
#######################################################
#                                                     #
#                        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   24 (  120),  selected   24 , name T0301TS102_2-D1
# Molecule2: number of CA atoms  200 ( 1505),  selected  200 , name T0301_D1.pdb
# PARAMETERS: T0301TS102_2-D1.T0301_D1.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    -       -      H       3           -
LGA    -       -      P       4           -
LGA    -       -      P       5           -
LGA    -       -      Q       6           -
LGA    -       -      I       7           -
LGA    -       -      R       8           -
LGA    Q       6      I       9           #
LGA    I       7      P      10          2.842
LGA    R       8      A      11          3.970
LGA    I       9      T      12          0.933
LGA    P      10      Y      13          3.577
LGA    A      11      L      14          3.924
LGA    T      12      R      15          2.244
LGA    Y      13      G      16           #
LGA    L     120      G      17           -
LGA    -       -      T      18           -
LGA    -       -      S      19           -
LGA    -       -      K      20           -
LGA    V     121      G      21          1.792
LGA    -       -      V      22           -
LGA    -       -      F      23           -
LGA    -       -      F      24           -
LGA    -       -      R      25           -
LGA    -       -      L      26           -
LGA    -       -      E      27           -
LGA    -       -      D      28           -
LGA    -       -      L      29           -
LGA    -       -      P      30           -
LGA    -       -      E      31           -
LGA    -       -      S      32           -
LGA    -       -      C      33           -
LGA    -       -      R      34           -
LGA    -       -      V      35           -
LGA    -       -      P      36           -
LGA    -       -      G      37           -
LGA    -       -      E      38           -
LGA    -       -      A      39           -
LGA    -       -      R      40           -
LGA    -       -      D      41           -
LGA    -       -      R      42           -
LGA    -       -      L      43           -
LGA    -       -      F      44           -
LGA    -       -      M      45           -
LGA    -       -      R      46           -
LGA    -       -      V      47           -
LGA    -       -      I      48           -
LGA    -       -      G      49           -
LGA    -       -      S      50           -
LGA    -       -      P      51           -
LGA    -       -      D      52           -
LGA    -       -      P      53           -
LGA    -       -      Y      54           -
LGA    -       -      A      55           -
LGA    -       -      A      56           -
LGA    -       -      H      57           -
LGA    -       -      I      58           -
LGA    -       -      D      59           -
LGA    -       -      G      60           -
LGA    -       -      M      61           -
LGA    -       -      G      62           -
LGA    -       -      G      63           -
LGA    -       -      A      64           -
LGA    -       -      T      65           -
LGA    -       -      S      66           -
LGA    -       -      S      67           -
LGA    -       -      T      68           -
LGA    -       -      S      69           -
LGA    -       -      K      70           -
LGA    D     122      C      71          0.436
LGA    P     123      V      72          0.953
LGA    -       -      I      73           -
LGA    -       -      L      74           -
LGA    -       -      S      75           -
LGA    -       -      K      76           -
LGA    -       -      S      77           -
LGA    -       -      S      78           -
LGA    -       -      Q      79           -
LGA    -       -      P      80           -
LGA    -       -      G      81           -
LGA    -       -      H      82           -
LGA    -       -      D      83           -
LGA    -       -      V      84           -
LGA    -       -      D      85           -
LGA    -       -      Y      86           -
LGA    -       -      L      87           -
LGA    A     124      Y      88          1.304
LGA    R     125      G      89          4.739
LGA    I     126      Q      90           -
LGA    -       -      V      91           -
LGA    -       -      S      92           -
LGA    -       -      I      93           -
LGA    -       -      D      94           -
LGA    -       -      K      95           -
LGA    -       -      P      96           -
LGA    -       -      F      97           -
LGA    -       -      V      98           -
LGA    -       -      D      99           -
LGA    -       -      W     100           -
LGA    -       -      S     101           -
LGA    -       -      G     102           -
LGA    -       -      N     103           -
LGA    -       -      C     104           -
LGA    -       -      G     105           -
LGA    -       -      N     106           -
LGA    P     127      L     107          3.021
LGA    E     128      S     108          2.193
LGA    D     129      T     109          1.475
LGA    E     173      G     110          1.766
LGA    V     175      A     111          0.897
LGA    L     176      G     112          0.307
LGA    E     177      A     113          1.634
LGA    F     178      F     114          0.994
LGA    -       -      A     115           -
LGA    -       -      L     116           -
LGA    -       -      H     117           -
LGA    -       -      A     118           -
LGA    -       -      G     119           -
LGA    -       -      L     120           -
LGA    -       -      V     121           -
LGA    -       -      D     122           -
LGA    -       -      P     123           -
LGA    -       -      A     124           -
LGA    -       -      R     125           -
LGA    -       -      I     126           -
LGA    -       -      P     127           -
LGA    -       -      E     128           -
LGA    -       -      D     129           -
LGA    -       -      G     130           -
LGA    -       -      I     131           -
LGA    -       -      C     132           -
LGA    -       -      E     133           -
LGA    -       -      V     134           -
LGA    -       -      R     135           -
LGA    -       -      I     136           -
LGA    -       -      W     137           -
LGA    -       -      Q     138           -
LGA    -       -      A     139           -
LGA    -       -      N     140           -
LGA    -       -      I     141           -
LGA    -       -      G     142           -
LGA    -       -      K     143           -
LGA    -       -      T     144           -
LGA    -       -      I     145           -
LGA    -       -      I     146           -
LGA    -       -      A     147           -
LGA    -       -      H     148           -
LGA    -       -      V     149           -
LGA    -       -      P     150           -
LGA    -       -      V     151           -
LGA    -       -      S     152           -
LGA    -       -      G     153           -
LGA    -       -      G     154           -
LGA    -       -      Q     155           -
LGA    -       -      V     156           -
LGA    -       -      Q     157           -
LGA    -       -      E     158           -
LGA    -       -      T     159           -
LGA    -       -      G     160           -
LGA    -       -      D     161           -
LGA    -       -      F     162           -
LGA    -       -      E     163           -
LGA    -       -      L     164           -
LGA    -       -      D     165           -
LGA    -       -      G     166           -
LGA    -       -      V     167           -
LGA    -       -      T     168           -
LGA    -       -      F     169           -
LGA    -       -      P     170           -
LGA    -       -      A     171           -
LGA    -       -      A     172           -
LGA    -       -      E     173           -
LGA    -       -      I     174           -
LGA    -       -      V     175           -
LGA    -       -      L     176           -
LGA    -       -      E     177           -
LGA    -       -      F     178           -
LGA    -       -      L     179           -
LGA    -       -      D     180           -
LGA    -       -      P     181           -
LGA    -       -      S     182           -
LGA    -       -      R     378           -
LGA    -       -      S     379           -
LGA    -       -      A     380           -
LGA    -       -      R     381           -
LGA    -       -      I     382           -
LGA    -       -      L     383           -
LGA    -       -      M     384           -
LGA    -       -      E     385           -
LGA    -       -      G     386           -
LGA    -       -      W     387           -
LGA    R     378      V     388          5.702
LGA    -       -      R     389           -
LGA    -       -      V     390           -
LGA    -       -      P     391           -
LGA    -       -      G     392           -
LGA    -       -      D     393           -
LGA    -       -      A     394           -
LGA    -       -      F     395           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   24  200    5.0     20    2.67     5.00      7.618     0.722

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.807357 * X  +   0.021192 * Y  +   0.589682 * Z  +  22.764732
  Y_new =   0.061400 * X  +  -0.996947 * Y  +  -0.048236 * Z  +  25.269215
  Z_new =   0.586860 * X  +   0.075150 * Y  +  -0.806193 * Z  +  -2.671914 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   3.048645   -0.092948  [ DEG:   174.6745     -5.3255 ]
  Theta =  -0.627175   -2.514417  [ DEG:   -35.9345   -144.0655 ]
  Phi   =   0.075904   -3.065688  [ DEG:     4.3490   -175.6510 ]
 
# 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: T0301TS102_2-D1                               
REMARK     2: T0301_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0301TS102_2-D1.T0301_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   24  200   5.0   20   2.67    5.00   7.618
REMARK  ---------------------------------------------------------- 
MOLECULE T0301TS102_2-D1
PFRMAT TS
TARGET T0301
MODEL 2
PARENT 1ji7_A
ATOM      1  N   GLN     6      59.906  38.306  14.500  1.00  1.00
ATOM      2  CA  GLN     6      61.036  38.177  13.537  1.00  1.00
ATOM      3  C   GLN     6      61.680  36.801  13.656  1.00  1.00
ATOM      4  O   GLN     6      61.250  35.970  14.458  1.00  1.00
ATOM      5  CB  GLN     6      62.070  39.263  13.798  1.00  1.00
ATOM      6  N   ILE     7      62.716  36.568  12.856  1.00  1.00
ATOM      7  CA  ILE     7      63.417  35.290  12.868  1.00  1.00
ATOM      8  C   ILE     7      64.872  35.468  13.290  1.00  1.00
ATOM      9  O   ILE     7      65.675  36.065  12.572  1.00  1.00
ATOM     10  CB  ILE     7      63.358  34.624  11.480  1.00  1.00
ATOM     11  N   ARG     8      65.204  34.937  14.460  1.00  1.00
ATOM     12  CA  ARG     8      66.555  35.040  14.994  1.00  1.00
ATOM     13  C   ARG     8      67.119  33.665  15.318  1.00  1.00
ATOM     14  O   ARG     8      66.576  32.943  16.149  1.00  1.00
ATOM     15  CB  ARG     8      66.548  35.910  16.248  1.00  1.00
ATOM     16  N   ILE     9      68.215  33.306  14.659  1.00  1.00
ATOM     17  CA  ILE     9      68.847  32.018  14.898  1.00  1.00
ATOM     18  C   ILE     9      69.587  31.995  16.228  1.00  1.00
ATOM     19  O   ILE     9      70.049  33.029  16.713  1.00  1.00
ATOM     20  CB  ILE     9      69.854  31.702  13.786  1.00  1.00
ATOM     21  N   PRO    10      69.696  30.812  16.844  1.00  1.00
ATOM     22  CA  PRO    10      70.413  30.726  18.116  1.00  1.00
ATOM     23  C   PRO    10      71.883  31.007  17.820  1.00  1.00
ATOM     24  O   PRO    10      72.334  30.833  16.687  1.00  1.00
ATOM     25  CB  PRO    10      70.157  29.291  18.566  1.00  1.00
ATOM     26  N   ALA    11      72.625  31.433  18.835  1.00  1.00
ATOM     27  CA  ALA    11      74.029  31.780  18.656  1.00  1.00
ATOM     28  C   ALA    11      74.869  30.769  17.885  1.00  1.00
ATOM     29  O   ALA    11      75.693  31.158  17.059  1.00  1.00
ATOM     30  CB  ALA    11      74.670  32.055  20.014  1.00  1.00
ATOM     31  N   THR    12      74.657  29.481  18.143  1.00  1.00
ATOM     32  CA  THR    12      75.437  28.439  17.478  1.00  1.00
ATOM     33  C   THR    12      75.118  28.211  16.003  1.00  1.00
ATOM     34  O   THR    12      75.758  27.389  15.350  1.00  1.00
ATOM     35  CB  THR    12      75.321  27.106  18.236  1.00  1.00
ATOM     36  N   TYR    13      74.138  28.936  15.474  1.00  1.00
ATOM     37  CA  TYR    13      73.784  28.782  14.068  1.00  1.00
ATOM     38  C   TYR    13      73.896  30.071  13.268  1.00  1.00
ATOM     39  O   TYR    13      73.415  30.149  12.143  1.00  1.00
ATOM     40  CB  TYR    13      72.362  28.230  13.936  1.00  1.00
ATOM     41  N   LEU   120      74.538  31.085  13.835  1.00  1.00
ATOM     42  CA  LEU   120      74.664  32.347  13.124  1.00  1.00
ATOM     43  C   LEU   120      75.697  32.353  11.997  1.00  1.00
ATOM     44  O   LEU   120      75.696  33.248  11.152  1.00  1.00
ATOM     45  CB  LEU   120      74.908  33.470  14.135  1.00  1.00
ATOM     46  N   VAL   121      76.565  31.349  11.955  1.00  1.00
ATOM     47  CA  VAL   121      77.547  31.292  10.877  1.00  1.00
ATOM     48  C   VAL   121      76.780  31.050   9.574  1.00  1.00
ATOM     49  O   VAL   121      75.679  30.498   9.592  1.00  1.00
ATOM     50  CB  VAL   121      78.560  30.160  11.111  1.00  1.00
ATOM     51  N   ASP   122      77.345  31.470   8.449  1.00  1.00
ATOM     52  CA  ASP   122      76.675  31.281   7.165  1.00  1.00
ATOM     53  C   ASP   122      76.380  29.812   6.881  1.00  1.00
ATOM     54  O   ASP   122      77.196  28.940   7.174  1.00  1.00
ATOM     55  CB  ASP   122      77.523  31.846   6.034  1.00  1.00
ATOM     56  N   PRO   123      75.205  29.518   6.299  1.00  1.00
ATOM     57  CA  PRO   123      74.840  28.133   5.989  1.00  1.00
ATOM     58  C   PRO   123      75.895  27.363   5.188  1.00  1.00
ATOM     59  O   PRO   123      76.062  26.156   5.372  1.00  1.00
ATOM     60  CB  PRO   123      73.521  28.286   5.224  1.00  1.00
ATOM     61  N   ALA   124      76.622  28.051   4.311  1.00  1.00
ATOM     62  CA  ALA   124      77.624  27.356   3.506  1.00  1.00
ATOM     63  C   ALA   124      78.715  26.728   4.380  1.00  1.00
ATOM     64  O   ALA   124      79.415  25.818   3.936  1.00  1.00
ATOM     65  CB  ALA   124      78.245  28.304   2.437  1.00  1.00
ATOM     66  N   ARG   125      78.832  27.191   5.624  1.00  1.00
ATOM     67  CA  ARG   125      79.832  26.651   6.546  1.00  1.00
ATOM     68  C   ARG   125      79.254  25.650   7.537  1.00  1.00
ATOM     69  O   ARG   125      79.981  25.087   8.354  1.00  1.00
ATOM     70  CB  ARG   125      80.508  27.778   7.332  1.00  1.00
ATOM     71  N   ILE   126      77.945  25.415   7.473  1.00  1.00
ATOM     72  CA  ILE   126      77.325  24.475   8.393  1.00  1.00
ATOM     73  C   ILE   126      77.802  23.054   8.173  1.00  1.00
ATOM     74  O   ILE   126      77.918  22.587   7.041  1.00  1.00
ATOM     75  CB  ILE   126      75.797  24.445   8.241  1.00  1.00
ATOM     76  N   PRO   127      78.060  22.361   9.272  1.00  1.00
ATOM     77  CA  PRO   127      78.448  20.964   9.204  1.00  1.00
ATOM     78  C   PRO   127      77.145  20.168   9.109  1.00  1.00
ATOM     79  O   PRO   127      76.047  20.733   9.201  1.00  1.00
ATOM     80  CB  PRO   127      79.163  20.552  10.488  1.00  1.00
ATOM     81  N   GLU   128      77.251  18.859   8.932  1.00  1.00
ATOM     82  CA  GLU   128      76.055  18.041   8.892  1.00  1.00
ATOM     83  C   GLU   128      75.309  18.155  10.230  1.00  1.00
ATOM     84  O   GLU   128      74.074  18.176  10.264  1.00  1.00
ATOM     85  CB  GLU   128      76.432  16.590   8.596  1.00  1.00
ATOM     86  N   ASP   129      76.045  18.256  11.338  1.00  1.00
ATOM     87  CA  ASP   129      75.386  18.384  12.632  1.00  1.00
ATOM     88  C   ASP   129      74.697  19.740  12.752  1.00  1.00
ATOM     89  O   ASP   129      73.628  19.841  13.348  1.00  1.00
ATOM     90  CB  ASP   129      76.372  18.212  13.793  1.00  1.00
ATOM     91  N   GLU   173      75.306  20.783  12.195  1.00  1.00
ATOM     92  CA  GLU   173      74.686  22.106  12.241  1.00  1.00
ATOM     93  C   GLU   173      73.347  22.068  11.501  1.00  1.00
ATOM     94  O   GLU   173      72.370  22.669  11.952  1.00  1.00
ATOM     95  CB  GLU   173      75.573  23.170  11.594  1.00  1.00
ATOM     96  N   VAL   175      73.303  21.376  10.364  1.00  1.00
ATOM     97  CA  VAL   175      72.056  21.255   9.610  1.00  1.00
ATOM     98  C   VAL   175      70.998  20.602  10.507  1.00  1.00
ATOM     99  O   VAL   175      69.853  21.053  10.563  1.00  1.00
ATOM    100  CB  VAL   175      72.266  20.414   8.326  1.00  1.00
ATOM    101  N   LEU   176      71.386  19.552  11.234  1.00  1.00
ATOM    102  CA  LEU   176      70.453  18.873  12.131  1.00  1.00
ATOM    103  C   LEU   176      70.006  19.818  13.250  1.00  1.00
ATOM    104  O   LEU   176      68.840  19.797  13.650  1.00  1.00
ATOM    105  CB  LEU   176      71.104  17.618  12.726  1.00  1.00
ATOM    106  N   GLU   177      70.924  20.633  13.766  1.00  1.00
ATOM    107  CA  GLU   177      70.575  21.586  14.821  1.00  1.00
ATOM    108  C   GLU   177      69.590  22.621  14.283  1.00  1.00
ATOM    109  O   GLU   177      68.680  23.054  14.994  1.00  1.00
ATOM    110  CB  GLU   177      71.829  22.287  15.350  1.00  1.00
ATOM    111  N   PHE   178      69.773  23.016  13.028  1.00  1.00
ATOM    112  CA  PHE   178      68.872  23.983  12.403  1.00  1.00
ATOM    113  C   PHE   178      67.469  23.370  12.328  1.00  1.00
ATOM    114  O   PHE   178      66.484  24.043  12.632  1.00  1.00
ATOM    115  CB  PHE   178      69.385  24.333  11.003  1.00  1.00
ATOM    379  N   ARG   378      69.290  37.535   4.950  1.00  1.00
ATOM    380  CA  ARG   378      69.646  38.331   6.124  1.00  1.00
ATOM    381  C   ARG   378      71.114  38.733   6.109  1.00  1.00
ATOM    382  O   ARG   378      71.392  39.937   6.291  1.00  1.00
ATOM    383  CB  ARG   378      69.349  37.557   7.413  1.00  1.00
TER
END
