
#######################################################
#                                                     #
#                        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 (  135),  selected   27 , name T0297TS239_3_2
# Molecule2: number of CA atoms  211 ( 1703),  selected  211 , name T0297.pdb
# PARAMETERS: T0297TS239_3_2.T0297.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      M       1           -
LGA    -       -      A       2           -
LGA    -       -      V       3           -
LGA    -       -      Q       4           -
LGA    -       -      L       5           -
LGA    -       -      L       6           -
LGA    -       -      E       7           -
LGA    -       -      N       8           -
LGA    -       -      W       9           -
LGA    -       -      L      10           -
LGA    -       -      L      11           -
LGA    -       -      K      12           -
LGA    -       -      E      13           -
LGA    M       1      Q      14          2.092
LGA    -       -      E      15           -
LGA    -       -      K      16           -
LGA    A       2      I      17          0.852
LGA    V       3      Q      18          6.223
LGA    -       -      T      19           -
LGA    -       -      K      20           -
LGA    -       -      Y      21           -
LGA    -       -      R      22           -
LGA    -       -      H      23           -
LGA    -       -      L      24           -
LGA    -       -      N      25           -
LGA    -       -      H      26           -
LGA    -       -      I      27           -
LGA    -       -      S      28           -
LGA    -       -      V      29           -
LGA    -       -      V      30           -
LGA    -       -      E      31           -
LGA    -       -      P      32           -
LGA    -       -      N      33           -
LGA    -       -      I      34           -
LGA    -       -      L      35           -
LGA    -       -      F      36           -
LGA    -       -      I      37           -
LGA    -       -      G      38           -
LGA    -       -      D      39           -
LGA    -       -      S      40           -
LGA    -       -      I      41           -
LGA    -       -      V      42           -
LGA    -       -      E      43           -
LGA    -       -      Y      44           -
LGA    -       -      Y      45           -
LGA    -       -      P      46           -
LGA    -       -      L      47           -
LGA    -       -      Q      48           -
LGA    -       -      E      49           -
LGA    -       -      L      50           -
LGA    -       -      F      51           -
LGA    -       -      G      52           -
LGA    -       -      T      53           -
LGA    -       -      S      54           -
LGA    -       -      K      55           -
LGA    -       -      T      56           -
LGA    -       -      I      57           -
LGA    -       -      V      58           -
LGA    -       -      N      59           -
LGA    -       -      R      60           -
LGA    Q       4      G      61          3.849
LGA    L       5      I      62          3.241
LGA    -       -      R      63           -
LGA    -       -      G      64           -
LGA    L       6      Y      65          4.073
LGA    E       7      Q      66          1.625
LGA    -       -      T      67           -
LGA    -       -      G      68           -
LGA    -       -      L      69           -
LGA    -       -      L      70           -
LGA    -       -      L      71           -
LGA    -       -      E      72           -
LGA    -       -      N      73           -
LGA    -       -      L      74           -
LGA    -       -      D      75           -
LGA    -       -      A      76           -
LGA    -       -      H      77           -
LGA    -       -      L      78           -
LGA    -       -      Y      79           -
LGA    -       -      G      80           -
LGA    -       -      G      81           -
LGA    -       -      A      82           -
LGA    -       -      V      83           -
LGA    -       -      D      84           -
LGA    -       -      K      85           -
LGA    -       -      I      86           -
LGA    -       -      F      87           -
LGA    -       -      L      88           -
LGA    -       -      L      89           -
LGA    -       -      I      90           -
LGA    -       -      G      91           -
LGA    -       -      T      92           -
LGA    N       8      N      93          3.999
LGA    W       9      D      94          3.092
LGA    -       -      I      95           -
LGA    -       -      G      96           -
LGA    -       -      K      97           -
LGA    -       -      D      98           -
LGA    L      10      V      99          2.091
LGA    L      11      P     100          1.158
LGA    K      12      V     101          0.417
LGA    E      13      N     102          1.283
LGA    -       -      E     103           -
LGA    -       -      A     104           -
LGA    Q      14      L     105          1.222
LGA    E      15      N     106          1.661
LGA    K      16      N     107          1.437
LGA    I      17      L     108          1.176
LGA    Q      18      E     109          1.141
LGA    T      19      A     110          0.949
LGA    K      20      I     111          0.725
LGA    Y      21      I     112          0.511
LGA    R      22      Q     113          0.702
LGA    H      23      S     114          0.364
LGA    L      24      V     115          0.752
LGA    N      25      A     116          0.734
LGA    H      26      R     117          1.105
LGA    I      27      D     118          1.096
LGA    -       -      Y     119           -
LGA    -       -      P     120           -
LGA    -       -      L     121           -
LGA    -       -      T     122           -
LGA    -       -      E     123           -
LGA    -       -      I     124           -
LGA    -       -      K     125           -
LGA    -       -      L     126           -
LGA    -       -      L     127           -
LGA    -       -      S     128           -
LGA    -       -      I     129           -
LGA    -       -      L     130           -
LGA    -       -      P     131           -
LGA    -       -      V     132           -
LGA    -       -      N     133           -
LGA    -       -      E     134           -
LGA    -       -      R     135           -
LGA    -       -      E     136           -
LGA    -       -      E     137           -
LGA    -       -      Y     138           -
LGA    -       -      Q     139           -
LGA    -       -      Q     140           -
LGA    -       -      A     141           -
LGA    -       -      V     142           -
LGA    -       -      Y     143           -
LGA    -       -      I     144           -
LGA    -       -      R     145           -
LGA    -       -      S     146           -
LGA    -       -      N     147           -
LGA    -       -      E     148           -
LGA    -       -      K     149           -
LGA    -       -      I     150           -
LGA    -       -      Q     151           -
LGA    -       -      N     152           -
LGA    -       -      W     153           -
LGA    -       -      N     154           -
LGA    -       -      Q     155           -
LGA    -       -      A     156           -
LGA    -       -      Y     157           -
LGA    -       -      Q     158           -
LGA    -       -      E     159           -
LGA    -       -      L     160           -
LGA    -       -      A     161           -
LGA    -       -      S     162           -
LGA    -       -      A     163           -
LGA    -       -      Y     164           -
LGA    -       -      M     165           -
LGA    -       -      Q     166           -
LGA    -       -      V     167           -
LGA    -       -      E     168           -
LGA    -       -      F     169           -
LGA    -       -      V     170           -
LGA    -       -      P     171           -
LGA    -       -      V     172           -
LGA    -       -      F     173           -
LGA    -       -      D     174           -
LGA    -       -      C     175           -
LGA    -       -      L     176           -
LGA    -       -      T     177           -
LGA    -       -      D     178           -
LGA    -       -      Q     179           -
LGA    -       -      A     180           -
LGA    -       -      G     181           -
LGA    -       -      Q     182           -
LGA    -       -      L     183           -
LGA    -       -      K     184           -
LGA    -       -      K     185           -
LGA    -       -      E     186           -
LGA    -       -      Y     187           -
LGA    -       -      T     188           -
LGA    -       -      T     189           -
LGA    -       -      D     190           -
LGA    -       -      G     191           -
LGA    -       -      L     192           -
LGA    -       -      H     193           -
LGA    -       -      L     194           -
LGA    -       -      S     195           -
LGA    -       -      I     196           -
LGA    -       -      A     197           -
LGA    -       -      G     198           -
LGA    -       -      Y     199           -
LGA    -       -      Q     200           -
LGA    -       -      A     201           -
LGA    -       -      L     202           -
LGA    -       -      S     203           -
LGA    -       -      K     204           -
LGA    -       -      S     205           -
LGA    -       -      L     206           -
LGA    -       -      K     207           -
LGA    -       -      D     208           -
LGA    -       -      Y     209           -
LGA    -       -      L     210           -
LGA    -       -      Y     211           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   27  211    5.0     27    2.25     3.70     10.952     1.151

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.858910 * X  +  -0.113979 * Y  +   0.499282 * Z  + -27.748117
  Y_new =  -0.320457 * X  +  -0.880085 * Y  +   0.350367 * Z  +  76.118607
  Z_new =   0.399477 * X  +  -0.460932 * Y  +  -0.792439 * Z  +  -3.704297 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.614766    0.526827  [ DEG:  -149.8150     30.1850 ]
  Theta =  -0.410946   -2.730647  [ DEG:   -23.5455   -156.4545 ]
  Phi   =  -0.357101    2.784492  [ DEG:   -20.4604    159.5396 ]
 
# 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: T0297TS239_3_2                                
REMARK     2: T0297.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0297TS239_3_2.T0297.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   27  211   5.0   27   2.25    3.70  10.952
REMARK  ---------------------------------------------------------- 
MOLECULE T0297TS239_3_2
REMARK PARENT number 2
PFRMAT TS
TARGET T0297
PARENT 1wab
ATOM      1  N   MET     1      19.183  85.519   2.658  1.00  9.99
ATOM      2  CA  MET     1      20.453  85.047   3.282  1.00  9.99
ATOM      3  C   MET     1      20.444  85.196   4.811  1.00  9.99
ATOM      4  O   MET     1      21.292  84.554   5.461  1.00  9.99
ATOM      5  CB  MET     1      21.627  85.803   2.660  1.00  9.99
ATOM      6  N   ALA     2      19.521  86.035   5.311  1.00  9.99
ATOM      7  CA  ALA     2      19.509  86.286   6.770  1.00  9.99
ATOM      8  C   ALA     2      18.197  85.805   7.364  1.00  9.99
ATOM      9  O   ALA     2      18.008  86.144   8.556  1.00  9.99
ATOM     10  CB  ALA     2      19.839  87.755   7.046  1.00  9.99
ATOM     11  N   VAL     3      17.387  85.097   6.598  1.00  9.99
ATOM     12  CA  VAL     3      16.136  84.542   7.205  1.00  9.99
ATOM     13  C   VAL     3      16.478  83.105   7.561  1.00  9.99
ATOM     14  O   VAL     3      16.583  82.280   6.659  1.00  9.99
ATOM     15  CB  VAL     3      15.044  84.619   6.160  1.00  9.99
ATOM     16  N   GLN     4      16.528  82.788   8.844  1.00  9.99
ATOM     17  CA  GLN     4      16.992  81.432   9.227  1.00  9.99
ATOM     18  C   GLN     4      16.039  80.380   8.713  1.00  9.99
ATOM     19  O   GLN     4      14.821  80.538   8.879  1.00  9.99
ATOM     20  CB  GLN     4      17.137  81.473  10.753  1.00  9.99
ATOM     21  N   LEU     5      16.594  79.334   8.112  1.00  9.99
ATOM     22  CA  LEU     5      15.743  78.262   7.590  1.00  9.99
ATOM     23  C   LEU     5      16.583  77.010   7.508  1.00  9.99
ATOM     24  O   LEU     5      17.808  77.114   7.236  1.00  9.99
ATOM     25  CB  LEU     5      15.129  78.649   6.199  1.00  9.99
ATOM     26  N   LEU     6      15.993  75.890   7.832  1.00  9.99
ATOM     27  CA  LEU     6      16.713  74.631   7.747  1.00  9.99
ATOM     28  C   LEU     6      16.764  74.179   6.298  1.00  9.99
ATOM     29  O   LEU     6      15.999  74.685   5.460  1.00  9.99
ATOM     30  CB  LEU     6      15.922  73.659   8.628  1.00  9.99
ATOM     31  N   GLU     7      17.668  73.244   6.025  1.00  9.99
ATOM     32  CA  GLU     7      17.604  72.621   4.659  1.00  9.99
ATOM     33  C   GLU     7      16.458  71.628   4.647  1.00  9.99
ATOM     34  O   GLU     7      16.374  70.687   5.465  1.00  9.99
ATOM     35  CB  GLU     7      18.972  72.040   4.328  1.00  9.99
ATOM     36  N   ASN     8      15.641  71.777   3.612  1.00  9.99
ATOM     37  CA  ASN     8      14.479  70.874   3.414  1.00  9.99
ATOM     38  C   ASN     8      14.992  69.564   2.817  1.00  9.99
ATOM     39  O   ASN     8      15.775  69.637   1.840  1.00  9.99
ATOM     40  CB  ASN     8      13.525  71.540   2.413  1.00  9.99
ATOM     41  N   TRP     9      14.506  68.453   3.350  1.00  9.99
ATOM     42  CA  TRP     9      14.963  67.148   2.858  1.00  9.99
ATOM     43  C   TRP     9      14.165  66.830   1.571  1.00  9.99
ATOM     44  O   TRP     9      12.930  66.578   1.727  1.00  9.99
ATOM     45  CB  TRP     9      14.818  66.061   3.915  1.00  9.99
ATOM     46  N   LEU    10      14.835  66.910   0.426  1.00  9.99
ATOM     47  CA  LEU    10      14.094  66.459  -0.788  1.00  9.99
ATOM     48  C   LEU    10      14.650  65.143  -1.324  1.00  9.99
ATOM     49  O   LEU    10      14.354  64.833  -2.506  1.00  9.99
ATOM     50  CB  LEU    10      14.101  67.550  -1.856  1.00  9.99
ATOM     51  N   LEU    11      15.465  64.473  -0.516  1.00  9.99
ATOM     52  CA  LEU    11      16.147  63.234  -0.996  1.00  9.99
ATOM     53  C   LEU    11      15.522  62.093  -0.207  1.00  9.99
ATOM     54  O   LEU    11      15.254  60.991  -0.782  1.00  9.99
ATOM     55  CB  LEU    11      17.666  63.315  -0.860  1.00  9.99
ATOM     56  N   LYS    12      15.416  62.214   1.117  1.00  9.99
ATOM     57  CA  LYS    12      14.618  61.238   1.909  1.00  9.99
ATOM     58  C   LYS    12      15.385  60.583   3.030  1.00  9.99
ATOM     59  O   LYS    12      14.728  59.881   3.870  1.00  9.99
ATOM     60  CB  LYS    12      14.058  60.161   0.965  1.00  9.99
ATOM     61  N   GLU    13      16.685  60.843   3.198  1.00  9.99
ATOM     62  CA  GLU    13      17.473  60.136   4.221  1.00  9.99
ATOM     63  C   GLU    13      17.734  61.024   5.462  1.00  9.99
ATOM     64  O   GLU    13      18.408  60.486   6.393  1.00  9.99
ATOM     65  CB  GLU    13      18.761  59.589   3.590  1.00  9.99
ATOM     66  N   GLN    14      17.280  62.262   5.447  1.00  9.99
ATOM     67  CA  GLN    14      17.306  63.073   6.704  1.00  9.99
ATOM     68  C   GLN    14      18.732  63.413   7.125  1.00  9.99
ATOM     69  O   GLN    14      18.914  63.751   8.343  1.00  9.99
ATOM     70  CB  GLN    14      16.580  62.311   7.825  1.00  9.99
ATOM     71  N   GLU    15      19.728  63.469   6.235  1.00  9.99
ATOM     72  CA  GLU    15      21.105  63.586   6.708  1.00  9.99
ATOM     73  C   GLU    15      21.388  64.958   7.328  1.00  9.99
ATOM     74  O   GLU    15      22.192  65.004   8.271  1.00  9.99
ATOM     75  CB  GLU    15      22.119  63.332   5.546  1.00  9.99
ATOM     76  N   LYS    16      20.822  66.007   6.726  1.00  9.99
ATOM     77  CA  LYS    16      21.145  67.351   7.275  1.00  9.99
ATOM     78  C   LYS    16      20.646  67.489   8.704  1.00  9.99
ATOM     79  O   LYS    16      21.414  67.970   9.575  1.00  9.99
ATOM     80  CB  LYS    16      20.508  68.396   6.350  1.00  9.99
ATOM     81  N   ILE    17      19.429  67.033   8.950  1.00  9.99
ATOM     82  CA  ILE    17      18.891  67.105  10.352  1.00  9.99
ATOM     83  C   ILE    17      19.668  66.146  11.250  1.00  9.99
ATOM     84  O   ILE    17      19.877  66.519  12.418  1.00  9.99
ATOM     85  CB  ILE    17      17.404  66.866  10.322  1.00  9.99
ATOM     86  N   GLN    18      20.144  65.004  10.766  1.00  9.99
ATOM     87  CA  GLN    18      20.993  64.148  11.590  1.00  9.99
ATOM     88  C   GLN    18      22.268  64.864  12.054  1.00  9.99
ATOM     89  O   GLN    18      22.714  64.703  13.199  1.00  9.99
ATOM     90  CB  GLN    18      21.337  62.846  10.873  1.00  9.99
ATOM     91  N   THR    19      22.886  65.550  11.084  1.00  9.99
ATOM     92  CA  THR    19      24.088  66.336  11.407  1.00  9.99
ATOM     93  C   THR    19      23.786  67.412  12.456  1.00  9.99
ATOM     94  O   THR    19      24.518  67.468  13.458  1.00  9.99
ATOM     95  CB  THR    19      24.617  66.944  10.096  1.00  9.99
ATOM     96  N   LYS    20      22.758  68.188  12.222  1.00  9.99
ATOM     97  CA  LYS    20      22.342  69.218  13.197  1.00  9.99
ATOM     98  C   LYS    20      22.138  68.595  14.580  1.00  9.99
ATOM     99  O   LYS    20      22.668  69.098  15.583  1.00  9.99
ATOM    100  CB  LYS    20      21.079  69.930  12.697  1.00  9.99
ATOM    101  N   TYR    21      21.398  67.497  14.587  1.00  9.99
ATOM    102  CA  TYR    21      21.137  66.822  15.905  1.00  9.99
ATOM    103  C   TYR    21      22.398  66.301  16.555  1.00  9.99
ATOM    104  O   TYR    21      22.529  66.392  17.812  1.00  9.99
ATOM    105  CB  TYR    21      20.064  65.724  15.797  1.00  9.99
ATOM    106  N   ARG    22      23.346  65.809  15.758  1.00  9.99
ATOM    107  CA  ARG    22      24.633  65.382  16.313  1.00  9.99
ATOM    108  C   ARG    22      25.331  66.557  16.999  1.00  9.99
ATOM    109  O   ARG    22      25.898  66.447  18.079  1.00  9.99
ATOM    110  CB  ARG    22      25.574  64.728  15.305  1.00  9.99
ATOM    111  N   HIS    23      25.352  67.713  16.300  1.00  9.99
ATOM    112  CA  HIS    23      26.019  68.910  16.823  1.00  9.99
ATOM    113  C   HIS    23      25.356  69.433  18.089  1.00  9.99
ATOM    114  O   HIS    23      26.080  69.857  19.011  1.00  9.99
ATOM    115  CB  HIS    23      25.995  69.974  15.697  1.00  9.99
ATOM    116  N   LEU    24      24.032  69.393  18.100  1.00  9.99
ATOM    117  CA  LEU    24      23.251  69.786  19.286  1.00  9.99
ATOM    118  C   LEU    24      23.725  68.889  20.445  1.00  9.99
ATOM    119  O   LEU    24      23.990  69.383  21.556  1.00  9.99
ATOM    120  CB  LEU    24      21.751  69.725  19.045  1.00  9.99
ATOM    121  N   ASN    25      23.791  67.611  20.165  1.00  9.99
ATOM    122  CA  ASN    25      24.242  66.657  21.222  1.00  9.99
ATOM    123  C   ASN    25      25.660  66.948  21.655  1.00  9.99
ATOM    124  O   ASN    25      26.002  66.836  22.853  1.00  9.99
ATOM    125  CB  ASN    25      24.016  65.217  20.745  1.00  9.99
ATOM    126  N   HIS    26      26.539  67.291  20.728  1.00  9.99
ATOM    127  CA  HIS    26      27.937  67.655  20.983  1.00  9.99
ATOM    128  C   HIS    26      28.002  68.822  21.969  1.00  9.99
ATOM    129  O   HIS    26      28.764  68.789  22.964  1.00  9.99
ATOM    130  CB  HIS    26      28.679  68.014  19.710  1.00  9.99
ATOM    131  N   ILE    27      27.195  69.842  21.652  1.00  9.99
ATOM    132  CA  ILE    27      27.200  71.045  22.513  1.00  9.99
ATOM    133  C   ILE    27      26.604  70.715  23.883  1.00  9.99
ATOM    134  O   ILE    27      27.080  71.317  24.879  1.00  9.99
ATOM    135  CB  ILE    27      26.449  72.207  21.854  1.00  9.99
TER
END
