
#######################################################
#                                                     #
#                        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 T0361TS239_5_1
# Molecule2: number of CA atoms  166 ( 1335),  selected  166 , name T0361.pdb
# PARAMETERS: T0361TS239_5_1.T0361.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      T       3           -
LGA    -       -      L       4           -
LGA    -       -      T       5           -
LGA    -       -      E       6           -
LGA    -       -      D       7           -
LGA    -       -      D       8           -
LGA    -       -      V       9           -
LGA    -       -      L      10           -
LGA    -       -      E      11           -
LGA    -       -      Q      12           -
LGA    M       1      L      13           #
LGA    A       2      D      14          1.831
LGA    T       3      A      15          3.114
LGA    L       4      Q      16          1.484
LGA    T       5      D      17           #
LGA    -       -      N      18           -
LGA    -       -      L      19           -
LGA    -       -      F      20           -
LGA    -       -      S      21           -
LGA    E       6      F      22          1.482
LGA    D       7      M      23          0.672
LGA    D       8      K      24          1.356
LGA    V       9      T      25          0.727
LGA    L      10      A      26          0.792
LGA    E      11      H      27          0.868
LGA    Q      12      S      28          0.270
LGA    L      13      I      29          0.388
LGA    D      14      L      30          0.410
LGA    A      15      L      31          0.361
LGA    Q      16      Q      32          0.180
LGA    D      17      G      33          0.899
LGA    N      18      I      34          0.581
LGA    L      19      R      35          0.590
LGA    F      20      Q      36          0.340
LGA    -       -      F      37           -
LGA    -       -      L      38           -
LGA    -       -      P      39           -
LGA    S      21      S      40          1.545
LGA    -       -      L      41           -
LGA    F      22      F      42          1.874
LGA    M      23      V      43          3.118
LGA    K      24      D      44          2.874
LGA    T      25      N      45           -
LGA    A      26      D      46           -
LGA    -       -      E      47           -
LGA    -       -      E      48           -
LGA    -       -      I      49           -
LGA    -       -      V      50           -
LGA    -       -      E      51           -
LGA    -       -      Y      52           -
LGA    -       -      A      53           -
LGA    -       -      V      54           -
LGA    -       -      K      55           -
LGA    -       -      P      56           -
LGA    -       -      L      57           -
LGA    -       -      L      58           -
LGA    -       -      A      59           -
LGA    -       -      Q      60           -
LGA    -       -      S      61           -
LGA    -       -      G      62           -
LGA    -       -      P      63           -
LGA    -       -      L      64           -
LGA    -       -      D      65           -
LGA    -       -      D      66           -
LGA    -       -      I      67           -
LGA    -       -      D      68           -
LGA    -       -      V      69           -
LGA    -       -      A      70           -
LGA    -       -      L      71           -
LGA    -       -      R      72           -
LGA    -       -      L      73           -
LGA    -       -      I      74           -
LGA    -       -      Y      75           -
LGA    -       -      A      76           -
LGA    -       -      L      77           -
LGA    -       -      G      78           -
LGA    H      27      K      79           #
LGA    -       -      M      80           -
LGA    -       -      D      81           -
LGA    -       -      K      82           -
LGA    -       -      W      83           -
LGA    -       -      L      84           -
LGA    -       -      Y      85           -
LGA    -       -      A      86           -
LGA    -       -      D      87           -
LGA    -       -      I      88           -
LGA    -       -      T      89           -
LGA    -       -      H      90           -
LGA    -       -      F      91           -
LGA    -       -      S      92           -
LGA    -       -      Q      93           -
LGA    -       -      Y      94           -
LGA    -       -      W      95           -
LGA    -       -      H      96           -
LGA    -       -      Y      97           -
LGA    -       -      L      98           -
LGA    -       -      N      99           -
LGA    -       -      E     100           -
LGA    -       -      Q     101           -
LGA    -       -      D     102           -
LGA    -       -      E     103           -
LGA    -       -      T     104           -
LGA    -       -      P     105           -
LGA    -       -      G     106           -
LGA    -       -      F     107           -
LGA    -       -      A     108           -
LGA    -       -      D     109           -
LGA    -       -      D     110           -
LGA    -       -      I     111           -
LGA    -       -      T     112           -
LGA    -       -      W     113           -
LGA    -       -      D     114           -
LGA    -       -      F     115           -
LGA    -       -      I     116           -
LGA    -       -      S     117           -
LGA    -       -      N     118           -
LGA    -       -      V     119           -
LGA    -       -      N     120           -
LGA    -       -      S     121           -
LGA    -       -      I     122           -
LGA    -       -      T     123           -
LGA    -       -      R     124           -
LGA    -       -      N     125           -
LGA    -       -      A     126           -
LGA    -       -      T     127           -
LGA    -       -      L     128           -
LGA    -       -      Y     129           -
LGA    -       -      D     130           -
LGA    -       -      A     131           -
LGA    -       -      L     132           -
LGA    -       -      K     133           -
LGA    -       -      A     134           -
LGA    -       -      M     135           -
LGA    -       -      K     136           -
LGA    -       -      F     137           -
LGA    -       -      A     138           -
LGA    -       -      D     139           -
LGA    -       -      F     140           -
LGA    -       -      A     141           -
LGA    -       -      V     142           -
LGA    -       -      W     143           -
LGA    -       -      S     144           -
LGA    -       -      E     145           -
LGA    -       -      A     146           -
LGA    -       -      R     147           -
LGA    -       -      F     148           -
LGA    -       -      S     149           -
LGA    -       -      G     150           -
LGA    -       -      M     151           -
LGA    -       -      V     152           -
LGA    -       -      K     153           -
LGA    -       -      T     154           -
LGA    -       -      A     155           -
LGA    -       -      L     156           -
LGA    -       -      T     157           -
LGA    -       -      L     158           -
LGA    -       -      A     159           -
LGA    -       -      V     160           -
LGA    -       -      T     161           -
LGA    -       -      T     162           -
LGA    -       -      T     163           -
LGA    -       -      L     164           -
LGA    -       -      K     165           -
LGA    -       -      E     166           -
LGA    -       -      L     167           -
LGA    -       -      T     168           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   27  166    5.0     22    1.47    13.64     12.655     1.399

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.991052 * X  +  -0.076414 * Y  +  -0.109441 * Z  +  72.217422
  Y_new =   0.131932 * X  +  -0.436389 * Y  +  -0.890033 * Z  +  34.175735
  Z_new =   0.020252 * X  +  -0.896507 * Y  +   0.442566 * Z  +  82.273331 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.112237    2.029355  [ DEG:   -63.7265    116.2735 ]
  Theta =  -0.020253   -3.121339  [ DEG:    -1.1604   -178.8396 ]
  Phi   =   3.009247   -0.132345  [ DEG:   172.4172     -7.5828 ]
 
# 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: T0361TS239_5_1                                
REMARK     2: T0361.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0361TS239_5_1.T0361.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   27  166   5.0   22   1.47   13.64  12.655
REMARK  ---------------------------------------------------------- 
MOLECULE T0361TS239_5_1
REMARK PARENT number 1
PFRMAT TS
TARGET T0361
PARENT 1f5q_B
ATOM      1  N   MET     1       7.461   8.994  35.356  1.00  9.99
ATOM      2  CA  MET     1       6.305   9.000  34.481  1.00  9.99
ATOM      3  C   MET     1       6.245   7.855  33.490  1.00  9.99
ATOM      4  O   MET     1       6.010   8.077  32.310  1.00  9.99
ATOM      5  CB  MET     1       6.313  10.318  33.728  1.00  9.99
ATOM      6  N   ALA     2       6.419   6.631  33.969  1.00  9.99
ATOM      7  CA  ALA     2       6.429   5.463  33.084  1.00  9.99
ATOM      8  C   ALA     2       5.450   4.334  33.426  1.00  9.99
ATOM      9  O   ALA     2       5.426   3.311  32.749  1.00  9.99
ATOM     10  CB  ALA     2       7.847   4.890  33.058  1.00  9.99
ATOM     11  N   THR     3       4.651   4.518  34.469  1.00  9.99
ATOM     12  CA  THR     3       3.707   3.497  34.900  1.00  9.99
ATOM     13  C   THR     3       2.653   3.057  33.899  1.00  9.99
ATOM     14  O   THR     3       2.274   1.892  33.887  1.00  9.99
ATOM     15  CB  THR     3       2.995   3.953  36.170  1.00  9.99
ATOM     16  N   LEU     4       2.188   3.974  33.059  1.00  9.99
ATOM     17  CA  LEU     4       1.131   3.672  32.089  1.00  9.99
ATOM     18  C   LEU     4       1.577   3.068  30.768  1.00  9.99
ATOM     19  O   LEU     4       0.755   2.859  29.866  1.00  9.99
ATOM     20  CB  LEU     4       0.313   4.938  31.810  1.00  9.99
ATOM     21  N   THR     5       2.867   2.788  30.652  1.00  9.99
ATOM     22  CA  THR     5       3.415   2.203  29.439  1.00  9.99
ATOM     23  C   THR     5       3.049   0.737  29.273  1.00  9.99
ATOM     24  O   THR     5       2.996  -0.010  30.238  1.00  9.99
ATOM     25  CB  THR     5       4.943   2.328  29.441  1.00  9.99
ATOM     26  N   GLU     6       2.797   0.338  28.032  1.00  9.99
ATOM     27  CA  GLU     6       2.486  -1.050  27.707  1.00  9.99
ATOM     28  C   GLU     6       3.538  -1.485  26.698  1.00  9.99
ATOM     29  O   GLU     6       4.031  -0.668  25.931  1.00  9.99
ATOM     30  CB  GLU     6       1.098  -1.170  27.093  1.00  9.99
ATOM     31  N   ASP     7       3.883  -2.766  26.695  1.00  9.99
ATOM     32  CA  ASP     7       4.907  -3.271  25.785  1.00  9.99
ATOM     33  C   ASP     7       5.059  -2.508  24.469  1.00  9.99
ATOM     34  O   ASP     7       6.157  -2.121  24.101  1.00  9.99
ATOM     35  CB  ASP     7       4.677  -4.761  25.476  1.00  9.99
ATOM     36  N   ASP     8       3.960  -2.268  23.772  1.00  9.99
ATOM     37  CA  ASP     8       4.040  -1.597  22.492  1.00  9.99
ATOM     38  C   ASP     8       4.702  -0.224  22.522  1.00  9.99
ATOM     39  O   ASP     8       5.397   0.144  21.568  1.00  9.99
ATOM     40  CB  ASP     8       2.658  -1.488  21.863  1.00  9.99
ATOM     41  N   VAL     9       4.483   0.533  23.598  1.00  9.99
ATOM     42  CA  VAL     9       5.071   1.860  23.730  1.00  9.99
ATOM     43  C   VAL     9       6.590   1.729  23.817  1.00  9.99
ATOM     44  O   VAL     9       7.332   2.490  23.186  1.00  9.99
ATOM     45  CB  VAL     9       4.563   2.560  24.989  1.00  9.99
ATOM     46  N   LEU    10       7.037   0.763  24.617  1.00  9.99
ATOM     47  CA  LEU    10       8.450   0.498  24.813  1.00  9.99
ATOM     48  C   LEU    10       9.063   0.049  23.490  1.00  9.99
ATOM     49  O   LEU    10      10.239   0.310  23.204  1.00  9.99
ATOM     50  CB  LEU    10       8.637  -0.598  25.869  1.00  9.99
ATOM     51  N   GLU    11       8.267  -0.641  22.682  1.00  9.99
ATOM     52  CA  GLU    11       8.755  -1.101  21.396  1.00  9.99
ATOM     53  C   GLU    11       8.908   0.074  20.451  1.00  9.99
ATOM     54  O   GLU    11       9.851   0.114  19.670  1.00  9.99
ATOM     55  CB  GLU    11       7.819  -2.151  20.810  1.00  9.99
ATOM     56  N   GLN    12       7.983   1.029  20.524  1.00  9.99
ATOM     57  CA  GLN    12       8.047   2.222  19.688  1.00  9.99
ATOM     58  C   GLN    12       9.348   2.967  19.927  1.00  9.99
ATOM     59  O   GLN    12       9.964   3.472  18.998  1.00  9.99
ATOM     60  CB  GLN    12       6.893   3.165  20.005  1.00  9.99
ATOM     61  N   LEU    13       9.737   3.033  21.195  1.00  9.99
ATOM     62  CA  LEU    13      10.951   3.708  21.638  1.00  9.99
ATOM     63  C   LEU    13      12.168   2.972  21.101  1.00  9.99
ATOM     64  O   LEU    13      13.138   3.579  20.658  1.00  9.99
ATOM     65  CB  LEU    13      10.980   3.741  23.175  1.00  9.99
ATOM     66  N   ASP    14      12.118   1.652  21.139  1.00  9.99
ATOM     67  CA  ASP    14      13.235   0.868  20.639  1.00  9.99
ATOM     68  C   ASP    14      13.362   1.100  19.142  1.00  9.99
ATOM     69  O   ASP    14      14.459   1.269  18.634  1.00  9.99
ATOM     70  CB  ASP    14      13.028  -0.635  20.926  1.00  9.99
ATOM     71  N   ALA    15      12.227   1.116  18.451  1.00  9.99
ATOM     72  CA  ALA    15      12.203   1.331  17.017  1.00  9.99
ATOM     73  C   ALA    15      12.788   2.704  16.710  1.00  9.99
ATOM     74  O   ALA    15      13.371   2.924  15.650  1.00  9.99
ATOM     75  CB  ALA    15      10.757   1.259  16.489  1.00  9.99
ATOM     76  N   GLN    16      12.634   3.630  17.645  1.00  9.99
ATOM     77  CA  GLN    16      13.148   4.968  17.437  1.00  9.99
ATOM     78  C   GLN    16      14.660   5.028  17.584  1.00  9.99
ATOM     79  O   GLN    16      15.303   5.861  16.955  1.00  9.99
ATOM     80  CB  GLN    16      12.507   5.954  18.405  1.00  9.99
ATOM     81  N   ASP    17      15.233   4.169  18.417  1.00  9.99
ATOM     82  CA  ASP    17      16.680   4.183  18.568  1.00  9.99
ATOM     83  C   ASP    17      17.279   3.393  17.411  1.00  9.99
ATOM     84  O   ASP    17      18.429   3.591  17.045  1.00  9.99
ATOM     85  CB  ASP    17      17.111   3.587  19.920  1.00  9.99
ATOM     86  N   ASN    18      16.483   2.505  16.831  1.00  9.99
ATOM     87  CA  ASN    18      16.926   1.708  15.698  1.00  9.99
ATOM     88  C   ASN    18      17.122   2.651  14.519  1.00  9.99
ATOM     89  O   ASN    18      18.124   2.592  13.808  1.00  9.99
ATOM     90  CB  ASN    18      15.876   0.654  15.340  1.00  9.99
ATOM     91  N   LEU    19      16.146   3.530  14.333  1.00  9.99
ATOM     92  CA  LEU    19      16.177   4.504  13.257  1.00  9.99
ATOM     93  C   LEU    19      17.280   5.533  13.451  1.00  9.99
ATOM     94  O   LEU    19      17.946   5.918  12.491  1.00  9.99
ATOM     95  CB  LEU    19      14.807   5.189  13.130  1.00  9.99
ATOM     96  N   PHE    20      17.483   5.970  14.688  1.00  9.99
ATOM     97  CA  PHE    20      18.520   6.945  14.979  1.00  9.99
ATOM     98  C   PHE    20      19.879   6.309  14.720  1.00  9.99
ATOM     99  O   PHE    20      20.796   6.960  14.231  1.00  9.99
ATOM    100  CB  PHE    20      18.418   7.421  16.433  1.00  9.99
ATOM    101  N   SER    21      24.279   5.848  11.126  1.00  9.99
ATOM    102  CA  SER    21      25.156   4.836  10.526  1.00  9.99
ATOM    103  C   SER    21      25.343   4.912   9.004  1.00  9.99
ATOM    104  O   SER    21      26.388   4.508   8.485  1.00  9.99
ATOM    105  CB  SER    21      24.667   3.431  10.900  1.00  9.99
ATOM    106  N   PHE    22      24.340   5.400   8.279  1.00  9.99
ATOM    107  CA  PHE    22      24.484   5.508   6.834  1.00  9.99
ATOM    108  C   PHE    22      25.423   6.698   6.562  1.00  9.99
ATOM    109  O   PHE    22      25.265   7.465   5.596  1.00  9.99
ATOM    110  CB  PHE    22      23.088   5.681   6.131  1.00  9.99
ATOM    111  N   MET    23      26.419   6.828   7.437  1.00  9.99
ATOM    112  CA  MET    23      27.380   7.901   7.318  1.00  9.99
ATOM    113  C   MET    23      28.445   7.661   6.266  1.00  9.99
ATOM    114  O   MET    23      28.279   6.890   5.312  1.00  9.99
ATOM    115  CB  MET    23      28.022   8.129   8.696  1.00  9.99
ATOM    116  N   LYS    24      29.563   8.345   6.465  1.00  9.99
ATOM    117  CA  LYS    24      30.710   8.292   5.571  1.00  9.99
ATOM    118  C   LYS    24      31.898   7.716   6.362  1.00  9.99
ATOM    119  O   LYS    24      32.200   8.190   7.447  1.00  9.99
ATOM    120  CB  LYS    24      31.009   9.739   5.056  1.00  9.99
ATOM    121  N   THR    25      32.550   6.683   5.829  1.00  9.99
ATOM    122  CA  THR    25      33.685   6.064   6.514  1.00  9.99
ATOM    123  C   THR    25      33.306   5.696   7.953  1.00  9.99
ATOM    124  O   THR    25      34.014   6.075   8.899  1.00  9.99
ATOM    125  CB  THR    25      34.887   7.025   6.574  1.00  9.99
ATOM    126  N   ALA    26      32.207   4.966   8.127  1.00  9.99
ATOM    127  CA  ALA    26      31.764   4.590   9.467  1.00  9.99
ATOM    128  C   ALA    26      32.846   3.912  10.312  1.00  9.99
ATOM    129  O   ALA    26      33.254   4.430  11.345  1.00  9.99
ATOM    130  CB  ALA    26      30.511   3.675   9.401  1.00  9.99
ATOM    131  N   HIS    27      33.320   2.759   9.870  1.00  9.99
ATOM    132  CA  HIS    27      34.328   2.011  10.608  1.00  9.99
ATOM    133  C   HIS    27      35.590   2.809  10.908  1.00  9.99
ATOM    134  O   HIS    27      36.175   2.683  11.979  1.00  9.99
ATOM    135  CB  HIS    27      34.699   0.735   9.836  1.00  9.99
TER
END
