
#######################################################
#                                                     #
#                        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   28 (  138),  selected   28 , name T0322TS239_5_1
# Molecule2: number of CA atoms  142 ( 1089),  selected  142 , name T0322.pdb
# PARAMETERS: T0322TS239_5_1.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    M       1      A      12           -
LGA    S       2      I      13           -
LGA    -       -      P      14           -
LGA    -       -      E      15           -
LGA    -       -      G      16           -
LGA    -       -      F      17           -
LGA    D       3      S      18          3.848
LGA    D       4      Q      19           #
LGA    -       -      L      20           -
LGA    -       -      N      21           -
LGA    -       -      W      22           -
LGA    -       -      S      23           -
LGA    -       -      R      24           -
LGA    -       -      G      25           -
LGA    -       -      F      26           -
LGA    -       -      G      27           -
LGA    -       -      R      28           -
LGA    -       -      Q      29           -
LGA    -       -      I      30           -
LGA    -       -      G      31           -
LGA    -       -      P      32           -
LGA    -       -      L      33           -
LGA    -       -      F      34           -
LGA    -       -      E      35           -
LGA    L       5      H      36          3.968
LGA    T       6      R      37          2.653
LGA    D       7      E      38          3.055
LGA    -       -      G      39           -
LGA    A       8      P      40          3.737
LGA    Q       9      G      41          2.873
LGA    T      10      Q      42          3.448
LGA    A      11      A      43          0.810
LGA    A      12      R      44          2.155
LGA    I      13      L      45          2.344
LGA    P      14      A      46           -
LGA    E      15      F      47           -
LGA    G      16      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    -       -      F      68           -
LGA    F      17      A      69          1.053
LGA    S      18      D      70          0.894
LGA    Q      19      M      71          3.144
LGA    -       -      A      72           -
LGA    Q      29      W      73          1.197
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    -       -      G     106           -
LGA    -       -      E     107           -
LGA    -       -      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    -       -      I     132           -
LGA    -       -      T     133           -
LGA    -       -      G     134           -
LGA    -       -      T     135           -
LGA    I      30      G     136          2.277
LGA    -       -      V     137           -
LGA    G      31      F     138          2.893
LGA    -       -      K     139           -
LGA    P      32      A     140           #
LGA    L      33      L     141           -
LGA    F      34      S     142           -
LGA    -       -      A     143           -
LGA    -       -      R     144           -
LGA    -       -      K     145           -
LGA    -       -      P     146           -
LGA    -       -      R     147           -
LGA    -       -      P     148           -
LGA    E      35      G     149           #
LGA    H      36      E     150          2.367
LGA    R      37      L     151          4.099
LGA    -       -      A     152           -
LGA    -       -      Y     153           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   28  142    5.0     18    2.80     5.56      8.633     0.621

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.086411 * X  +  -0.551876 * Y  +   0.829437 * Z  +  23.038128
  Y_new =  -0.203060 * X  +  -0.805318 * Y  +  -0.556983 * Z  +   5.730142
  Z_new =   0.975346 * X  +  -0.216555 * Y  +  -0.042476 * Z  +  -2.590622 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.764481    1.377112  [ DEG:  -101.0973     78.9027 ]
  Theta =  -1.348283   -1.793310  [ DEG:   -77.2509   -102.7491 ]
  Phi   =  -1.973127    1.168466  [ DEG:  -113.0518     66.9482 ]
 
# 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_5_1                                
REMARK     2: T0322.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0322TS239_5_1.T0322.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   28  142   5.0   18   2.80    5.56   8.633
REMARK  ---------------------------------------------------------- 
MOLECULE T0322TS239_5_1
REMARK PARENT number 1
PFRMAT TS
TARGET T0322
PARENT 1vh5_A
ATOM      1  N   MET     1      25.123 -15.172   0.436  1.00  9.99
ATOM      2  CA  MET     1      23.933 -15.475  -0.365  1.00  9.99
ATOM      3  C   MET     1      22.667 -14.885   0.245  1.00  9.99
ATOM      4  O   MET     1      22.181 -15.360   1.269  1.00  9.99
ATOM      5  CB  MET     1      23.760 -16.988  -0.551  1.00  9.99
ATOM      6  N   SER     2      22.082 -13.887  -0.411  1.00  9.99
ATOM      7  CA  SER     2      20.907 -13.212   0.190  1.00  9.99
ATOM      8  C   SER     2      19.573 -13.827  -0.215  1.00  9.99
ATOM      9  O   SER     2      18.569 -13.634   0.457  1.00  9.99
ATOM     10  CB  SER     2      20.927 -11.696  -0.124  1.00  9.99
ATOM     11  N   ASP     3      14.795 -17.505  -2.672  1.00  9.99
ATOM     12  CA  ASP     3      14.159 -18.239  -3.754  1.00  9.99
ATOM     13  C   ASP     3      15.197 -18.443  -4.810  1.00  9.99
ATOM     14  O   ASP     3      16.041 -17.587  -5.041  1.00  9.99
ATOM     15  CB  ASP     3      13.006 -17.455  -4.379  1.00  9.99
ATOM     16  N   ASP     4      15.122 -19.583  -5.486  1.00  9.99
ATOM     17  CA  ASP     4      15.997 -19.812  -6.631  1.00  9.99
ATOM     18  C   ASP     4      15.246 -19.463  -7.921  1.00  9.99
ATOM     19  O   ASP     4      14.062 -19.741  -8.073  1.00  9.99
ATOM     20  CB  ASP     4      16.500 -21.268  -6.647  1.00  9.99
ATOM     21  N   LEU     5      15.942 -18.808  -8.829  1.00  9.99
ATOM     22  CA  LEU     5      15.400 -18.507 -10.147  1.00  9.99
ATOM     23  C   LEU     5      16.521 -18.541 -11.176  1.00  9.99
ATOM     24  O   LEU     5      17.655 -18.186 -10.871  1.00  9.99
ATOM     25  CB  LEU     5      14.641 -17.128 -10.125  1.00  9.99
ATOM     26  N   THR     6      16.214 -19.031 -12.377  1.00  9.99
ATOM     27  CA  THR     6      17.149 -18.928 -13.489  1.00  9.99
ATOM     28  C   THR     6      16.979 -17.570 -14.146  1.00  9.99
ATOM     29  O   THR     6      15.933 -16.928 -13.981  1.00  9.99
ATOM     30  CB  THR     6      16.872 -19.993 -14.553  1.00  9.99
ATOM     31  N   ASP     7      17.989 -17.159 -14.913  1.00  9.99
ATOM     32  CA  ASP     7      17.887 -15.955 -15.735  1.00  9.99
ATOM     33  C   ASP     7      16.734 -16.068 -16.719  1.00  9.99
ATOM     34  O   ASP     7      16.006 -15.121 -16.963  1.00  9.99
ATOM     35  CB  ASP     7      19.196 -15.663 -16.473  1.00  9.99
ATOM     36  N   ALA     8      16.559 -17.262 -17.275  1.00  9.99
ATOM     37  CA  ALA     8      15.447 -17.533 -18.163  1.00  9.99
ATOM     38  C   ALA     8      14.077 -17.214 -17.552  1.00  9.99
ATOM     39  O   ALA     8      13.251 -16.549 -18.186  1.00  9.99
ATOM     40  CB  ALA     8      15.484 -19.007 -18.588  1.00  9.99
ATOM     41  N   GLN     9      13.812 -17.723 -16.347  1.00  9.99
ATOM     42  CA  GLN     9      12.502 -17.539 -15.717  1.00  9.99
ATOM     43  C   GLN     9      12.303 -16.076 -15.274  1.00  9.99
ATOM     44  O   GLN     9      11.183 -15.553 -15.315  1.00  9.99
ATOM     45  CB  GLN     9      12.300 -18.529 -14.542  1.00  9.99
ATOM     46  N   THR    10      13.405 -15.436 -14.885  1.00  9.99
ATOM     47  CA  THR    10      13.422 -14.008 -14.543  1.00  9.99
ATOM     48  C   THR    10      13.001 -13.186 -15.774  1.00  9.99
ATOM     49  O   THR    10      12.093 -12.357 -15.718  1.00  9.99
ATOM     50  CB  THR    10      14.833 -13.610 -14.110  1.00  9.99
ATOM     51  N   ALA    11      13.637 -13.465 -16.911  1.00  9.99
ATOM     52  CA  ALA    11      13.338 -12.754 -18.144  1.00  9.99
ATOM     53  C   ALA    11      11.955 -13.044 -18.708  1.00  9.99
ATOM     54  O   ALA    11      11.369 -12.196 -19.372  1.00  9.99
ATOM     55  CB  ALA    11      14.442 -12.980 -19.166  1.00  9.99
ATOM     56  N   ALA    12      11.420 -14.238 -18.419  1.00  9.99
ATOM     57  CA  ALA    12      10.078 -14.578 -18.860  1.00  9.99
ATOM     58  C   ALA    12       9.000 -13.702 -18.227  1.00  9.99
ATOM     59  O   ALA    12       7.930 -13.525 -18.797  1.00  9.99
ATOM     60  CB  ALA    12       9.787 -16.055 -18.601  1.00  9.99
ATOM     61  N   ILE    13       9.298 -13.118 -17.062  1.00  9.99
ATOM     62  CA  ILE    13       8.300 -12.327 -16.334  1.00  9.99
ATOM     63  C   ILE    13       7.818 -11.094 -17.094  1.00  9.99
ATOM     64  O   ILE    13       6.674 -10.654 -16.942  1.00  9.99
ATOM     65  CB  ILE    13       8.890 -11.846 -15.008  1.00  9.99
ATOM     66  N   PRO    14       8.718 -10.539 -17.898  1.00  9.99
ATOM     67  CA  PRO    14       8.519  -9.264 -18.560  1.00  9.99
ATOM     68  C   PRO    14       7.640  -9.311 -19.794  1.00  9.99
ATOM     69  O   PRO    14       7.259  -8.263 -20.316  1.00  9.99
ATOM     70  CB  PRO    14       9.901  -8.689 -18.912  1.00  9.99
ATOM     71  N   GLU    15       7.318 -10.513 -20.291  1.00  9.99
ATOM     72  CA  GLU    15       6.578 -10.637 -21.561  1.00  9.99
ATOM     73  C   GLU    15       5.187 -10.056 -21.452  1.00  9.99
ATOM     74  O   GLU    15       4.415 -10.445 -20.567  1.00  9.99
ATOM     75  CB  GLU    15       6.449 -12.112 -22.002  1.00  9.99
ATOM     76  N   GLY    16       4.877  -9.122 -22.346  1.00  9.99
ATOM     77  CA  GLY    16       3.567  -8.517 -22.388  1.00  9.99
ATOM     78  C   GLY    16       3.355  -7.412 -21.358  1.00  9.99
ATOM     79  O   GLY    16       2.220  -6.977 -21.154  1.00  9.99
ATOM     80  N   PHE    17       4.437  -6.960 -20.720  1.00  9.99
ATOM     81  CA  PHE    17       4.350  -5.832 -19.766  1.00  9.99
ATOM     82  C   PHE    17       5.497  -4.872 -20.013  1.00  9.99
ATOM     83  O   PHE    17       6.244  -5.024 -20.967  1.00  9.99
ATOM     84  CB  PHE    17       4.205  -6.307 -18.299  1.00  9.99
ATOM     85  N   SER    18       5.664  -3.886 -19.134  1.00  9.99
ATOM     86  CA  SER    18       6.591  -2.802 -19.435  1.00  9.99
ATOM     87  C   SER    18       8.038  -3.291 -19.587  1.00  9.99
ATOM     88  O   SER    18       8.782  -2.775 -20.416  1.00  9.99
ATOM     89  CB  SER    18       6.511  -1.707 -18.364  1.00  9.99
ATOM     90  N   GLN    19       8.438  -4.242 -18.753  1.00  9.99
ATOM     91  CA  GLN    19       9.803  -4.746 -18.810  1.00  9.99
ATOM     92  C   GLN    19      10.082  -5.302 -20.236  1.00  9.99
ATOM     93  O   GLN    19      11.106  -4.991 -20.836  1.00  9.99
ATOM     94  CB  GLN    19      10.085  -5.805 -17.710  1.00  9.99
ATOM     95  N   GLN    29       9.142  -6.085 -20.757  1.00  9.99
ATOM     96  CA  GLN    29       9.248  -6.636 -22.101  1.00  9.99
ATOM     97  C   GLN    29       9.212  -5.549 -23.158  1.00  9.99
ATOM     98  O   GLN    29      10.029  -5.549 -24.085  1.00  9.99
ATOM     99  CB  GLN    29       8.116  -7.654 -22.320  1.00  9.99
ATOM    100  N   ILE    30       8.280  -4.622 -23.009  1.00  9.99
ATOM    101  CA  ILE    30       8.126  -3.502 -23.954  1.00  9.99
ATOM    102  C   ILE    30       9.414  -2.709 -24.114  1.00  9.99
ATOM    103  O   ILE    30       9.755  -2.306 -25.217  1.00  9.99
ATOM    104  CB  ILE    30       6.978  -2.592 -23.499  1.00  9.99
ATOM    105  N   GLY    31      10.119  -2.467 -23.005  1.00  9.99
ATOM    106  CA  GLY    31      11.338  -1.680 -23.063  1.00  9.99
ATOM    107  C   GLY    31      12.614  -2.497 -23.307  1.00  9.99
ATOM    108  O   GLY    31      13.722  -1.932 -23.315  1.00  9.99
ATOM    109  N   PRO    32      12.465  -3.821 -23.447  1.00  9.99
ATOM    110  CA  PRO    32      13.620  -4.720 -23.633  1.00  9.99
ATOM    111  C   PRO    32      14.596  -4.664 -22.475  1.00  9.99
ATOM    112  O   PRO    32      15.800  -4.705 -22.674  1.00  9.99
ATOM    113  CB  PRO    32      14.352  -4.408 -24.960  1.00  9.99
ATOM    114  N   LEU    33      14.056  -4.554 -21.270  1.00  9.99
ATOM    115  CA  LEU    33      14.891  -4.753 -20.098  1.00  9.99
ATOM    116  C   LEU    33      15.232  -6.252 -19.998  1.00  9.99
ATOM    117  O   LEU    33      14.318  -7.098 -20.064  1.00  9.99
ATOM    118  CB  LEU    33      14.155  -4.203 -18.855  1.00  9.99
ATOM    119  N   PHE    34      16.524  -6.560 -19.835  1.00  9.99
ATOM    120  CA  PHE    34      16.998  -7.941 -19.830  1.00  9.99
ATOM    121  C   PHE    34      17.819  -8.148 -18.560  1.00  9.99
ATOM    122  O   PHE    34      18.850  -7.498 -18.363  1.00  9.99
ATOM    123  CB  PHE    34      17.926  -8.203 -21.030  1.00  9.99
ATOM    124  N   GLU    35      17.401  -9.102 -17.732  1.00  9.99
ATOM    125  CA  GLU    35      18.267  -9.538 -16.622  1.00  9.99
ATOM    126  C   GLU    35      19.487 -10.302 -17.160  1.00  9.99
ATOM    127  O   GLU    35      19.346 -11.164 -18.026  1.00  9.99
ATOM    128  CB  GLU    35      17.459 -10.378 -15.609  1.00  9.99
ATOM    129  N   HIS    36      20.659  -9.949 -16.667  1.00  9.99
ATOM    130  CA  HIS    36      21.933 -10.449 -17.188  1.00  9.99
ATOM    131  C   HIS    36      22.734 -11.242 -16.181  1.00  9.99
ATOM    132  O   HIS    36      23.615 -12.027 -16.570  1.00  9.99
ATOM    133  CB  HIS    36      22.821  -9.281 -17.582  1.00  9.99
ATOM    134  N   ARG    37      22.562 -10.983 -14.885  1.00  9.99
ATOM    135  CA  ARG    37      23.419 -11.614 -13.899  1.00  9.99
ATOM    136  C   ARG    37      22.727 -11.687 -12.556  1.00  9.99
ATOM    137  O   ARG    37      22.178 -10.676 -12.086  1.00  9.99
ATOM    138  CB  ARG    37      24.742 -10.840 -13.797  1.00  9.99
TER
END
