
#######################################################
#                                                     #
#                        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_3
# Molecule2: number of CA atoms  287 ( 2364),  selected  287 , name T0320.pdb
# PARAMETERS: T0320TS599_3.T0320.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      M       1           -
LGA    -       -      Q       2           -
LGA    -       -      L       3           -
LGA    -       -      S       4           -
LGA    -       -      K       5           -
LGA    -       -      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    L     206      I      27           #
LGA    L     207      -       -           -
LGA    Y     208      -       -           -
LGA    S     209      -       -           -
LGA    N     210      A      28          4.454
LGA    E     211      S      29           -
LGA    P     212      T      30          5.043
LGA    -       -      Q      31           -
LGA    -       -      E      32           -
LGA    -       -      A      33           -
LGA    I     213      I      34           #
LGA    C     214      R      35           -
LGA    G     215      L      36           -
LGA    L     216      -       -           -
LGA    Y     217      -       -           -
LGA    G     218      -       -           -
LGA    K     219      -       -           -
LGA    G     220      -       -           -
LGA    F     221      -       -           -
LGA    T     222      -       -           -
LGA    S     223      -       -           -
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      T      37          1.872
LGA    H     253      R      38          1.045
LGA    A     254      K      39          2.252
LGA    F     255      Y      40          3.554
LGA    G     256      L      41          4.189
LGA    -       -      L      42           -
LGA    -       -      S      43           -
LGA    -       -      E      44           -
LGA    K     257      I      45           #
LGA    D     258      F      46          3.165
LGA    A     259      V      47           -
LGA    E     260      R      48           -
LGA    G     261      W      49           #
LGA    E     262      S      50          2.066
LGA    R     263      P      51          2.895
LGA    S     264      L      52          1.379
LGA    S     265      N      53          2.363
LGA    A     266      G      54          2.291
LGA    I     267      E      55           #
LGA    -       -      I      56           -
LGA    -       -      S      57           -
LGA    -       -      F      58           -
LGA    -       -      S      59           -
LGA    -       -      Y      60           -
LGA    -       -      N      61           -
LGA    -       -      G      62           -
LGA    -       -      G      63           -
LGA    -       -      K      64           -
LGA    -       -      D      65           -
LGA    -       -      C      66           -
LGA    -       -      Q      67           -
LGA    -       -      V      68           -
LGA    -       -      L      69           -
LGA    -       -      L      70           -
LGA    -       -      L      71           -
LGA    -       -      L      72           -
LGA    -       -      Y      73           -
LGA    -       -      L      74           -
LGA    -       -      S      75           -
LGA    -       -      C      76           -
LGA    -       -      L      77           -
LGA    -       -      W      78           -
LGA    -       -      E      79           -
LGA    -       -      Y      80           -
LGA    -       -      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    N     268      Q     100          5.008
LGA    T     269      R     101          2.598
LGA    S     270      L     102          4.646
LGA    P     271      P     103           #
LGA    -       -      T     104           -
LGA    -       -      V     105           -
LGA    -       -      F     106           -
LGA    -       -      I     107           -
LGA    -       -      D     108           -
LGA    -       -      Q     109           -
LGA    -       -      E     110           -
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    I     272      S     130          2.673
LGA    S     273      L     131           #
LGA    V     274      Y     132           -
LGA    V     275      E     133           -
LGA    -       -      S     134           -
LGA    -       -      Q     135           -
LGA    -       -      R     136           -
LGA    -       -      V     142           -
LGA    -       -      N     143           -
LGA    -       -      M     144           -
LGA    -       -      A     145           -
LGA    -       -      D     146           -
LGA    -       -      A     147           -
LGA    -       -      F     148           -
LGA    -       -      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    D     276      I     161          2.353
LGA    K     277      V     162          4.333
LGA    E     278      -       -           -
LGA    R     279      I     163          3.766
LGA    F     280      G     164          2.453
LGA    S     281      I     165          3.170
LGA    K     282      -       -           -
LGA    Y     283      -       -           -
LGA    H     284      R     166          1.749
LGA    D     285      H     167          2.650
LGA    N     286      T     168          4.384
LGA    Y     287      D     169          5.168
LGA    -       -      P     170           -
LGA    -       -      F     171           -
LGA    -       -      G     172           -
LGA    -       -      E     173           -
LGA    -       -      A     174           -
LGA    -       -      L     175           -
LGA    -       -      K     176           -
LGA    -       -      P     177           -
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    -       -      P     193           -
LGA    -       -      L     194           -
LGA    -       -      L     195           -
LGA    -       -      H     196           -
LGA    -       -      W     197           -
LGA    Y     288      D     198          2.249
LGA    P     289      L     199          0.911
LGA    -       -      T     200           -
LGA    G     290      N     201          1.301
LGA    W     291      I     202          2.735
LGA    -       -      W     203           -
LGA    -       -      S     204           -
LGA    Y     292      F     205          1.537
LGA    L     293      L     206          3.494
LGA    -       -      L     207           -
LGA    -       -      Y     208           -
LGA    V     294      S     209          1.474
LGA    D     295      N     210          4.896
LGA    D     296      E     211          4.442
LGA    -       -      P     212           -
LGA    -       -      I     213           -
LGA    -       -      C     214           -
LGA    -       -      G     215           -
LGA    -       -      L     216           -
LGA    -       -      Y     217           -
LGA    -       -      G     218           -
LGA    -       -      K     219           -
LGA    -       -      G     220           -
LGA    -       -      F     221           -
LGA    -       -      T     222           -
LGA    -       -      S     223           -
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    T     297      A     254          4.035
LGA    L     298      F     255          2.720
LGA    E     299      G     256          2.736
LGA    R     300      K     257          2.540
LGA    A     301      -       -           -
LGA    G     302      -       -           -
LGA    R     303      D     258          3.123
LGA    -       -      R     263           -
LGA    I     304      S     264          4.416
LGA    K     305      S     265           -
LGA    N     306      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           -
LGA    -       -      R     300           -
LGA    -       -      A     301           -
LGA    -       -      G     302           -
LGA    -       -      R     303           -
LGA    -       -      I     304           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  101  287    5.0     41    3.25     2.44      7.957     1.223

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.274351 * X  +  -0.861045 * Y  +  -0.428174 * Z  +  10.446544
  Y_new =  -0.350919 * X  +  -0.504198 * Y  +   0.789076 * Z  +  23.790440
  Z_new =  -0.895314 * X  +  -0.066229 * Y  +  -0.440484 * Z  +  21.530745 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.992355    0.149238  [ DEG:  -171.4493      8.5507 ]
  Theta =   1.109136    2.032457  [ DEG:    63.5488    116.4512 ]
  Phi   =  -0.907247    2.234345  [ DEG:   -51.9814    128.0186 ]
 
# 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_3                                  
REMARK     2: T0320.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0320TS599_3.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   41   3.25    2.44   7.957
REMARK  ---------------------------------------------------------- 
MOLECULE T0320TS599_3
PFRMAT TS                                                                       
TARGET T0320                                                                    
MODEL  3                                                                        
PARENT N/A                                                                      
ATOM    206  CA  LEU   206      -2.306  21.358  19.580  1.00  0.00              
ATOM    207  CA  LEU   207      -4.538  20.851  23.113  1.00  0.00              
ATOM    208  CA  TYR   208      -5.150  18.327  26.450  1.00  0.00              
ATOM    209  CA  SER   209      -4.187  18.530  22.472  1.00  0.00              
ATOM    210  CA  ASN   210      -0.944  16.775  22.533  1.00  0.00              
ATOM    211  CA  GLU   211       1.239  19.474  21.159  1.00  0.00              
ATOM    212  CA  PRO   212       4.746  19.836  22.485  1.00  0.00              
ATOM    213  CA  ILE   213       5.282  23.542  23.609  1.00  0.00              
ATOM    214  CA  CYS   214       7.649  25.207  24.745  1.00  0.00              
ATOM    215  CA  GLY   215       6.741  28.864  26.502  1.00  0.00              
ATOM    216  CA  LEU   216       9.255  31.147  25.879  1.00  0.00              
ATOM    217  CA  TYR   217       9.498  30.228  22.179  1.00  0.00              
ATOM    218  CA  GLY   218       5.738  30.294  21.412  1.00  0.00              
ATOM    219  CA  LYS   219       5.414  33.587  23.087  1.00  0.00              
ATOM    220  CA  GLY   220       8.080  35.307  21.079  1.00  0.00              
ATOM    221  CA  PHE   221      10.949  35.430  23.505  1.00  0.00              
ATOM    222  CA  THR   222      14.133  35.222  21.626  1.00  0.00              
ATOM    223  CA  SER   223      16.686  33.416  24.082  1.00  0.00              
ATOM    224  CA  ILE   224      17.930  30.191  22.318  1.00  0.00              
ATOM    225  CA  GLY   225      21.220  29.623  23.777  1.00  0.00              
ATOM    226  CA  GLY   226      23.840  27.972  21.677  1.00  0.00              
ATOM    227  CA  ILE   227      22.174  24.667  20.783  1.00  0.00              
ATOM    228  CA  ASN   228      23.597  23.929  17.396  1.00  0.00              
ATOM    229  CA  ASN   229      25.269  20.688  18.590  1.00  0.00              
ATOM    230  CA  SER   230      22.252  19.223  20.263  1.00  0.00              
ATOM    231  CA  LEU   231      20.114  19.278  17.218  1.00  0.00              
ATOM    232  CA  PRO   232      22.151  17.707  14.466  1.00  0.00              
ATOM    233  CA  ASN   233      19.595  15.538  12.611  1.00  0.00              
ATOM    234  CA  PRO   234      20.486  12.153  13.854  1.00  0.00              
ATOM    235  CA  HIS   235      16.956  10.678  14.189  1.00  0.00              
ATOM    236  CA  LEU   236      15.017  13.015  11.861  1.00  0.00              
ATOM    237  CA  ARG   237      11.435  12.329  11.389  1.00  0.00              
ATOM    238  CA  LYS   238       9.878  14.298   8.257  1.00  0.00              
ATOM    239  CA  ASP   239       6.241  14.351   8.256  1.00  0.00              
ATOM    240  CA  SER   240       5.546  16.394   5.325  1.00  0.00              
ATOM    241  CA  ASN   241       5.812  14.895   1.929  1.00  0.00              
ATOM    242  CA  ASN   242       9.104  16.121   0.697  1.00  0.00              
ATOM    243  CA  PRO   243      11.144  14.039   3.158  1.00  0.00              
ATOM    244  CA  ALA   244      12.879  16.842   4.902  1.00  0.00              
ATOM    245  CA  LEU   245      12.968  15.603   8.500  1.00  0.00              
ATOM    246  CA  HIS   246      12.745  18.323  11.319  1.00  0.00              
ATOM    247  CA  PHE   247      11.569  16.993  14.619  1.00  0.00              
ATOM    248  CA  GLU   248       9.928  19.293  17.157  1.00  0.00              
ATOM    249  CA  TRP   249      10.252  18.420  20.726  1.00  0.00              
ATOM    250  CA  GLU   250       7.485  19.347  23.261  1.00  0.00              
ATOM    251  CA  ILE   251       8.855  20.160  27.017  1.00  0.00              
ATOM    252  CA  ILE   252       7.010  18.490  29.680  1.00  0.00              
ATOM    253  CA  HIS   253       5.678  21.023  32.106  1.00  0.00              
ATOM    254  CA  ALA   254       8.209  20.639  34.859  1.00  0.00              
ATOM    255  CA  PHE   255      11.164  21.376  32.626  1.00  0.00              
ATOM    256  CA  GLY   256      10.027  24.552  31.022  1.00  0.00              
ATOM    257  CA  LYS   257       9.130  25.957  34.410  1.00  0.00              
ATOM    258  CA  ASP   258      12.042  25.472  36.613  1.00  0.00              
ATOM    259  CA  ALA   259      14.752  26.719  34.398  1.00  0.00              
ATOM    260  CA  GLU   260      12.894  29.700  32.917  1.00  0.00              
ATOM    261  CA  GLY   261      12.032  31.250  36.304  1.00  0.00              
ATOM    262  CA  GLU   262      15.653  31.179  37.425  1.00  0.00              
ATOM    263  CA  ARG   263      16.963  32.596  34.148  1.00  0.00              
ATOM    264  CA  SER   264      14.510  35.362  33.996  1.00  0.00              
ATOM    265  CA  SER   265      15.393  36.405  37.503  1.00  0.00              
ATOM    266  CA  ALA   266      19.089  36.613  37.008  1.00  0.00              
ATOM    267  CA  ILE   267      19.432  38.098  33.659  1.00  0.00              
ATOM    268  CA  ASN   268      16.545  40.516  33.533  1.00  0.00              
ATOM    269  CA  THR   269      16.383  41.724  29.952  1.00  0.00              
ATOM    270  CA  SER   270      12.883  40.674  28.975  1.00  0.00              
ATOM    271  CA  PRO   271      13.479  38.883  25.643  1.00  0.00              
ATOM    272  CA  ILE   272      16.849  37.440  26.364  1.00  0.00              
ATOM    273  CA  SER   273      16.738  33.555  26.096  1.00  0.00              
ATOM    274  CA  VAL   274      19.229  31.893  28.190  1.00  0.00              
ATOM    275  CA  VAL   275      19.116  28.167  27.528  1.00  0.00              
ATOM    276  CA  ASP   276      19.895  25.912  30.448  1.00  0.00              
ATOM    277  CA  LYS   277      22.462  23.281  29.371  1.00  0.00              
ATOM    278  CA  GLU   278      20.609  20.585  31.336  1.00  0.00              
ATOM    279  CA  ARG   279      17.320  21.050  29.466  1.00  0.00              
ATOM    280  CA  PHE   280      18.935  20.860  25.966  1.00  0.00              
ATOM    281  CA  SER   281      20.842  17.624  26.715  1.00  0.00              
ATOM    282  CA  LYS   282      17.772  15.711  28.088  1.00  0.00              
ATOM    283  CA  TYR   283      15.345  16.512  25.298  1.00  0.00              
ATOM    284  CA  HIS   284      17.916  15.734  22.541  1.00  0.00              
ATOM    285  CA  ASP   285      19.613  12.486  23.699  1.00  0.00              
ATOM    286  CA  ASN   286      16.989  10.105  22.893  1.00  0.00              
ATOM    287  CA  TYR   287      15.734  11.188  19.470  1.00  0.00              
ATOM    288  CA  TYR   288      11.941  10.837  19.803  1.00  0.00              
ATOM    289  CA  PRO   289      10.199  13.359  17.614  1.00  0.00              
ATOM    290  CA  GLY   290       7.497  15.201  19.453  1.00  0.00              
ATOM    291  CA  TRP   291       5.933  18.172  17.670  1.00  0.00              
ATOM    292  CA  TYR   292       5.019  20.957  19.687  1.00  0.00              
ATOM    293  CA  LEU   293       2.698  23.389  17.674  1.00  0.00              
ATOM    294  CA  VAL   294       3.329  27.160  18.139  1.00  0.00              
ATOM    295  CA  ASP   295       0.581  29.614  18.397  1.00  0.00              
ATOM    296  CA  ASP   296       1.185  30.861  14.821  1.00  0.00              
ATOM    297  CA  THR   297       1.071  27.351  13.412  1.00  0.00              
ATOM    298  CA  LEU   298      -1.886  26.163  15.293  1.00  0.00              
ATOM    299  CA  GLU   299      -3.876  29.232  14.326  1.00  0.00              
ATOM    300  CA  ARG   300      -2.967  28.821  10.664  1.00  0.00              
ATOM    301  CA  ALA   301      -4.052  25.104  10.735  1.00  0.00              
ATOM    302  CA  GLY   302      -7.371  25.740  12.377  1.00  0.00              
ATOM    303  CA  ARG   303      -9.038  28.325  10.227  1.00  0.00              
ATOM    304  CA  ILE   304      -8.738  25.752   6.915  1.00  0.00              
ATOM    305  CA  LYS   305      -9.601  22.413   9.264  1.00  0.00              
ATOM    306  CA  ASN   306     -10.264  25.741   6.789  1.00  0.00              
TER                                                                             
END
