
#######################################################
#                                                     #
#                        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_2-D2
# Molecule2: number of CA atoms  148 ( 1130),  selected  148 , name T0321_D2.pdb
# PARAMETERS: T0321TS074_2-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    V      97      S     145          2.109
LGA    I      98      I     146          0.985
LGA    F      99      L     147          2.865
LGA    S     100      E     148          3.413
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    D     101      L     158          1.949
LGA    -       -      P     159           -
LGA    -       -      A     160           -
LGA    A     102      S     161          2.169
LGA    K     103      E     162          1.670
LGA    R     104      F     163          2.617
LGA    V     105      I     164          1.793
LGA    -       -      L     165           -
LGA    E     106      P     166          3.616
LGA    D     107      E     167          1.702
LGA    R     108      C     168          1.861
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    -       -      S     190           -
LGA    -       -      R     191           -
LGA    -       -      N     192           -
LGA    -       -      A     193           -
LGA    -       -      R     194           -
LGA    -       -      R     195           -
LGA    -       -      I     196           -
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    -       -      G     213           -
LGA    -       -      L     214           -
LGA    -       -      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     12    2.35     8.33      6.194     0.491

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.649469 * X  +   0.703678 * Y  +  -0.288146 * Z  + -78.480812
  Y_new =   0.758940 * X  +  -0.623263 * Y  +   0.188557 * Z  +  47.790680
  Z_new =  -0.046907 * X  +  -0.341147 * Y  +  -0.938839 * Z  + 130.654999 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.793056    0.348537  [ DEG:  -160.0303     19.9697 ]
  Theta =   0.046924    3.094668  [ DEG:     2.6886    177.3114 ]
  Phi   =   0.862969   -2.278624  [ DEG:    49.4445   -130.5555 ]
 
# 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_2-D2                               
REMARK     2: T0321_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0321TS074_2-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   12   2.35    8.33   6.194
REMARK  ---------------------------------------------------------- 
MOLECULE T0321TS074_2-D2
PFRMAT TS
TARGET T0321
MODEL  2
PARENT N/A
ATOM    817  N   VAL    97      22.775  42.328  63.977  1.00  1.00
ATOM    818  CA  VAL    97      22.209  43.059  62.849  1.00  1.00
ATOM    819  C   VAL    97      20.689  42.925  62.841  1.00  1.00
ATOM    820  O   VAL    97      20.137  41.963  63.387  1.00  1.00
ATOM    821  HN  VAL    97      23.365  41.565  63.711  1.00  1.00
ATOM    822  CB  VAL    97      22.794  42.575  61.531  1.00  1.00
ATOM    823  CG1 VAL    97      22.183  43.192  60.259  1.00  1.00
ATOM    824  CG2 VAL    97      22.671  41.064  61.257  1.00  1.00
ATOM    825  N   ILE    98      20.023  43.994  62.388  1.00  1.00
ATOM    826  CA  ILE    98      18.557  43.970  62.335  1.00  1.00
ATOM    827  C   ILE    98      18.104  43.746  60.898  1.00  1.00
ATOM    828  O   ILE    98      18.364  44.580  60.033  1.00  1.00
ATOM    829  HN  ILE    98      20.428  44.851  62.066  1.00  1.00
ATOM    830  CB  ILE    98      17.996  45.277  62.882  1.00  1.00
ATOM    831  CG1 ILE    98      18.444  45.598  64.316  1.00  1.00
ATOM    832  CG2 ILE    98      16.471  45.237  62.705  1.00  1.00
ATOM    833  CD1 ILE    98      18.031  44.537  65.326  1.00  1.00
ATOM    834  N   PHE    99      17.530  42.572  60.629  1.00  1.00
ATOM    835  CA  PHE    99      17.135  42.237  59.263  1.00  1.00
ATOM    836  C   PHE    99      15.848  42.959  58.875  1.00  1.00
ATOM    837  O   PHE    99      14.806  42.784  59.502  1.00  1.00
ATOM    838  HN  PHE    99      17.330  41.855  61.297  1.00  1.00
ATOM    839  CB  PHE    99      16.975  40.725  59.095  1.00  1.00
ATOM    840  CG  PHE    99      18.254  39.895  59.255  1.00  1.00
ATOM    841  CD1 PHE    99      19.465  40.538  58.885  1.00  1.00
ATOM    842  CD2 PHE    99      18.213  38.537  59.184  1.00  1.00
ATOM    843  CE1 PHE    99      20.642  39.788  58.758  1.00  1.00
ATOM    844  CE2 PHE    99      19.377  37.785  59.042  1.00  1.00
ATOM    845  CZ  PHE    99      20.580  38.426  58.826  1.00  1.00
ATOM    846  N   SER   100      15.969  43.882  57.934  1.00  1.00
ATOM    847  CA  SER   100      14.854  44.691  57.454  1.00  1.00
ATOM    848  C   SER   100      14.127  43.941  56.344  1.00  1.00
ATOM    849  O   SER   100      12.924  44.115  56.148  1.00  1.00
ATOM    850  HN  SER   100      16.840  44.085  57.487  1.00  1.00
ATOM    851  CB  SER   100      15.355  46.037  56.924  1.00  1.00
ATOM    852  OG  SER   100      16.295  45.930  55.736  1.00  1.00
ATOM    853  N   ASP   101      14.867  43.104  55.623  1.00  1.00
ATOM    854  CA  ASP   101      14.303  42.316  54.532  1.00  1.00
ATOM    855  C   ASP   101      14.026  40.885  54.981  1.00  1.00
ATOM    856  O   ASP   101      14.952  40.117  55.251  1.00  1.00
ATOM    857  HN  ASP   101      15.845  42.952  55.770  1.00  1.00
ATOM    858  CB  ASP   101      15.255  42.322  53.333  1.00  1.00
ATOM    859  CG  ASP   101      15.328  43.675  52.653  1.00  1.00
ATOM    860  OD1 ASP   101      14.850  44.520  52.617  1.00  1.00
ATOM    861  OD2 ASP   101      16.521  43.254  51.729  1.00  1.00
ATOM    862  N   ALA   102      12.739  40.505  55.053  1.00  1.00
ATOM    863  CA  ALA   102      12.267  39.180  55.468  1.00  1.00
ATOM    864  C   ALA   102      12.980  38.005  54.808  1.00  1.00
ATOM    865  O   ALA   102      13.276  37.006  55.463  1.00  1.00
ATOM    866  HN  ALA   102      12.005  41.142  54.814  1.00  1.00
ATOM    867  CB  ALA   102      10.785  39.210  55.106  1.00  1.00
ATOM    868  N   LYS   103      13.248  38.125  53.511  1.00  1.00
ATOM    869  CA  LYS   103      13.902  37.055  52.765  1.00  1.00
ATOM    870  C   LYS   103      15.335  36.787  53.214  1.00  1.00
ATOM    871  O   LYS   103      15.928  35.778  52.833  1.00  1.00
ATOM    872  HN  LYS   103      13.029  38.930  52.961  1.00  1.00
ATOM    873  CB  LYS   103      13.896  37.378  51.266  1.00  1.00
ATOM    874  CG  LYS   103      14.467  36.320  50.513  1.00  1.00
ATOM    875  CD  LYS   103      13.542  35.017  50.557  1.00  1.00
ATOM    876  CE  LYS   103      13.926  33.777  49.845  1.00  1.00
ATOM    877  NZ  LYS   103      12.917  32.666  50.014  1.00  1.00
ATOM    878  N   ARG   104      15.888  37.679  54.029  1.00  1.00
ATOM    879  CA  ARG   104      17.261  37.528  54.497  1.00  1.00
ATOM    880  C   ARG   104      17.395  36.918  55.890  1.00  1.00
ATOM    881  O   ARG   104      18.509  36.663  56.352  1.00  1.00
ATOM    882  HN  ARG   104      15.428  38.496  54.376  1.00  1.00
ATOM    883  CB  ARG   104      17.969  38.883  54.471  1.00  1.00
ATOM    884  CG  ARG   104      19.431  38.818  54.874  1.00  1.00
ATOM    885  CD  ARG   104      19.862  40.325  54.750  1.00  1.00
ATOM    886  NE  ARG   104      19.091  41.037  55.763  1.00  1.00
ATOM    887  CZ  ARG   104      19.110  42.360  55.903  1.00  1.00
ATOM    888  NH1 ARG   104      19.927  43.091  55.142  1.00  1.00
ATOM    889  NH2 ARG   104      18.350  42.906  56.845  1.00  1.00
ATOM    890  N   VAL   105      16.274  36.685  56.557  1.00  1.00
ATOM    891  CA  VAL   105      16.304  36.109  57.897  1.00  1.00
ATOM    892  C   VAL   105      16.563  34.605  57.877  1.00  1.00
ATOM    893  O   VAL   105      15.815  33.831  57.275  1.00  1.00
ATOM    894  HN  VAL   105      15.352  36.873  56.217  1.00  1.00
ATOM    895  CB  VAL   105      14.993  36.379  58.665  1.00  1.00
ATOM    896  CG1 VAL   105      14.776  37.878  58.797  1.00  1.00
ATOM    897  CG2 VAL   105      15.060  35.744  60.053  1.00  1.00
ATOM    898  N   GLU   106      17.641  34.208  58.546  1.00  1.00
ATOM    899  CA  GLU   106      18.039  32.812  58.644  1.00  1.00
ATOM    900  C   GLU   106      17.577  32.241  59.977  1.00  1.00
ATOM    901  O   GLU   106      17.169  31.083  60.060  1.00  1.00
ATOM    902  HN  GLU   106      18.250  34.839  59.024  1.00  1.00
ATOM    903  CB  GLU   106      19.559  32.699  58.546  1.00  1.00
ATOM    904  CG  GLU   106      20.133  33.118  57.212  1.00  1.00
ATOM    905  CD  GLU   106      19.733  32.257  56.049  1.00  1.00
ATOM    906  OE1 GLU   106      19.668  31.036  56.173  1.00  1.00
ATOM    907  OE2 GLU   106      19.497  32.874  54.967  1.00  1.00
ATOM    908  N   ASP   107      17.645  33.065  61.019  1.00  1.00
ATOM    909  CA  ASP   107      17.245  32.640  62.353  1.00  1.00
ATOM    910  C   ASP   107      16.782  33.833  63.179  1.00  1.00
ATOM    911  O   ASP   107      17.110  34.980  62.875  1.00  1.00
ATOM    912  HN  ASP   107      17.967  34.010  60.972  1.00  1.00
ATOM    913  CB  ASP   107      18.410  31.953  63.050  1.00  1.00
ATOM    914  CG  ASP   107      19.642  32.832  63.273  1.00  1.00
ATOM    915  OD1 ASP   107      19.930  33.741  62.961  1.00  1.00
ATOM    916  OD2 ASP   107      20.445  31.783  64.005  1.00  1.00
ATOM    917  N   ARG   108      16.009  33.549  64.220  1.00  1.00
ATOM    918  CA  ARG   108      15.504  34.584  65.112  1.00  1.00
ATOM    919  C   ARG   108      16.563  34.898  66.158  1.00  1.00
ATOM    920  O   ARG   108      17.452  34.087  66.412  1.00  1.00
ATOM    921  HN  ARG   108      15.721  32.624  64.465  1.00  1.00
ATOM    922  CB  ARG   108      14.242  34.098  65.823  1.00  1.00
ATOM    923  CG  ARG   108      13.523  35.075  66.754  1.00  1.00
ATOM    924  CD  ARG   108      13.027  36.162  65.910  1.00  1.00
ATOM    925  NE  ARG   108      12.343  37.090  66.803  1.00  1.00
ATOM    926  CZ  ARG   108      12.967  38.050  67.481  1.00  1.00
ATOM    927  NH1 ARG   108      14.296  38.140  67.421  1.00  1.00
ATOM    928  NH2 ARG   108      12.241  38.856  68.247  1.00  1.00
TER
END
