
#######################################################
#                                                     #
#                        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   18 (   88),  selected   18 , name T0301TS239_5_2-D1
# Molecule2: number of CA atoms  200 ( 1505),  selected  200 , name T0301_D1.pdb
# PARAMETERS: T0301TS239_5_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    -       -      I       9           -
LGA    -       -      P      10           -
LGA    -       -      A      11           -
LGA    -       -      T      12           -
LGA    -       -      Y      13           -
LGA    -       -      L      14           -
LGA    -       -      R      15           -
LGA    -       -      G      16           -
LGA    -       -      G      17           -
LGA    -       -      T      18           -
LGA    -       -      S      19           -
LGA    -       -      K      20           -
LGA    -       -      G      21           -
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    R     378      A      64          3.495
LGA    S     379      T      65          1.525
LGA    A     380      S      66          2.179
LGA    R     381      S      67          2.351
LGA    I     382      T      68           #
LGA    -       -      S      69           -
LGA    -       -      K      70           -
LGA    -       -      C      71           -
LGA    -       -      V      72           -
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    L     383      Y      88           #
LGA    -       -      G      89           -
LGA    -       -      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    M     384      C     104          4.378
LGA    E     385      G     105          2.534
LGA    -       -      N     106           -
LGA    -       -      L     107           -
LGA    -       -      S     108           -
LGA    G     386      T     109          1.892
LGA    W     387      G     110          4.561
LGA    V     388      A     111          3.821
LGA    R     389      G     112          1.583
LGA    V     390      A     113          2.359
LGA    P     391      F     114          1.913
LGA    G     392      A     115          2.854
LGA    D     393      L     116          3.940
LGA    A     394      -       -           -
LGA    F     395      H     117          2.426
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    -       -      V     388           -
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)   18  200    5.0     15    2.95     0.00      5.463     0.492

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.489473 * X  +   0.495555 * Y  +   0.717525 * Z  +  65.114410
  Y_new =   0.792437 * X  +   0.596196 * Y  +   0.128815 * Z  +  11.330206
  Z_new =  -0.363951 * X  +   0.631644 * Y  +  -0.684518 * Z  +  25.041178 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.396346   -0.745247  [ DEG:   137.3005    -42.6995 ]
  Theta =   0.372506    2.769087  [ DEG:    21.3430    158.6570 ]
  Phi   =   2.124115   -1.017478  [ DEG:   121.7028    -58.2972 ]
 
# 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: T0301TS239_5_2-D1                             
REMARK     2: T0301_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0301TS239_5_2-D1.T0301_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   18  200   5.0   15   2.95    0.00   5.463
REMARK  ---------------------------------------------------------- 
MOLECULE T0301TS239_5_2-D1
REMARK PARENT number 2
PFRMAT TS
TARGET T0301
PARENT 1xub_A
ATOM    554  N   ARG   378      90.349  39.016  14.513  1.00  9.99
ATOM    555  CA  ARG   378      89.960  38.432  13.236  1.00  9.99
ATOM    556  C   ARG   378      89.571  36.989  13.449  1.00  9.99
ATOM    557  O   ARG   378      90.364  36.199  13.927  1.00  9.99
ATOM    558  CB  ARG   378      91.086  38.540  12.228  1.00  9.99
ATOM    559  N   SER   379      88.327  36.638  13.088  1.00  9.99
ATOM    560  CA  SER   379      87.852  35.283  13.306  1.00  9.99
ATOM    561  C   SER   379      88.442  34.247  12.376  1.00  9.99
ATOM    562  O   SER   379      89.023  34.578  11.358  1.00  9.99
ATOM    563  CB  SER   379      86.383  35.389  13.095  1.00  9.99
ATOM    564  N   ALA   380      88.212  32.977  12.772  1.00  9.99
ATOM    565  CA  ALA   380      88.361  31.820  11.912  1.00  9.99
ATOM    566  C   ALA   380      87.066  31.137  11.798  1.00  9.99
ATOM    567  O   ALA   380      86.106  31.468  12.500  1.00  9.99
ATOM    568  CB  ALA   380      89.425  30.930  12.510  1.00  9.99
ATOM    569  N   ARG   381      86.939  30.226  10.809  1.00  9.99
ATOM    570  CA  ARG   381      85.648  29.631  10.539  1.00  9.99
ATOM    571  C   ARG   381      85.823  28.301   9.794  1.00  9.99
ATOM    572  O   ARG   381      86.835  28.088   9.128  1.00  9.99
ATOM    573  CB  ARG   381      84.767  30.596   9.698  1.00  9.99
ATOM    574  N   ILE   382      84.805  27.516   9.908  1.00  9.99
ATOM    575  CA  ILE   382      84.696  26.251   9.180  1.00  9.99
ATOM    576  C   ILE   382      83.252  25.820   9.068  1.00  9.99
ATOM    577  O   ILE   382      82.377  26.386   9.751  1.00  9.99
ATOM    578  CB  ILE   382      85.640  25.201   9.826  1.00  9.99
ATOM    579  N   LEU   383      82.971  24.795   8.281  1.00  9.99
ATOM    580  CA  LEU   383      81.609  24.264   8.186  1.00  9.99
ATOM    581  C   LEU   383      81.256  23.617   9.529  1.00  9.99
ATOM    582  O   LEU   383      82.118  22.939  10.178  1.00  9.99
ATOM    583  CB  LEU   383      81.531  23.160   7.181  1.00  9.99
ATOM    584  N   MET   384      80.052  23.812  10.042  1.00  9.99
ATOM    585  CA  MET   384      79.611  23.211  11.251  1.00  9.99
ATOM    586  C   MET   384      79.636  21.689  11.125  1.00  9.99
ATOM    587  O   MET   384      80.000  21.000  12.106  1.00  9.99
ATOM    588  CB  MET   384      78.200  23.683  11.583  1.00  9.99
ATOM    589  N   GLU   385      79.086  21.142  10.056  1.00  9.99
ATOM    590  CA  GLU   385      78.997  19.719   9.807  1.00  9.99
ATOM    591  C   GLU   385      78.012  19.013  10.699  1.00  9.99
ATOM    592  O   GLU   385      78.069  17.765  10.804  1.00  9.99
ATOM    593  CB  GLU   385      80.398  19.104   9.959  1.00  9.99
ATOM    594  N   GLY   386      77.009  19.716  11.176  1.00  9.99
ATOM    595  CA  GLY   386      75.877  19.180  11.967  1.00  9.99
ATOM    596  C   GLY   386      74.528  19.756  11.503  1.00  9.99
ATOM    597  O   GLY   386      73.639  20.052  12.244  1.00  9.99
ATOM    598  N   TRP   387      74.401  19.861  10.147  1.00  9.99
ATOM    599  CA  TRP   387      73.332  20.690   9.588  1.00  9.99
ATOM    600  C   TRP   387      71.975  20.119   9.887  1.00  9.99
ATOM    601  O   TRP   387      71.057  20.836  10.333  1.00  9.99
ATOM    602  CB  TRP   387      73.495  20.899   8.099  1.00  9.99
ATOM    603  N   VAL   388      71.745  18.809   9.589  1.00  9.99
ATOM    604  CA  VAL   388      70.425  18.255   9.814  1.00  9.99
ATOM    605  C   VAL   388      69.995  18.407  11.301  1.00  9.99
ATOM    606  O   VAL   388      68.834  18.756  11.539  1.00  9.99
ATOM    607  CB  VAL   388      70.276  16.789   9.320  1.00  9.99
ATOM    608  N   ARG   389      70.913  18.094  12.197  1.00  9.99
ATOM    609  CA  ARG   389      70.604  18.212  13.632  1.00  9.99
ATOM    610  C   ARG   389      70.224  19.678  14.041  1.00  9.99
ATOM    611  O   ARG   389      69.211  19.918  14.700  1.00  9.99
ATOM    612  CB  ARG   389      71.810  17.800  14.397  1.00  9.99
ATOM    613  N   VAL   390      71.003  20.645  13.501  1.00  9.99
ATOM    614  CA  VAL   390      70.750  22.020  13.871  1.00  9.99
ATOM    615  C   VAL   390      69.418  22.513  13.273  1.00  9.99
ATOM    616  O   VAL   390      68.640  23.182  13.945  1.00  9.99
ATOM    617  CB  VAL   390      71.900  22.886  13.409  1.00  9.99
ATOM    618  N   PRO   391      69.189  22.215  11.973  1.00  9.99
ATOM    619  CA  PRO   391      68.001  22.611  11.310  1.00  9.99
ATOM    620  C   PRO   391      66.760  22.023  11.995  1.00  9.99
ATOM    621  O   PRO   391      65.795  22.721  12.167  1.00  9.99
ATOM    622  CB  PRO   391      68.097  22.202   9.837  1.00  9.99
ATOM    623  N   GLY   392      66.863  20.755  12.384  1.00  9.99
ATOM    624  CA  GLY   392      65.794  20.084  13.169  1.00  9.99
ATOM    625  C   GLY   392      65.458  20.918  14.448  1.00  9.99
ATOM    626  O   GLY   392      64.289  21.186  14.711  1.00  9.99
ATOM    627  N   ASP   393      66.529  21.256  15.159  1.00  9.99
ATOM    628  CA  ASP   393      66.393  21.983  16.401  1.00  9.99
ATOM    629  C   ASP   393      65.748  23.312  16.169  1.00  9.99
ATOM    630  O   ASP   393      64.900  23.761  16.980  1.00  9.99
ATOM    631  CB  ASP   393      67.670  22.053  17.043  1.00  9.99
ATOM    632  N   ALA   394      66.104  23.987  15.074  1.00  9.99
ATOM    633  CA  ALA   394      65.427  25.250  14.735  1.00  9.99
ATOM    634  C   ALA   394      64.045  25.182  14.164  1.00  9.99
ATOM    635  O   ALA   394      63.340  26.190  14.125  1.00  9.99
ATOM    636  CB  ALA   394      66.331  26.028  13.750  1.00  9.99
ATOM    637  N   PHE   395      63.658  23.984  13.700  1.00  9.99
ATOM    638  CA  PHE   395      62.346  23.808  13.141  1.00  9.99
ATOM    639  C   PHE   395      62.196  24.106  11.665  1.00  9.99
ATOM    640  O   PHE   395      61.064  24.402  11.194  1.00  9.99
ATOM    641  CB  PHE   395      61.377  24.679  13.957  1.00  9.99
TER
END
