
#######################################################
#                                                     #
#                        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   12 (  112),  selected   12 , name T0321TS074_5-D2
# Molecule2: number of CA atoms  148 ( 1130),  selected  148 , name T0321_D2.pdb
# PARAMETERS: T0321TS074_5-D2.T0321_D2.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    -       -      V      97           -
LGA    -       -      I      98           -
LGA    -       -      F      99           -
LGA    -       -      S     100           -
LGA    -       -      D     101           -
LGA    -       -      A     102           -
LGA    -       -      N     110           -
LGA    -       -      D     111           -
LGA    -       -      P     112           -
LGA    -       -      F     113           -
LGA    -       -      I     114           -
LGA    -       -      M     115           -
LGA    -       -      S     116           -
LGA    -       -      Q     117           -
LGA    -       -      N     118           -
LGA    -       -      E     119           -
LGA    -       -      V     120           -
LGA    -       -      K     121           -
LGA    -       -      G     122           -
LGA    -       -      K     123           -
LGA    -       -      K     124           -
LGA    -       -      V     125           -
LGA    -       -      G     126           -
LGA    -       -      V     127           -
LGA    -       -      V     128           -
LGA    -       -      G     129           -
LGA    -       -      H     130           -
LGA    -       -      F     131           -
LGA    -       -      P     132           -
LGA    -       -      H     133           -
LGA    -       -      L     134           -
LGA    -       -      E     135           -
LGA    -       -      S     136           -
LGA    -       -      L     137           -
LGA    -       -      L     138           -
LGA    -       -      E     139           -
LGA    -       -      P     140           -
LGA    -       -      I     141           -
LGA    -       -      C     142           -
LGA    -       -      D     143           -
LGA    -       -      L     144           -
LGA    -       -      S     145           -
LGA    -       -      I     146           -
LGA    -       -      L     147           -
LGA    -       -      E     148           -
LGA    -       -      W     149           -
LGA    -       -      S     150           -
LGA    -       -      P     151           -
LGA    -       -      E     152           -
LGA    -       -      E     153           -
LGA    -       -      G     154           -
LGA    -       -      D     155           -
LGA    -       -      Y     156           -
LGA    -       -      P     157           -
LGA    -       -      L     158           -
LGA    -       -      P     159           -
LGA    -       -      A     160           -
LGA    -       -      S     161           -
LGA    -       -      E     162           -
LGA    -       -      F     163           -
LGA    -       -      I     164           -
LGA    V      97      L     165          0.981
LGA    I      98      P     166          2.668
LGA    -       -      E     167           -
LGA    -       -      C     168           -
LGA    -       -      D     169           -
LGA    -       -      Y     170           -
LGA    -       -      V     171           -
LGA    -       -      Y     172           -
LGA    -       -      I     173           -
LGA    -       -      T     174           -
LGA    -       -      C     175           -
LGA    -       -      A     176           -
LGA    -       -      S     177           -
LGA    -       -      V     178           -
LGA    -       -      V     179           -
LGA    -       -      D     180           -
LGA    -       -      K     181           -
LGA    -       -      T     182           -
LGA    -       -      L     183           -
LGA    -       -      P     184           -
LGA    -       -      R     185           -
LGA    -       -      L     186           -
LGA    -       -      L     187           -
LGA    -       -      E     188           -
LGA    -       -      L     189           -
LGA    F      99      S     190          0.546
LGA    S     100      R     191          1.691
LGA    D     101      N     192          1.706
LGA    A     102      A     193          1.242
LGA    K     103      R     194          1.331
LGA    R     104      R     195          1.555
LGA    V     105      I     196          2.066
LGA    -       -      T     197           -
LGA    -       -      L     198           -
LGA    -       -      V     199           -
LGA    -       -      G     200           -
LGA    -       -      P     201           -
LGA    -       -      G     202           -
LGA    -       -      T     203           -
LGA    -       -      P     204           -
LGA    -       -      L     205           -
LGA    -       -      A     206           -
LGA    -       -      P     207           -
LGA    -       -      V     208           -
LGA    -       -      L     209           -
LGA    -       -      F     210           -
LGA    -       -      E     211           -
LGA    -       -      H     212           -
LGA    E     106      G     213          4.318
LGA    D     107      L     214          3.449
LGA    R     108      Q     215           -
LGA    -       -      E     216           -
LGA    -       -      L     217           -
LGA    -       -      S     218           -
LGA    -       -      G     219           -
LGA    -       -      F     220           -
LGA    -       -      M     221           -
LGA    -       -      V     222           -
LGA    -       -      K     223           -
LGA    -       -      D     224           -
LGA    -       -      N     225           -
LGA    -       -      A     226           -
LGA    -       -      R     227           -
LGA    -       -      A     228           -
LGA    -       -      F     229           -
LGA    -       -      R     230           -
LGA    -       -      I     231           -
LGA    -       -      V     232           -
LGA    -       -      A     233           -
LGA    -       -      G     234           -
LGA    -       -      A     235           -
LGA    -       -      E     236           -
LGA    -       -      K     237           -
LGA    -       -      V     238           -
LGA    -       -      K     239           -
LGA    -       -      I     240           -
LGA    -       -      Y     241           -
LGA    -       -      S     242           -
LGA    -       -      A     243           -
LGA    -       -      G     244           -
LGA    -       -      Q     245           -
LGA    -       -      K     246           -
LGA    -       -      V     247           -
LGA    -       -      T     248           -
LGA    -       -      I     249           -
LGA    -       -      K     250           -
LGA    -       -      K     251           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   12  148    5.0     11    2.23    18.18      6.237     0.472

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.876154 * X  +   0.181049 * Y  +   0.446740 * Z  +  15.712608
  Y_new =  -0.152969 * X  +  -0.774449 * Y  +   0.613864 * Z  +  45.612656
  Z_new =   0.457116 * X  +  -0.606177 * Y  +  -0.650841 * Z  +  59.126423 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.391712    0.749881  [ DEG:  -137.0350     42.9650 ]
  Theta =  -0.474750   -2.666842  [ DEG:   -27.2012   -152.7988 ]
  Phi   =  -0.172849    2.968743  [ DEG:    -9.9035    170.0965 ]
 
# 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: T0321TS074_5-D2                               
REMARK     2: T0321_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0321TS074_5-D2.T0321_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   12  148   5.0   11   2.23   18.18   6.237
REMARK  ---------------------------------------------------------- 
MOLECULE T0321TS074_5-D2
PFRMAT TS
TARGET T0321
MODEL  5
PARENT N/A
ATOM    817  N   VAL    97      15.958  35.526  61.311  1.00  1.00
ATOM    818  CA  VAL    97      15.119  36.341  60.442  1.00  1.00
ATOM    819  C   VAL    97      13.813  35.575  60.166  1.00  1.00
ATOM    820  O   VAL    97      12.720  36.142  60.146  1.00  1.00
ATOM    821  HN  VAL    97      16.774  35.159  60.864  1.00  1.00
ATOM    822  CB  VAL    97      15.868  36.666  59.098  1.00  1.00
ATOM    823  CG1 VAL    97      17.166  37.434  59.358  1.00  1.00
ATOM    824  CG2 VAL    97      14.996  37.498  58.173  1.00  1.00
ATOM    825  N   ILE    98      13.954  34.283  59.926  1.00  1.00
ATOM    826  CA  ILE    98      12.777  33.448  59.681  1.00  1.00
ATOM    827  C   ILE    98      12.162  33.035  61.013  1.00  1.00
ATOM    828  O   ILE    98      12.804  32.355  61.809  1.00  1.00
ATOM    829  HN  ILE    98      14.820  33.785  59.891  1.00  1.00
ATOM    830  CB  ILE    98      13.142  32.250  58.816  1.00  1.00
ATOM    831  CG1 ILE    98      13.773  32.729  57.481  1.00  1.00
ATOM    832  CG2 ILE    98      11.891  31.368  58.689  1.00  1.00
ATOM    833  CD1 ILE    98      12.677  33.645  56.727  1.00  1.00
ATOM    834  N   PHE    99      10.916  33.412  61.223  1.00  1.00
ATOM    835  CA  PHE    99      10.243  33.258  62.507  1.00  1.00
ATOM    836  C   PHE    99       9.803  31.846  62.863  1.00  1.00
ATOM    837  O   PHE    99       9.697  31.511  64.042  1.00  1.00
ATOM    838  HN  PHE    99      10.348  33.828  60.513  1.00  1.00
ATOM    839  CB  PHE    99       9.039  34.188  62.580  1.00  1.00
ATOM    840  CG  PHE    99       9.372  35.680  62.560  1.00  1.00
ATOM    841  CD1 PHE    99      10.592  36.107  63.102  1.00  1.00
ATOM    842  CD2 PHE    99       8.445  36.623  62.196  1.00  1.00
ATOM    843  CE1 PHE    99      10.841  37.460  63.218  1.00  1.00
ATOM    844  CE2 PHE    99       8.671  37.972  62.279  1.00  1.00
ATOM    845  CZ  PHE    99       9.923  38.402  62.791  1.00  1.00
ATOM    846  N   SER   100       9.545  31.025  61.853  1.00  1.00
ATOM    847  CA  SER   100       9.070  29.660  62.065  1.00  1.00
ATOM    848  C   SER   100       9.825  28.881  63.150  1.00  1.00
ATOM    849  O   SER   100      11.036  28.708  63.084  1.00  1.00
ATOM    850  HN  SER   100       9.652  31.273  60.890  1.00  1.00
ATOM    851  CB  SER   100       9.082  28.887  60.726  1.00  1.00
ATOM    852  OG  SER   100      10.448  28.720  60.070  1.00  1.00
ATOM    853  N   ASP   101       9.075  28.464  64.167  1.00  1.00
ATOM    854  CA  ASP   101       9.579  27.671  65.277  1.00  1.00
ATOM    855  C   ASP   101      10.500  28.335  66.302  1.00  1.00
ATOM    856  O   ASP   101      11.035  27.670  67.188  1.00  1.00
ATOM    857  HN  ASP   101       8.100  28.674  64.228  1.00  1.00
ATOM    858  CB  ASP   101      10.236  26.405  64.731  1.00  1.00
ATOM    859  CG  ASP   101       9.225  25.438  64.153  1.00  1.00
ATOM    860  OD1 ASP   101       8.079  25.503  64.340  1.00  1.00
ATOM    861  OD2 ASP   101       9.823  24.491  63.479  1.00  1.00
ATOM    862  N   ALA   102      10.679  29.641  66.192  1.00  1.00
ATOM    863  CA  ALA   102      11.504  30.343  67.144  1.00  1.00
ATOM    864  C   ALA   102      10.670  30.637  68.390  1.00  1.00
ATOM    865  O   ALA   102       9.434  30.660  68.335  1.00  1.00
ATOM    866  HN  ALA   102      10.285  30.226  65.485  1.00  1.00
ATOM    867  CB  ALA   102      12.011  31.649  66.535  1.00  1.00
ATOM    868  N   LYS   103      11.349  30.850  69.511  1.00  1.00
ATOM    869  CA  LYS   103      10.689  31.173  70.782  1.00  1.00
ATOM    870  C   LYS   103      10.350  32.654  70.902  1.00  1.00
ATOM    871  O   LYS   103       9.389  33.028  71.573  1.00  1.00
ATOM    872  HN  LYS   103      12.346  30.805  69.571  1.00  1.00
ATOM    873  CB  LYS   103      11.549  30.712  71.969  1.00  1.00
ATOM    874  CG  LYS   103      10.858  30.968  73.296  1.00  1.00
ATOM    875  CD  LYS   103      11.785  30.478  74.434  1.00  1.00
ATOM    876  CE  LYS   103      13.047  31.216  74.669  1.00  1.00
ATOM    877  NZ  LYS   103      13.860  30.640  75.804  1.00  1.00
ATOM    878  N   ARG   104      11.137  33.492  70.242  1.00  1.00
ATOM    879  CA  ARG   104      10.901  34.930  70.248  1.00  1.00
ATOM    880  C   ARG   104       9.710  35.228  69.347  1.00  1.00
ATOM    881  O   ARG   104       8.939  36.156  69.605  1.00  1.00
ATOM    882  HN  ARG   104      11.932  33.213  69.705  1.00  1.00
ATOM    883  CB  ARG   104      12.143  35.676  69.738  1.00  1.00
ATOM    884  CG  ARG   104      13.368  35.475  70.586  1.00  1.00
ATOM    885  CD  ARG   104      12.987  36.219  71.905  1.00  1.00
ATOM    886  NE  ARG   104      14.132  36.073  72.796  1.00  1.00
ATOM    887  CZ  ARG   104      14.174  36.582  74.025  1.00  1.00
ATOM    888  NH1 ARG   104      13.164  37.336  74.460  1.00  1.00
ATOM    889  NH2 ARG   104      15.260  36.368  74.760  1.00  1.00
ATOM    890  N   VAL   105       9.575  34.427  68.292  1.00  1.00
ATOM    891  CA  VAL   105       8.507  34.574  67.306  1.00  1.00
ATOM    892  C   VAL   105       7.127  34.153  67.815  1.00  1.00
ATOM    893  O   VAL   105       6.949  33.056  68.345  1.00  1.00
ATOM    894  HN  VAL   105      10.199  33.669  68.106  1.00  1.00
ATOM    895  CB  VAL   105       8.832  33.759  66.033  1.00  1.00
ATOM    896  CG1 VAL   105      10.153  34.237  65.440  1.00  1.00
ATOM    897  CG2 VAL   105       7.720  33.918  65.002  1.00  1.00
ATOM    898  N   GLU   106       6.151  35.034  67.623  1.00  1.00
ATOM    899  CA  GLU   106       4.787  34.785  68.059  1.00  1.00
ATOM    900  C   GLU   106       3.966  34.069  66.992  1.00  1.00
ATOM    901  O   GLU   106       3.478  32.965  67.224  1.00  1.00
ATOM    902  HN  GLU   106       6.278  35.919  67.174  1.00  1.00
ATOM    903  CB  GLU   106       4.106  36.101  68.426  1.00  1.00
ATOM    904  CG  GLU   106       2.799  35.863  68.917  1.00  1.00
ATOM    905  CD  GLU   106       2.018  37.237  69.329  1.00  1.00
ATOM    906  OE1 GLU   106       2.598  38.309  69.186  1.00  1.00
ATOM    907  OE2 GLU   106       0.847  37.121  69.799  1.00  1.00
ATOM    908  N   ASP   107       3.809  34.704  65.831  1.00  1.00
ATOM    909  CA  ASP   107       3.039  34.103  64.734  1.00  1.00
ATOM    910  C   ASP   107       3.935  33.515  63.654  1.00  1.00
ATOM    911  O   ASP   107       4.838  34.208  63.139  1.00  1.00
ATOM    912  HN  ASP   107       4.186  35.605  65.617  1.00  1.00
ATOM    913  CB  ASP   107       2.076  35.115  64.126  1.00  1.00
ATOM    914  CG  ASP   107       1.089  34.442  62.732  1.00  1.00
ATOM    915  OD1 ASP   107       1.103  33.694  62.530  1.00  1.00
ATOM    916  OD2 ASP   107       0.766  35.946  62.494  1.00  1.00
ATOM    917  N   ARG   108       3.691  32.255  63.270  1.00  1.00
ATOM    918  CA  ARG   108       4.533  31.612  62.229  1.00  1.00
ATOM    919  C   ARG   108       4.418  32.324  60.889  1.00  1.00
ATOM    920  O   ARG   108       5.314  32.220  60.046  1.00  1.00
ATOM    921  HN  ARG   108       2.966  31.665  63.626  1.00  1.00
ATOM    922  CB  ARG   108       4.152  30.117  62.060  1.00  1.00
ATOM    923  CG  ARG   108       4.529  29.267  63.380  1.00  1.00
ATOM    924  CD  ARG   108       3.996  27.866  62.801  1.00  1.00
ATOM    925  NE  ARG   108       4.914  27.643  61.691  1.00  1.00
ATOM    926  CZ  ARG   108       6.108  27.073  61.830  1.00  1.00
ATOM    927  NH1 ARG   108       6.546  26.751  63.048  1.00  1.00
ATOM    928  NH2 ARG   108       6.854  26.895  60.745  1.00  1.00
TER
END
