -       -      P      14           -
LGA    -       -      E      15           -
LGA    -       -      G      16           -
LGA    -       -      F      17           -
LGA    -       -      S      18           -
LGA    -       -      Q      19           -
LGA    -       -      L      20           -
LGA    -       -      N      21           -
LGA    -       -      W      22           -
LGA    -       -      S      23           -
LGA    M       1      R      24          1.331
LGA    S       2      G      25          1.919
LGA    -       -      F      26           -
LGA    -       -      G      27           -
LGA    -       -      R      28           -
LGA    D       3      Q      29          1.603
LGA    D       4      I      30          2.667
LGA    L       5      G      31          2.429
LGA    -       -      P      32           -
LGA    T       6      L      33          1.157
LGA    -       -      F      34           -
LGA    -       -      E      35           -
LGA    -       -      H      36           -
LGA    -       -      R      37           -
LGA    -       -      E      38           -
LGA    -       -      G      39           -
LGA    -       -      P      40           -
LGA    -       -      G      41           -
LGA    -       -      Q      42           -
LGA    -       -      A      43           -
LGA    -       -      R      44           -
LGA    D       7      L      45          3.271
LGA    A       8      A      46          1.266
LGA    Q       9      F      47          3.922
LGA    -       -      R      48           -
LGA    -       -      V      49           -
LGA    -       -      E      50           -
LGA    -       -      E      51           -
LGA    -       -      H      52           -
LGA    -       -      H      53           -
LGA    -       -      T      54           -
LGA    -       -      N      55           -
LGA    -       -      G      56           -
LGA    -       -      L      57           -
LGA    -       -      G      58           -
LGA    -       -      N      59           -
LGA    -       -      C      60           -
LGA    -       -      H      61           -
LGA    -       -      G      62           -
LGA    -       -      G      63           -
LGA    -       -      M      64           -
LGA    -       -      L      65           -
LGA    -       -      M      66           -
LGA    -       -      S      67           -
LGA    T      10      F      68          2.208
LGA    A      11      A      69          4.286
LGA    -       -      D      70           -
LGA    -       -      M      71           -
LGA    -       -      A      72           -
LGA    -       -      W      73           -
LGA    -       -      G      74           -
LGA    -       -      R      75           -
LGA    -       -      I      76           -
LGA    -       -      I      77           -
LGA    -       -      S      78           -
LGA    -       -      L      79           -
LGA    -       -      Q      80           -
LGA    -       -      K      81           -
LGA    -       -      S      82           -
LGA    -       -      Y      83           -
LGA    -       -      S      84           -
LGA    -       -      W      85           -
LGA    -       -      V      86           -
LGA    -       -      T      87           -
LGA    -       -      V      88           -
LGA    -       -      R      89           -
LGA    -       -      L      90           -
LGA    -       -      M      91           -
LGA    -       -      C      92           -
LGA    -       -      D      93           -
LGA    -       -      F      94           -
LGA    -       -      L      95           -
LGA    -       -      S      96           -
LGA    -       -      G      97           -
LGA    -       -      A      98           -
LGA    -       -      K      99           -
LGA    -       -      L     100           -
LGA    -       -      G     101           -
LGA    -       -      D     102           -
LGA    -       -      W     103           -
LGA    -       -      V     104           -
LGA    -       -      E     105           -
LGA    A      12      G     106          3.278
LGA    I      13      E     107           -
LGA    P      14      G     108           #
LGA    -       -      E     109           -
LGA    -       -      L     110           -
LGA    -       -      I     111           -
LGA    -       -      S     112           -
LGA    -       -      E     113           -
LGA    -       -      E     114           -
LGA    -       -      D     115           -
LGA    -       -      M     116           -
LGA    -       -      L     117           -
LGA    -       -      F     118           -
LGA    -       -      T     119           -
LGA    -       -      V     120           -
LGA    -       -      R     121           -
LGA    -       -      G     122           -
LGA    -       -      R     123           -
LGA    -       -      I     124           -
LGA    -       -      W     125           -
LGA    -       -      A     126           -
LGA    -       -      G     127           -
LGA    -       -      E     128           -
LGA    -       -      R     129           -
LGA    -       -      T     130           -
LGA    -       -      L     131           -
LGA    E      15      I     132          3.308
LGA    G      16      T     133          0.869
LGA    F      17      G     134          1.287
LGA    S      18      T     135          1.086
LGA    Q      19      G     136          3.071
LGA    S     142      V     137           -
LGA    -       -      F     138           -
LGA    -       -      K     139           -
LGA    -       -      A     140           -
LGA    -       -      L     141           -
LGA    -       -      S     142           -
LGA    -       -      A     143           -
LGA    -       -      R     144           -
LGA    -       -      K     145           -
LGA    -       -      P     146           -
LGA    -       -      R     147           -
LGA    -       -      P     148           -
LGA    -       -      G     149           -
LGA    -       -      E     150           -
LGA    -       -      L     151           -
LGA    -       -      A     152           -
LGA    -       -      Y     153           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   20  142    5.0     17    2.52    11.76      8.016     0.649

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.344785 * X  +  -0.784576 * Y  +   0.515329 * Z  +  19.239841
  Y_new =   0.689648 * X  +  -0.584158 * Y  +  -0.427954 * Z  +  12.595601
  Z_new =   0.636796 * X  +   0.207843 * Y  +   0.742490 * Z  + -17.751245 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.272941   -2.868651  [ DEG:    15.6384   -164.3616 ]
  Theta =  -0.690335   -2.451257  [ DEG:   -39.5533   -140.4467 ]
  Phi   =   2.034398   -1.107194  [ DEG:   116.5624    -63.4376 ]
 
# 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: T0322TS239_4_2                                
REMARK     2: T0322.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0322TS239_4_2.T0322.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   20  142   5.0   17   2.52   11.76   8.016
REMARK  ---------------------------------------------------------- 
MOLECULE T0322TS239_4_2
REMARK PARENT number 2
PFRMAT TS
TARGET T0322
PARENT 1vh5_A
ATOM      1  N   MET     1      11.855   2.989  -0.327  1.00  9.99
ATOM      2  CA  MET     1      10.822   2.271  -1.079  1.00  9.99
ATOM      3  C   MET     1       9.824   3.222  -1.731  1.00  9.99
ATOM      4  O   MET     1       9.002   3.834  -1.053  1.00  9.99
ATOM      5  CB  MET     1      10.075   1.275  -0.183  1.00  9.99
ATOM      6  N   SER     2       9.841   3.308  -3.058  1.00  9.99
ATOM      7  CA  SER     2       8.962   4.292  -3.734  1.00  9.99
ATOM      8  C   SER     2       7.595   3.733  -4.113  1.00  9.99
ATOM      9  O   SER     2       6.655   4.485  -4.332  1.00  9.99
ATOM     10  CB  SER     2       9.668   4.896  -4.973  1.00  9.99
ATOM     11  N   ASP     3       2.279   0.074  -4.970  1.00  9.99
ATOM     12  CA  ASP     3       1.612  -1.169  -5.322  1.00  9.99
ATOM     13  C   ASP     3       2.650  -2.244  -5.290  1.00  9.99
ATOM     14  O   ASP     3       3.800  -2.025  -5.646  1.00  9.99
ATOM     15  CB  ASP     3       1.028  -1.127  -6.734  1.00  9.99
ATOM     16  N   ASP     4       2.238  -3.438  -4.881  1.00  9.99
ATOM     17  CA  ASP     4       3.137  -4.586  -4.952  1.00  9.99
ATOM     18  C   ASP     4       2.857  -5.372  -6.237  1.00  9.99
ATOM     19  O   ASP     4       1.716  -5.544  -6.650  1.00  9.99
ATOM     20  CB  ASP     4       2.984  -5.473  -3.701  1.00  9.99
ATOM     21  N   LEU     5       3.918  -5.805  -6.887  1.00  9.99
ATOM     22  CA  LEU     5       3.809  -6.662  -8.060  1.00  9.99
ATOM     23  C   LEU     5       4.986  -7.625  -8.095  1.00  9.99
ATOM     24  O   LEU     5       6.086  -7.279  -7.676  1.00  9.99
ATOM     25  CB  LEU     5       3.701  -5.789  -9.365  1.00  9.99
ATOM     26  N   THR     6       4.736  -8.857  -8.538  1.00  9.99
ATOM     27  CA  THR     6       5.821  -9.794  -8.800  1.00  9.99
ATOM     28  C   THR     6       6.357  -9.543 -10.198  1.00  9.99
ATOM     29  O   THR     6       5.660  -8.947 -11.031  1.00  9.99
ATOM     30  CB  THR     6       5.332 -11.243  -8.746  1.00  9.99
ATOM     31  N   ASP     7       7.570 -10.028 -10.457  1.00  9.99
ATOM     32  CA  ASP     7       8.133 -10.007 -11.805  1.00  9.99
ATOM     33  C   ASP     7       7.245 -10.768 -12.776  1.00  9.99
ATOM     34  O   ASP     7       7.036 -10.362 -13.905  1.00  9.99
ATOM     35  CB  ASP     7       9.559 -10.564 -11.831  1.00  9.99
ATOM     36  N   ALA     8       6.699 -11.887 -12.308  1.00  9.99
ATOM     37  CA  ALA     8       5.764 -12.664 -13.096  1.00  9.99
ATOM     38  C   ALA     8       4.561 -11.856 -13.600  1.00  9.99
ATOM     39  O   ALA     8       4.222 -11.920 -14.786  1.00  9.99
ATOM     40  CB  ALA     8       5.265 -13.853 -12.263  1.00  9.99
ATOM     41  N   GLN     9       3.888 -11.137 -12.701  1.00  9.99
ATOM     42  CA  GLN     9       2.679 -10.396 -13.073  1.00  9.99
ATOM     43  C   GLN     9       3.025  -9.184 -13.960  1.00  9.99
ATOM     44  O   GLN     9       2.253  -8.816 -14.852  1.00  9.99
ATOM     45  CB  GLN     9       1.868  -9.980 -11.820  1.00  9.99
ATOM     46  N   THR    10       4.199  -8.603 -13.711  1.00  9.99
ATOM     47  CA  THR    10       4.742  -7.514 -14.531  1.00  9.99
ATOM     48  C   THR    10       4.940  -8.013 -15.973  1.00  9.99
ATOM     49  O   THR    10       4.465  -7.412 -16.937  1.00  9.99
ATOM     50  CB  THR    10       6.082  -7.063 -13.948  1.00  9.99
ATOM     51  N   ALA    11       5.604  -9.160 -16.110  1.00  9.99
ATOM     52  CA  ALA    11       5.865  -9.735 -17.420  1.00  9.99
ATOM     53  C   ALA    11       4.620 -10.234 -18.138  1.00  9.99
ATOM     54  O   ALA    11       4.576 -10.240 -19.363  1.00  9.99
ATOM     55  CB  ALA    11       6.947 -10.801 -17.324  1.00  9.99
ATOM     56  N   ALA    12       3.594 -10.627 -17.371  1.00  9.99
ATOM     57  CA  ALA    12       2.342 -11.058 -17.969  1.00  9.99
ATOM     58  C   ALA    12       1.626  -9.942 -18.727  1.00  9.99
ATOM     59  O   ALA    12       0.854 -10.209 -19.640  1.00  9.99
ATOM     60  CB  ALA    12       1.421 -11.659 -16.909  1.00  9.99
ATOM     61  N   ILE    13       1.914  -8.686 -18.375  1.00  9.99
ATOM     62  CA  ILE    13       1.217  -7.548 -18.985  1.00  9.99
ATOM     63  C   ILE    13       1.442  -7.424 -20.490  1.00  9.99
ATOM     64  O   ILE    13       0.578  -6.944 -21.230  1.00  9.99
ATOM     65  CB  ILE    13       1.692  -6.246 -18.342  1.00  9.99
ATOM     66  N   PRO    14       2.625  -7.849 -20.920  1.00  9.99
ATOM     67  CA  PRO    14       3.101  -7.646 -22.275  1.00  9.99
ATOM     68  C   PRO    14       2.531  -8.600 -23.306  1.00  9.99
ATOM     69  O   PRO    14       2.725  -8.396 -24.504  1.00  9.99
ATOM     70  CB  PRO    14       4.636  -7.735 -22.259  1.00  9.99
ATOM     71  N   GLU    15       1.840  -9.660 -22.866  1.00  9.99
ATOM     72  CA  GLU    15       1.369 -10.702 -23.800  1.00  9.99
ATOM     73  C   GLU    15       0.351 -10.153 -24.773  1.00  9.99
ATOM     74  O   GLU    15      -0.665  -9.580 -24.360  1.00  9.99
ATOM     75  CB  GLU    15       0.726 -11.888 -23.050  1.00  9.99
ATOM     76  N   GLY    16       0.631 -10.324 -26.062  1.00  9.99
ATOM     77  CA  GLY    16      -0.276  -9.894 -27.100  1.00  9.99
ATOM     78  C   GLY    16      -0.201  -8.404 -27.418  1.00  9.99
ATOM     79  O   GLY    16      -1.068  -7.885 -28.122  1.00  9.99
ATOM     80  N   PHE    17       0.830  -7.725 -26.909  1.00  9.99
ATOM     81  CA  PHE    17       1.041  -6.296 -27.229  1.00  9.99
ATOM     82  C   PHE    17       2.507  -6.057 -27.534  1.00  9.99
ATOM     83  O   PHE    17       3.288  -6.992 -27.612  1.00  9.99
ATOM     84  CB  PHE    17       0.438  -5.353 -26.157  1.00  9.99
ATOM     85  N   SER    18       2.899  -4.794 -27.681  1.00  9.99
ATOM     86  CA  SER    18       4.231  -4.508 -28.201  1.00  9.99
ATOM     87  C   SER    18       5.344  -5.044 -27.291  1.00  9.99
ATOM     88  O   SER    18       6.377  -5.497 -27.777  1.00  9.99
ATOM     89  CB  SER    18       4.412  -3.003 -28.431  1.00  9.99
ATOM     90  N   GLN    19       5.149  -4.940 -25.983  1.00  9.99
ATOM     91  CA  GLN    19       6.166  -5.399 -25.048  1.00  9.99
ATOM     92  C   GLN    19       6.452  -6.907 -25.305  1.00  9.99
ATOM     93  O   GLN    19       7.606  -7.315 -25.395  1.00  9.99
ATOM     94  CB  GLN    19       5.770  -5.128 -23.571  1.00  9.99
ATOM    639  N   SER   142      -6.840  10.575 -12.020  1.00  9.99
ATOM    640  CA  SER   142      -7.500  10.259 -10.769  1.00  9.99
ATOM    641  C   SER   142      -8.668   9.349 -11.049  1.00  9.99
ATOM    642  O   SER   142      -9.007   8.510 -10.227  1.00  9.99
ATOM    643  CB  SER   142      -7.938  11.562 -10.038  1.00  9.99
TER
END
