
#######################################################
#                                                     #
#                        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  101 (  101),  selected  101 , name T0320TS599_5
# Molecule2: number of CA atoms  287 ( 2364),  selected  287 , name T0320.pdb
# PARAMETERS: T0320TS599_5.T0320.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    L     206      M       1           -
LGA    L     207      Q       2           -
LGA    Y     208      L       3           -
LGA    S     209      S       4           -
LGA    N     210      K       5           -
LGA    E     211      A       6           -
LGA    -       -      A       7           -
LGA    -       -      E       8           -
LGA    -       -      M       9           -
LGA    -       -      C      10           -
LGA    -       -      Y      11           -
LGA    -       -      E      12           -
LGA    -       -      I      13           -
LGA    -       -      T      14           -
LGA    -       -      N      15           -
LGA    -       -      S      16           -
LGA    -       -      Y      17           -
LGA    -       -      L      18           -
LGA    -       -      H      19           -
LGA    -       -      I      20           -
LGA    -       -      D      21           -
LGA    -       -      Q      22           -
LGA    -       -      K      23           -
LGA    -       -      S      24           -
LGA    -       -      Q      25           -
LGA    -       -      I      26           -
LGA    -       -      I      27           -
LGA    -       -      A      28           -
LGA    -       -      S      29           -
LGA    -       -      T      30           -
LGA    -       -      Q      31           -
LGA    -       -      E      32           -
LGA    -       -      A      33           -
LGA    -       -      I      34           -
LGA    -       -      R      35           -
LGA    -       -      L      36           -
LGA    -       -      T      37           -
LGA    -       -      R      38           -
LGA    -       -      K      39           -
LGA    -       -      Y      40           -
LGA    -       -      L      41           -
LGA    -       -      L      42           -
LGA    -       -      S      43           -
LGA    -       -      E      44           -
LGA    -       -      I      45           -
LGA    -       -      F      46           -
LGA    -       -      V      47           -
LGA    -       -      R      48           -
LGA    -       -      W      49           -
LGA    -       -      S      50           -
LGA    -       -      P      51           -
LGA    -       -      L      52           -
LGA    -       -      N      53           -
LGA    -       -      G      54           -
LGA    -       -      E      55           -
LGA    -       -      I      56           -
LGA    -       -      S      57           -
LGA    -       -      F      58           -
LGA    -       -      S      59           -
LGA    P     212      Y      60           #
LGA    I     213      N      61          2.616
LGA    C     214      G      62          1.946
LGA    G     215      G      63          3.233
LGA    L     216      K      64           #
LGA    Y     217      D      65           -
LGA    G     218      C      66           -
LGA    K     219      Q      67           -
LGA    G     220      -       -           -
LGA    F     221      V      68           #
LGA    T     222      L      69           -
LGA    S     223      L      70           -
LGA    I     224      L      71          4.770
LGA    G     225      -       -           -
LGA    G     226      -       -           -
LGA    I     227      L      72          4.757
LGA    -       -      Y      73           -
LGA    -       -      L      74           -
LGA    -       -      S      75           -
LGA    N     228      C      76          4.180
LGA    N     229      L      77          4.011
LGA    S     230      W      78           -
LGA    L     231      E      79           -
LGA    P     232      Y      80           -
LGA    N     233      F      81           -
LGA    -       -      F      82           -
LGA    -       -      I      83           -
LGA    -       -      K      84           -
LGA    -       -      A      85           -
LGA    -       -      Q      86           -
LGA    -       -      N      87           -
LGA    -       -      S      88           -
LGA    -       -      F      97           -
LGA    -       -      P      98           -
LGA    -       -      M      99           -
LGA    -       -      Q     100           -
LGA    -       -      R     101           -
LGA    -       -      L     102           -
LGA    P     234      P     103           #
LGA    H     235      T     104           #
LGA    L     236      V     105          3.645
LGA    R     237      F     106          4.116
LGA    K     238      I     107          2.243
LGA    -       -      D     108           -
LGA    D     239      Q     109          1.990
LGA    S     240      E     110          2.249
LGA    -       -      E     111           -
LGA    -       -      T     112           -
LGA    -       -      F     113           -
LGA    -       -      P     114           -
LGA    -       -      T     115           -
LGA    -       -      L     116           -
LGA    -       -      E     117           -
LGA    -       -      N     118           -
LGA    -       -      F     119           -
LGA    -       -      V     120           -
LGA    -       -      L     121           -
LGA    -       -      E     122           -
LGA    -       -      T     123           -
LGA    -       -      S     124           -
LGA    -       -      E     125           -
LGA    -       -      R     126           -
LGA    -       -      Y     127           -
LGA    -       -      C     128           -
LGA    -       -      L     129           -
LGA    -       -      S     130           -
LGA    -       -      L     131           -
LGA    -       -      Y     132           -
LGA    -       -      E     133           -
LGA    -       -      S     134           -
LGA    -       -      Q     135           -
LGA    N     241      R     136          3.069
LGA    N     242      V     142           -
LGA    P     243      N     143           -
LGA    A     244      M     144           -
LGA    L     245      A     145           -
LGA    H     246      D     146           -
LGA    F     247      A     147           -
LGA    E     248      F     148           -
LGA    W     249      R     149           -
LGA    -       -      D     150           -
LGA    -       -      F     151           -
LGA    -       -      I     152           -
LGA    -       -      K     153           -
LGA    -       -      I     154           -
LGA    -       -      Y     155           -
LGA    -       -      P     156           -
LGA    -       -      E     157           -
LGA    -       -      T     158           -
LGA    -       -      E     159           -
LGA    -       -      A     160           -
LGA    -       -      I     161           -
LGA    E     250      V     162          1.865
LGA    I     251      I     163          3.046
LGA    -       -      G     164           -
LGA    -       -      I     165           -
LGA    I     252      R     166           #
LGA    H     253      H     167           -
LGA    -       -      T     168           -
LGA    -       -      D     169           -
LGA    -       -      P     170           -
LGA    -       -      F     171           -
LGA    -       -      G     172           -
LGA    -       -      E     173           -
LGA    -       -      A     174           -
LGA    -       -      L     175           -
LGA    -       -      K     176           -
LGA    A     254      P     177          3.092
LGA    -       -      I     178           -
LGA    -       -      Q     179           -
LGA    -       -      R     180           -
LGA    -       -      T     181           -
LGA    -       -      D     182           -
LGA    -       -      S     183           -
LGA    -       -      N     184           -
LGA    -       -      W     185           -
LGA    -       -      P     186           -
LGA    -       -      D     187           -
LGA    -       -      F     188           -
LGA    -       -      M     189           -
LGA    -       -      R     190           -
LGA    -       -      L     191           -
LGA    -       -      Q     192           -
LGA    F     255      P     193          1.966
LGA    G     256      L     194          2.663
LGA    K     257      L     195          1.856
LGA    D     258      H     196          1.155
LGA    A     259      W     197          1.237
LGA    E     260      D     198          3.435
LGA    G     261      -       -           -
LGA    E     262      -       -           -
LGA    R     263      L     199          3.334
LGA    S     264      -       -           -
LGA    S     265      -       -           -
LGA    A     266      -       -           -
LGA    I     267      -       -           -
LGA    N     268      T     200          2.521
LGA    T     269      N     201           -
LGA    S     270      I     202           -
LGA    P     271      -       -           -
LGA    I     272      -       -           -
LGA    S     273      W     203          3.001
LGA    V     274      S     204           #
LGA    -       -      F     205           -
LGA    V     275      L     206          2.284
LGA    D     276      L     207          2.786
LGA    -       -      Y     208           -
LGA    -       -      S     209           -
LGA    -       -      N     210           -
LGA    K     277      E     211          2.690
LGA    E     278      P     212           -
LGA    R     279      -       -           -
LGA    F     280      -       -           -
LGA    S     281      -       -           -
LGA    K     282      -       -           -
LGA    Y     283      -       -           -
LGA    H     284      -       -           -
LGA    D     285      -       -           -
LGA    N     286      -       -           -
LGA    Y     287      -       -           -
LGA    Y     288      -       -           -
LGA    P     289      -       -           -
LGA    G     290      -       -           -
LGA    W     291      -       -           -
LGA    Y     292      I     213           #
LGA    L     293      C     214           -
LGA    -       -      G     215           -
LGA    -       -      L     216           -
LGA    V     294      Y     217          3.469
LGA    D     295      G     218           -
LGA    -       -      K     219           -
LGA    -       -      G     220           -
LGA    D     296      F     221          1.423
LGA    T     297      T     222          2.853
LGA    L     298      S     223          4.289
LGA    -       -      I     224           -
LGA    -       -      G     225           -
LGA    -       -      G     226           -
LGA    -       -      I     227           -
LGA    -       -      N     228           -
LGA    -       -      N     229           -
LGA    -       -      S     230           -
LGA    -       -      L     231           -
LGA    -       -      P     232           -
LGA    -       -      N     233           -
LGA    -       -      P     234           -
LGA    -       -      H     235           -
LGA    -       -      L     236           -
LGA    -       -      R     237           -
LGA    -       -      K     238           -
LGA    -       -      D     239           -
LGA    -       -      S     240           -
LGA    -       -      N     241           -
LGA    -       -      N     242           -
LGA    -       -      P     243           -
LGA    -       -      A     244           -
LGA    -       -      L     245           -
LGA    -       -      H     246           -
LGA    -       -      F     247           -
LGA    -       -      E     248           -
LGA    -       -      W     249           -
LGA    -       -      E     250           -
LGA    -       -      I     251           -
LGA    -       -      I     252           -
LGA    -       -      H     253           -
LGA    -       -      A     254           -
LGA    -       -      F     255           -
LGA    -       -      G     256           -
LGA    -       -      K     257           -
LGA    -       -      D     258           -
LGA    -       -      R     263           -
LGA    -       -      S     264           -
LGA    -       -      S     265           -
LGA    -       -      A     266           -
LGA    -       -      I     267           -
LGA    -       -      N     268           -
LGA    -       -      T     269           -
LGA    -       -      S     270           -
LGA    -       -      P     271           -
LGA    -       -      I     272           -
LGA    -       -      S     273           -
LGA    -       -      V     274           -
LGA    -       -      V     275           -
LGA    -       -      D     276           -
LGA    -       -      K     277           -
LGA    -       -      E     278           -
LGA    -       -      R     279           -
LGA    -       -      F     280           -
LGA    -       -      S     281           -
LGA    -       -      K     282           -
LGA    -       -      Y     283           -
LGA    -       -      H     284           -
LGA    -       -      D     285           -
LGA    -       -      N     286           -
LGA    -       -      Y     287           -
LGA    -       -      Y     288           -
LGA    -       -      P     289           -
LGA    -       -      G     290           -
LGA    -       -      W     291           -
LGA    -       -      Y     292           -
LGA    -       -      L     293           -
LGA    -       -      V     294           -
LGA    -       -      D     295           -
LGA    -       -      D     296           -
LGA    -       -      T     297           -
LGA    -       -      L     298           -
LGA    E     299      E     299          4.864
LGA    R     300      R     300          3.208
LGA    A     301      A     301          4.939
LGA    G     302      G     302           #
LGA    R     303      R     303           -
LGA    I     304      I     304           -
LGA    K     305      -       -           -
LGA    N     306      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  101  287    5.0     35    3.17    17.14      6.965     1.072

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.296771 * X  +   0.554583 * Y  +   0.777409 * Z  +  13.813084
  Y_new =  -0.245234 * X  +  -0.831043 * Y  +   0.499228 * Z  +  22.743879
  Z_new =   0.922923 * X  +  -0.042491 * Y  +   0.382633 * Z  +  19.145241 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.110595    3.030998  [ DEG:    -6.3366    173.6634 ]
  Theta =  -1.175605   -1.965988  [ DEG:   -67.3572   -112.6428 ]
  Phi   =  -2.450996    0.690597  [ DEG:  -140.4317     39.5683 ]
 
# 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: T0320TS599_5                                  
REMARK     2: T0320.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0320TS599_5.T0320.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  101  287   5.0   35   3.17   17.14   6.965
REMARK  ---------------------------------------------------------- 
MOLECULE T0320TS599_5
PFRMAT TS                                                                       
TARGET T0320                                                                    
MODEL  5                                                                        
PARENT N/A                                                                      
ATOM    206  CA  LEU   206      29.010  16.603   7.518  1.00  0.00              
ATOM    207  CA  LEU   207      29.277  17.870  11.334  1.00  0.00              
ATOM    208  CA  TYR   208      28.552  21.544  12.981  1.00  0.00              
ATOM    209  CA  SER   209      28.642  25.423  11.394  1.00  0.00              
ATOM    210  CA  ASN   210      28.831  27.517  14.551  1.00  0.00              
ATOM    211  CA  GLU   211      25.617  29.586  14.199  1.00  0.00              
ATOM    212  CA  PRO   212      23.469  30.250  17.174  1.00  0.00              
ATOM    213  CA  ILE   213      20.074  28.820  16.270  1.00  0.00              
ATOM    214  CA  CYS   214      17.083  28.703  18.578  1.00  0.00              
ATOM    215  CA  GLY   215      14.276  26.211  17.080  1.00  0.00              
ATOM    216  CA  LEU   216      10.880  28.021  17.435  1.00  0.00              
ATOM    217  CA  TYR   217      12.691  31.234  16.359  1.00  0.00              
ATOM    218  CA  GLY   218      14.535  29.902  13.306  1.00  0.00              
ATOM    219  CA  LYS   219      11.434  28.402  11.892  1.00  0.00              
ATOM    220  CA  GLY   220       9.397  31.561  12.171  1.00  0.00              
ATOM    221  CA  PHE   221       6.926  30.679  14.945  1.00  0.00              
ATOM    222  CA  THR   222       6.493  33.726  17.076  1.00  0.00              
ATOM    223  CA  SER   223       3.635  32.581  19.411  1.00  0.00              
ATOM    224  CA  ILE   224       5.445  31.953  22.565  1.00  0.00              
ATOM    225  CA  GLY   225       2.731  31.641  25.086  1.00  0.00              
ATOM    226  CA  GLY   226       3.520  32.059  28.688  1.00  0.00              
ATOM    227  CA  ILE   227       6.160  29.396  29.413  1.00  0.00              
ATOM    228  CA  ASN   228       8.714  31.340  31.357  1.00  0.00              
ATOM    229  CA  ASN   229       9.710  28.632  33.912  1.00  0.00              
ATOM    230  CA  SER   230      10.059  25.845  31.350  1.00  0.00              
ATOM    231  CA  LEU   231      12.583  27.431  29.118  1.00  0.00              
ATOM    232  CA  PRO   232      15.505  28.659  31.250  1.00  0.00              
ATOM    233  CA  ASN   233      18.730  27.025  29.704  1.00  0.00              
ATOM    234  CA  PRO   234      20.542  30.066  28.065  1.00  0.00              
ATOM    235  CA  HIS   235      22.515  28.062  25.366  1.00  0.00              
ATOM    236  CA  LEU   236      23.443  29.831  22.478  1.00  0.00              
ATOM    237  CA  ARG   237      27.114  28.876  20.710  1.00  0.00              
ATOM    238  CA  LYS   238      28.699  30.854  18.828  1.00  0.00              
ATOM    239  CA  ASP   239      31.735  29.755  16.707  1.00  0.00              
ATOM    240  CA  SER   240      32.182  31.405  13.384  1.00  0.00              
ATOM    241  CA  ASN   241      32.542  35.182  13.215  1.00  0.00              
ATOM    242  CA  ASN   242      29.204  36.061  11.532  1.00  0.00              
ATOM    243  CA  PRO   243      27.228  33.357  13.063  1.00  0.00              
ATOM    244  CA  ALA   244      24.980  35.230  15.448  1.00  0.00              
ATOM    245  CA  LEU   245      21.600  33.957  16.137  1.00  0.00              
ATOM    246  CA  HIS   246      20.535  33.634  19.766  1.00  0.00              
ATOM    247  CA  PHE   247      18.426  30.546  20.501  1.00  0.00              
ATOM    248  CA  GLU   248      17.906  29.843  24.043  1.00  0.00              
ATOM    249  CA  TRP   249      17.204  26.072  25.163  1.00  0.00              
ATOM    250  CA  GLU   250      17.329  25.015  28.639  1.00  0.00              
ATOM    251  CA  ILE   251      18.105  21.209  29.154  1.00  0.00              
ATOM    252  CA  ILE   252      16.821  20.338  32.637  1.00  0.00              
ATOM    253  CA  HIS   253      17.369  16.591  32.755  1.00  0.00              
ATOM    254  CA  ALA   254      13.692  15.584  32.654  1.00  0.00              
ATOM    255  CA  PHE   255      12.620  17.719  29.692  1.00  0.00              
ATOM    256  CA  GLY   256      15.242  16.813  27.116  1.00  0.00              
ATOM    257  CA  LYS   257      15.106  13.186  27.943  1.00  0.00              
ATOM    258  CA  ASP   258      11.407  12.401  27.858  1.00  0.00              
ATOM    259  CA  ALA   259      10.233  14.335  24.846  1.00  0.00              
ATOM    260  CA  GLU   260      13.029  13.467  22.388  1.00  0.00              
ATOM    261  CA  GLY   261      12.850   9.700  22.962  1.00  0.00              
ATOM    262  CA  GLU   262       9.099   9.724  22.450  1.00  0.00              
ATOM    263  CA  ARG   263       9.235  11.633  19.162  1.00  0.00              
ATOM    264  CA  SER   264      11.930   9.439  17.593  1.00  0.00              
ATOM    265  CA  SER   265       9.862   6.341  18.519  1.00  0.00              
ATOM    266  CA  ALA   266       6.485   7.537  17.286  1.00  0.00              
ATOM    267  CA  ILE   267       7.418   9.054  13.934  1.00  0.00              
ATOM    268  CA  ASN   268       5.882  12.496  14.132  1.00  0.00              
ATOM    269  CA  THR   269       3.717  12.623  11.046  1.00  0.00              
ATOM    270  CA  SER   270       5.515  14.870   8.643  1.00  0.00              
ATOM    271  CA  PRO   271       8.886  13.017   8.917  1.00  0.00              
ATOM    272  CA  ILE   272      10.472  16.388   9.660  1.00  0.00              
ATOM    273  CA  SER   273       8.128  17.948  12.124  1.00  0.00              
ATOM    274  CA  VAL   274       7.497  21.583  11.801  1.00  0.00              
ATOM    275  CA  VAL   275       5.217  22.907  14.443  1.00  0.00              
ATOM    276  CA  ASP   276       2.817  25.671  13.361  1.00  0.00              
ATOM    277  CA  LYS   277       3.179  28.754  15.400  1.00  0.00              
ATOM    278  CA  GLU   278      -0.514  29.192  16.060  1.00  0.00              
ATOM    279  CA  ARG   279      -0.929  25.766  17.713  1.00  0.00              
ATOM    280  CA  PHE   280       2.012  26.173  20.093  1.00  0.00              
ATOM    281  CA  SER   281       1.017  29.566  21.346  1.00  0.00              
ATOM    282  CA  LYS   282      -2.328  28.591  22.358  1.00  0.00              
ATOM    283  CA  TYR   283      -1.838  25.421  24.454  1.00  0.00              
ATOM    284  CA  HIS   284       0.929  26.469  26.611  1.00  0.00              
ATOM    285  CA  ASP   285       0.107  25.205  29.930  1.00  0.00              
ATOM    286  CA  ASN   286       2.895  22.732  30.629  1.00  0.00              
ATOM    287  CA  TYR   287       5.923  24.250  28.768  1.00  0.00              
ATOM    288  CA  TYR   288       7.574  21.949  27.372  1.00  0.00              
ATOM    289  CA  PRO   289      10.525  23.071  24.875  1.00  0.00              
ATOM    290  CA  GLY   290       9.675  24.252  21.664  1.00  0.00              
ATOM    291  CA  TRP   291      11.707  21.865  19.082  1.00  0.00              
ATOM    292  CA  TYR   292      10.799  22.142  16.122  1.00  0.00              
ATOM    293  CA  LEU   293      12.602  19.379  13.712  1.00  0.00              
ATOM    294  CA  VAL   294      13.312  20.273  10.320  1.00  0.00              
ATOM    295  CA  ASP   295      14.538  17.605   7.652  1.00  0.00              
ATOM    296  CA  ASP   296      17.965  18.648   7.690  1.00  0.00              
ATOM    297  CA  THR   297      18.333  18.124  11.285  1.00  0.00              
ATOM    298  CA  LEU   298      16.808  14.650  11.076  1.00  0.00              
ATOM    299  CA  GLU   299      19.158  13.696   8.330  1.00  0.00              
ATOM    300  CA  ARG   300      22.256  14.787  10.282  1.00  0.00              
ATOM    301  CA  ALA   301      20.992  12.862  13.271  1.00  0.00              
ATOM    302  CA  GLY   302      20.437   9.720  11.180  1.00  0.00              
ATOM    303  CA  ARG   303      16.766   9.194  11.745  1.00  0.00              
ATOM    304  CA  ILE   304      16.698   5.797  13.179  1.00  0.00              
ATOM    305  CA  LYS   305      13.422   5.611  14.591  1.00  0.00              
ATOM    306  CA  ASN   306      16.006   8.898  14.984  1.00  0.00              
TER                                                                             
END
