
#######################################################
#                                                     #
#                        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   89 (   89),  selected   89 , name T0386TS599_1
# Molecule2: number of CA atoms  291 ( 2337),  selected  291 , name T0386.pdb
# PARAMETERS: T0386TS599_1.T0386.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    Q     211      K       9           -
LGA    H     212      N      10           -
LGA    L     213      T      11           -
LGA    F     214      E      12           -
LGA    E     215      I      13           -
LGA    D     216      I      14           -
LGA    I     217      S      15           -
LGA    S     218      P      16           -
LGA    N     219      H      17           -
LGA    P     220      H      18           -
LGA    E     221      Y      19           -
LGA    K     222      V      20           -
LGA    I     223      Y      21           -
LGA    R     224      P      22           -
LGA    L     225      N      23           -
LGA    L     226      T      24           -
LGA    K     227      T      25           -
LGA    E     228      T      26           -
LGA    F     229      L      27           -
LGA    M     230      K      28           -
LGA    -       -      N      29           -
LGA    -       -      K      30           -
LGA    -       -      Y      31           -
LGA    -       -      G      32           -
LGA    -       -      I      33           -
LGA    -       -      K      34           -
LGA    -       -      N      35           -
LGA    -       -      L      36           -
LGA    -       -      N      37           -
LGA    -       -      A      38           -
LGA    -       -      F      39           -
LGA    -       -      L      40           -
LGA    -       -      E      41           -
LGA    -       -      K      42           -
LGA    -       -      C      43           -
LGA    -       -      S      44           -
LGA    -       -      H      45           -
LGA    -       -      D      46           -
LGA    -       -      T      47           -
LGA    -       -      A      48           -
LGA    -       -      K      49           -
LGA    -       -      A      50           -
LGA    -       -      M      51           -
LGA    -       -      I      52           -
LGA    -       -      N      53           -
LGA    -       -      L      54           -
LGA    -       -      R      55           -
LGA    -       -      E      56           -
LGA    -       -      E      57           -
LGA    -       -      S      58           -
LGA    -       -      L      59           -
LGA    -       -      P      60           -
LGA    -       -      E      61           -
LGA    -       -      Y      62           -
LGA    -       -      F      63           -
LGA    -       -      D      64           -
LGA    -       -      T      65           -
LGA    -       -      A      66           -
LGA    -       -      Y      67           -
LGA    -       -      L      68           -
LGA    -       -      C      69           -
LGA    -       -      H      70           -
LGA    -       -      I      71           -
LGA    -       -      H      72           -
LGA    -       -      Q      73           -
LGA    -       -      Q      74           -
LGA    -       -      L      75           -
LGA    -       -      F      76           -
LGA    -       -      K      77           -
LGA    -       -      N      78           -
LGA    -       -      T      79           -
LGA    -       -      F      80           -
LGA    -       -      E      81           -
LGA    -       -      W      82           -
LGA    -       -      A      83           -
LGA    -       -      G      84           -
LGA    -       -      Y      85           -
LGA    -       -      L      86           -
LGA    -       -      R      87           -
LGA    -       -      H      88           -
LGA    -       -      I      89           -
LGA    -       -      P      90           -
LGA    -       -      F      91           -
LGA    -       -      T      92           -
LGA    -       -      F      93           -
LGA    -       -      A      94           -
LGA    -       -      D      95           -
LGA    -       -      G      96           -
LGA    -       -      T      97           -
LGA    -       -      T      98           -
LGA    -       -      A      99           -
LGA    -       -      A     100           -
LGA    -       -      M     101           -
LGA    -       -      P     102           -
LGA    -       -      E     103           -
LGA    -       -      M     104           -
LGA    -       -      K     105           -
LGA    -       -      R     106           -
LGA    -       -      T     107           -
LGA    H     231      G     108           #
LGA    T     232      -       -           -
LGA    M     233      -       -           -
LGA    K     234      W     109          3.047
LGA    N     235      K     110          2.373
LGA    T     236      N     111          4.814
LGA    G     237      A     112          1.275
LGA    R     238      F     113          1.731
LGA    N     239      -       -           -
LGA    V     240      -       -           -
LGA    N     241      -       -           -
LGA    D     242      A     114          4.870
LGA    R     243      I     115           -
LGA    P     244      G     116           -
LGA    V     245      D     117           -
LGA    M     246      E     118           -
LGA    V     247      I     119           -
LGA    A     248      Q     120           -
LGA    K     249      E     121           -
LGA    -       -      G     122           -
LGA    -       -      L     123           -
LGA    -       -      Q     124           -
LGA    -       -      R     125           -
LGA    -       -      L     126           -
LGA    -       -      D     127           -
LGA    -       -      Q     128           -
LGA    -       -      T     129           -
LGA    -       -      L     130           -
LGA    -       -      A     131           -
LGA    -       -      E     132           -
LGA    -       -      K     133           -
LGA    -       -      N     134           -
LGA    -       -      N     135           -
LGA    -       -      L     136           -
LGA    -       -      Q     137           -
LGA    -       -      G     138           -
LGA    -       -      L     139           -
LGA    -       -      T     140           -
LGA    E     250      R     141          2.517
LGA    G     251      E     142          2.643
LGA    -       -      E     143           -
LGA    -       -      F     144           -
LGA    E     252      N     145          2.357
LGA    T     253      S     146          1.971
LGA    Y     254      E     147          3.269
LGA    -       -      A     148           -
LGA    -       -      I     149           -
LGA    T     255      E     150          1.922
LGA    G     256      L     151          2.797
LGA    -       -      F     152           -
LGA    -       -      N     153           -
LGA    -       -      S     154           -
LGA    T     257      L     155          0.294
LGA    Y     258      N     156          4.150
LGA    -       -      Q     157           -
LGA    -       -      L     158           -
LGA    -       -      H     159           -
LGA    -       -      P     160           -
LGA    -       -      F     161           -
LGA    -       -      R     162           -
LGA    -       -      E     163           -
LGA    -       -      G     164           -
LGA    -       -      N     165           -
LGA    -       -      G     166           -
LGA    -       -      R     167           -
LGA    -       -      T     168           -
LGA    R     259      Q     169          1.110
LGA    G     260      R     170          3.142
LGA    A     261      L     171          1.728
LGA    G     262      F     172           -
LGA    -       -      F     173           -
LGA    -       -      E     174           -
LGA    -       -      N     175           -
LGA    -       -      L     176           -
LGA    -       -      A     177           -
LGA    -       -      K     178           -
LGA    -       -      A     179           -
LGA    -       -      A     180           -
LGA    -       -      G     181           -
LGA    -       -      H     182           -
LGA    -       -      Q     183           -
LGA    L     263      L     184           #
LGA    E     264      N     185          1.223
LGA    G     265      -       -           -
LGA    F     266      F     186          3.008
LGA    A     267      S     187           -
LGA    -       -      L     188           -
LGA    -       -      I     189           -
LGA    -       -      T     190           -
LGA    -       -      K     191           -
LGA    -       -      E     192           -
LGA    -       -      R     193           -
LGA    L     268      M     194          1.726
LGA    -       -      M     195           -
LGA    -       -      V     196           -
LGA    N     269      A     197          0.603
LGA    V     270      S     198          2.902
LGA    K     271      V     199          2.850
LGA    -       -      A     200           -
LGA    G     272      V     201          2.817
LGA    A     273      A     202          5.009
LGA    -       -      E     203           -
LGA    -       -      N     204           -
LGA    -       -      G     205           -
LGA    -       -      D     206           -
LGA    Y     274      L     207           #
LGA    -       -      E     208           -
LGA    -       -      P     209           -
LGA    I     275      M     210          4.585
LGA    -       -      Q     211           -
LGA    -       -      H     212           -
LGA    -       -      L     213           -
LGA    I     276      F     214          2.991
LGA    G     277      E     215           #
LGA    N     278      D     216          3.668
LGA    I     279      I     217          3.127
LGA    D     280      S     218          2.600
LGA    H     281      N     219          1.881
LGA    -       -      P     220           -
LGA    -       -      E     221           -
LGA    L     282      K     222          1.601
LGA    P     283      I     223          4.699
LGA    P     284      R     224          2.217
LGA    E     285      L     225          3.203
LGA    Q     286      L     226          2.542
LGA    L     287      K     227          1.660
LGA    K     288      E     228          1.758
LGA    I     289      F     229          1.287
LGA    L     290      M     230          1.884
LGA    -       -      H     231           -
LGA    -       -      T     232           -
LGA    -       -      M     233           -
LGA    K     291      K     234           #
LGA    P     292      N     235           -
LGA    G     293      T     236           -
LGA    -       -      G     237           -
LGA    -       -      R     238           -
LGA    -       -      N     239           -
LGA    D     294      V     240           #
LGA    K     295      -       -           -
LGA    I     296      N     241           #
LGA    -       -      D     242           -
LGA    T     297      R     243           #
LGA    F     298      P     244           #
LGA    T     299      V     245           -
LGA    -       -      M     246           -
LGA    -       -      V     247           -
LGA    -       -      A     248           -
LGA    -       -      K     249           -
LGA    -       -      E     250           -
LGA    -       -      G     251           -
LGA    -       -      E     252           -
LGA    -       -      T     253           -
LGA    -       -      Y     254           -
LGA    -       -      T     255           -
LGA    -       -      G     256           -
LGA    -       -      T     257           -
LGA    -       -      Y     258           -
LGA    -       -      R     259           -
LGA    -       -      G     260           -
LGA    -       -      A     261           -
LGA    -       -      G     262           -
LGA    -       -      L     263           -
LGA    -       -      E     264           -
LGA    -       -      G     265           -
LGA    -       -      F     266           -
LGA    -       -      A     267           -
LGA    -       -      L     268           -
LGA    -       -      N     269           -
LGA    -       -      V     270           -
LGA    -       -      K     271           -
LGA    -       -      G     272           -
LGA    -       -      A     273           -
LGA    -       -      Y     274           -
LGA    -       -      I     275           -
LGA    -       -      I     276           -
LGA    -       -      G     277           -
LGA    -       -      N     278           -
LGA    -       -      I     279           -
LGA    -       -      D     280           -
LGA    -       -      H     281           -
LGA    -       -      L     282           -
LGA    -       -      P     283           -
LGA    -       -      P     284           -
LGA    -       -      E     285           -
LGA    -       -      Q     286           -
LGA    -       -      L     287           -
LGA    -       -      K     288           -
LGA    -       -      I     289           -
LGA    -       -      L     290           -
LGA    -       -      K     291           -
LGA    -       -      P     292           -
LGA    -       -      G     293           -
LGA    -       -      D     294           -
LGA    -       -      K     295           -
LGA    -       -      I     296           -
LGA    -       -      T     297           -
LGA    -       -      F     298           -
LGA    -       -      T     299           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   89  291    5.0     41    2.82     7.32      8.528     1.402

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.390361 * X  +  -0.793540 * Y  +   0.466811 * Z  +  14.794199
  Y_new =  -0.263241 * X  +  -0.582074 * Y  +  -0.769347 * Z  +  57.354099
  Z_new =   0.882226 * X  +   0.177440 * Y  +  -0.436111 * Z  +  64.825325 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.755180   -0.386413  [ DEG:   157.8602    -22.1398 ]
  Theta =  -1.080569   -2.061024  [ DEG:   -61.9120   -118.0880 ]
  Phi   =  -0.593304    2.548289  [ DEG:   -33.9938    146.0062 ]
 
# 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: T0386TS599_1                                  
REMARK     2: T0386.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0386TS599_1.T0386.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   89  291   5.0   41   2.82    7.32   8.528
REMARK  ---------------------------------------------------------- 
MOLECULE T0386TS599_1
PFRMAT TS                                                                       
TARGET T0386                                                                    
MODEL  1                                                                        
PARENT N/A                                                                      
ATOM    211  CA  GLN   211      21.514  72.244  70.359  1.00  0.00              
ATOM    212  CA  HIS   212      19.038  68.998  69.470  1.00  0.00              
ATOM    213  CA  LEU   213      17.785  65.003  69.861  1.00  0.00              
ATOM    214  CA  PHE   214      19.680  68.072  70.081  1.00  0.00              
ATOM    215  CA  GLU   215      21.157  66.769  73.353  1.00  0.00              
ATOM    216  CA  ASP   216      22.291  63.580  71.651  1.00  0.00              
ATOM    217  CA  ILE   217      23.957  65.447  68.760  1.00  0.00              
ATOM    218  CA  SER   218      25.744  67.752  71.213  1.00  0.00              
ATOM    219  CA  ASN   219      27.127  64.784  73.157  1.00  0.00              
ATOM    220  CA  PRO   220      30.140  63.734  71.047  1.00  0.00              
ATOM    221  CA  GLU   221      30.302  60.014  71.439  1.00  0.00              
ATOM    222  CA  LYS   222      26.654  59.454  70.466  1.00  0.00              
ATOM    223  CA  ILE   223      26.801  61.961  67.579  1.00  0.00              
ATOM    224  CA  ARG   224      29.954  60.794  65.727  1.00  0.00              
ATOM    225  CA  LEU   225      28.776  57.224  65.820  1.00  0.00              
ATOM    226  CA  LEU   226      25.233  57.860  64.726  1.00  0.00              
ATOM    227  CA  LYS   227      26.538  59.960  61.802  1.00  0.00              
ATOM    228  CA  GLU   228      28.698  57.043  60.656  1.00  0.00              
ATOM    229  CA  PHE   229      25.729  54.634  60.897  1.00  0.00              
ATOM    230  CA  MET   230      23.465  56.918  58.936  1.00  0.00              
ATOM    231  CA  HIS   231      26.178  57.291  56.265  1.00  0.00              
ATOM    232  CA  THR   232      26.387  53.517  55.910  1.00  0.00              
ATOM    233  CA  MET   233      22.580  53.299  55.578  1.00  0.00              
ATOM    234  CA  LYS   234      22.535  55.979  52.857  1.00  0.00              
ATOM    235  CA  ASN   235      25.273  54.219  50.829  1.00  0.00              
ATOM    236  CA  THR   236      23.419  50.978  51.076  1.00  0.00              
ATOM    237  CA  GLY   237      20.347  52.980  49.885  1.00  0.00              
ATOM    238  CA  ARG   238      19.152  50.072  48.022  1.00  0.00              
ATOM    239  CA  ASN   239      19.545  47.788  51.112  1.00  0.00              
ATOM    240  CA  VAL   240      17.770  50.248  53.409  1.00  0.00              
ATOM    241  CA  ASN   241      14.721  50.776  51.135  1.00  0.00              
ATOM    242  CA  ASP   242      14.257  46.990  51.051  1.00  0.00              
ATOM    243  CA  ARG   243      14.589  46.581  54.858  1.00  0.00              
ATOM    244  CA  PRO   244      12.550  49.204  56.656  1.00  0.00              
ATOM    245  CA  VAL   245      10.469  48.268  59.665  1.00  0.00              
ATOM    246  CA  MET   246       8.138  50.778  61.220  1.00  0.00              
ATOM    247  CA  VAL   247       7.028  50.362  64.843  1.00  0.00              
ATOM    248  CA  ALA   248       4.245  52.481  66.168  1.00  0.00              
ATOM    249  CA  LYS   249       3.743  53.576  69.775  1.00  0.00              
ATOM    250  CA  GLU   250       0.805  51.145  70.211  1.00  0.00              
ATOM    251  CA  GLY   251       2.775  48.067  69.376  1.00  0.00              
ATOM    252  CA  GLU   252       1.901  47.604  65.745  1.00  0.00              
ATOM    253  CA  THR   253       4.697  46.396  63.567  1.00  0.00              
ATOM    254  CA  TYR   254       4.689  47.840  60.077  1.00  0.00              
ATOM    255  CA  THR   255       6.878  46.448  57.383  1.00  0.00              
ATOM    256  CA  GLY   256       7.959  48.879  54.747  1.00  0.00              
ATOM    257  CA  THR   257       9.799  51.751  53.295  1.00  0.00              
ATOM    258  CA  TYR   258       9.685  54.386  55.967  1.00  0.00              
ATOM    259  CA  ARG   259       8.792  58.010  55.318  1.00  0.00              
ATOM    260  CA  GLY   260       6.147  58.713  58.003  1.00  0.00              
ATOM    261  CA  ALA   261       5.725  62.111  59.549  1.00  0.00              
ATOM    262  CA  GLY   262       7.636  62.499  62.762  1.00  0.00              
ATOM    263  CA  LEU   263       5.243  64.402  64.939  1.00  0.00              
ATOM    264  CA  GLU   264       5.457  62.846  68.346  1.00  0.00              
ATOM    265  CA  GLY   265       9.033  61.797  68.785  1.00  0.00              
ATOM    266  CA  PHE   266      10.854  59.721  66.169  1.00  0.00              
ATOM    267  CA  ALA   267      13.426  57.214  67.157  1.00  0.00              
ATOM    268  CA  LEU   268      15.581  55.701  64.582  1.00  0.00              
ATOM    269  CA  ASN   269      17.227  52.414  65.125  1.00  0.00              
ATOM    270  CA  VAL   270      19.886  51.338  62.873  1.00  0.00              
ATOM    271  CA  LYS   271      20.607  47.701  62.299  1.00  0.00              
ATOM    272  CA  GLY   272      18.638  47.111  59.037  1.00  0.00              
ATOM    273  CA  ALA   273      16.398  50.173  59.440  1.00  0.00              
ATOM    274  CA  TYR   274      13.926  50.269  62.272  1.00  0.00              
ATOM    275  CA  ILE   275      11.701  53.336  62.889  1.00  0.00              
ATOM    276  CA  ILE   276      10.163  53.764  66.183  1.00  0.00              
ATOM    277  CA  GLY   277       7.485  56.156  66.709  1.00  0.00              
ATOM    278  CA  ASN   278       6.809  57.262  70.159  1.00  0.00              
ATOM    279  CA  ILE   279       4.050  59.606  70.735  1.00  0.00              
ATOM    280  CA  ASP   280       1.844  57.378  72.808  1.00  0.00              
ATOM    281  CA  HIS   281       4.541  56.257  75.229  1.00  0.00              
ATOM    282  CA  LEU   282       6.101  59.426  76.306  1.00  0.00              
ATOM    283  CA  PRO   283       5.561  60.765  79.843  1.00  0.00              
ATOM    284  CA  PRO   284       4.682  64.403  80.140  1.00  0.00              
ATOM    285  CA  GLU   285       8.105  65.275  81.583  1.00  0.00              
ATOM    286  CA  GLN   286       9.861  63.564  78.616  1.00  0.00              
ATOM    287  CA  LEU   287       7.803  65.296  76.032  1.00  0.00              
ATOM    288  CA  LYS   288       8.595  68.720  77.392  1.00  0.00              
ATOM    289  CA  ILE   289      12.342  68.184  77.582  1.00  0.00              
ATOM    290  CA  LEU   290      12.640  66.888  74.072  1.00  0.00              
ATOM    291  CA  LYS   291      10.436  68.733  71.660  1.00  0.00              
ATOM    292  CA  PRO   292       8.252  67.627  68.737  1.00  0.00              
ATOM    293  CA  GLY   293      10.358  66.885  65.744  1.00  0.00              
ATOM    294  CA  ASP   294      13.339  65.694  67.736  1.00  0.00              
ATOM    295  CA  LYS   295      15.156  62.789  66.232  1.00  0.00              
ATOM    296  CA  ILE   296      17.002  60.265  68.298  1.00  0.00              
ATOM    297  CA  THR   297      19.449  57.823  66.510  1.00  0.00              
ATOM    298  CA  PHE   298      20.379  54.520  68.000  1.00  0.00              
ATOM    299  CA  THR   299      22.761  51.734  65.919  1.00  0.00              
TER                                                                             
END
