
#######################################################
#                                                     #
#                        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_4
# Molecule2: number of CA atoms  291 ( 2337),  selected  291 , name T0386.pdb
# PARAMETERS: T0386TS599_4.T0386.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      K       9           -
LGA    -       -      N      10           -
LGA    -       -      T      11           -
LGA    -       -      E      12           -
LGA    -       -      I      13           -
LGA    -       -      I      14           -
LGA    Q     211      S      15          2.462
LGA    H     212      P      16          5.221
LGA    -       -      H      17           -
LGA    -       -      H      18           -
LGA    -       -      Y      19           -
LGA    -       -      V      20           -
LGA    -       -      Y      21           -
LGA    -       -      P      22           -
LGA    -       -      N      23           -
LGA    -       -      T      24           -
LGA    -       -      T      25           -
LGA    -       -      T      26           -
LGA    -       -      L      27           -
LGA    -       -      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    L     213      T      98           #
LGA    F     214      A      99          2.672
LGA    E     215      A     100          4.170
LGA    D     216      M     101          1.373
LGA    I     217      P     102           #
LGA    S     218      -       -           -
LGA    N     219      -       -           -
LGA    P     220      -       -           -
LGA    E     221      E     103          3.283
LGA    K     222      M     104          2.152
LGA    I     223      K     105           #
LGA    R     224      R     106           -
LGA    L     225      T     107           -
LGA    -       -      G     108           -
LGA    -       -      W     109           -
LGA    -       -      K     110           -
LGA    -       -      N     111           -
LGA    -       -      A     112           -
LGA    -       -      F     113           -
LGA    L     226      A     114          4.154
LGA    K     227      I     115          4.124
LGA    -       -      G     116           -
LGA    -       -      D     117           -
LGA    E     228      E     118          2.195
LGA    F     229      I     119          3.552
LGA    M     230      Q     120          3.653
LGA    H     231      E     121          1.972
LGA    T     232      G     122          1.087
LGA    M     233      L     123          1.783
LGA    K     234      Q     124          1.298
LGA    N     235      R     125          0.412
LGA    T     236      L     126          1.107
LGA    G     237      D     127          0.856
LGA    R     238      Q     128          0.545
LGA    N     239      T     129          0.735
LGA    V     240      L     130          0.748
LGA    N     241      A     131          0.871
LGA    D     242      E     132          0.897
LGA    R     243      K     133          1.497
LGA    -       -      N     134           -
LGA    -       -      N     135           -
LGA    P     244      L     136          2.540
LGA    V     245      Q     137           -
LGA    -       -      G     138           -
LGA    -       -      L     139           -
LGA    -       -      T     140           -
LGA    -       -      R     141           -
LGA    -       -      E     142           -
LGA    -       -      E     143           -
LGA    M     246      F     144          0.816
LGA    V     247      N     145          0.642
LGA    A     248      S     146           #
LGA    K     249      E     147           -
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      A     148          3.347
LGA    L     268      I     149          3.236
LGA    N     269      E     150          1.599
LGA    V     270      L     151          5.305
LGA    K     271      F     152           -
LGA    G     272      -       -           -
LGA    A     273      N     153          1.542
LGA    Y     274      S     154          4.266
LGA    I     275      L     155           #
LGA    -       -      N     156           -
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    -       -      Q     169           -
LGA    -       -      R     170           -
LGA    -       -      L     171           -
LGA    -       -      F     172           -
LGA    -       -      F     173           -
LGA    -       -      E     174           -
LGA    -       -      N     175           -
LGA    I     276      L     176          5.212
LGA    G     277      A     177          4.188
LGA    N     278      -       -           -
LGA    I     279      -       -           -
LGA    D     280      -       -           -
LGA    H     281      -       -           -
LGA    L     282      -       -           -
LGA    P     283      K     178          4.380
LGA    P     284      A     179           -
LGA    -       -      A     180           -
LGA    -       -      G     181           -
LGA    -       -      H     182           -
LGA    E     285      Q     183           #
LGA    Q     286      L     184          1.953
LGA    L     287      -       -           -
LGA    K     288      N     185          2.045
LGA    I     289      F     186          3.983
LGA    L     290      S     187           -
LGA    K     291      L     188           -
LGA    P     292      I     189           -
LGA    G     293      T     190           -
LGA    -       -      K     191           -
LGA    -       -      E     192           -
LGA    -       -      R     193           -
LGA    -       -      M     194           -
LGA    -       -      M     195           -
LGA    -       -      V     196           -
LGA    D     294      A     197           #
LGA    -       -      S     198           -
LGA    -       -      V     199           -
LGA    -       -      A     200           -
LGA    -       -      V     201           -
LGA    -       -      A     202           -
LGA    -       -      E     203           -
LGA    -       -      N     204           -
LGA    -       -      G     205           -
LGA    -       -      D     206           -
LGA    -       -      L     207           -
LGA    -       -      E     208           -
LGA    -       -      P     209           -
LGA    K     295      M     210           #
LGA    I     296      Q     211           #
LGA    T     297      H     212           -
LGA    F     298      L     213           -
LGA    T     299      F     214           -
LGA    -       -      E     215           -
LGA    -       -      D     216           -
LGA    -       -      I     217           -
LGA    -       -      S     218           -
LGA    -       -      N     219           -
LGA    -       -      P     220           -
LGA    -       -      E     221           -
LGA    -       -      K     222           -
LGA    -       -      I     223           -
LGA    -       -      R     224           -
LGA    -       -      L     225           -
LGA    -       -      L     226           -
LGA    -       -      K     227           -
LGA    -       -      E     228           -
LGA    -       -      F     229           -
LGA    -       -      M     230           -
LGA    -       -      H     231           -
LGA    -       -      T     232           -
LGA    -       -      M     233           -
LGA    -       -      K     234           -
LGA    -       -      N     235           -
LGA    -       -      T     236           -
LGA    -       -      G     237           -
LGA    -       -      R     238           -
LGA    -       -      N     239           -
LGA    -       -      V     240           -
LGA    -       -      N     241           -
LGA    -       -      D     242           -
LGA    -       -      R     243           -
LGA    -       -      P     244           -
LGA    -       -      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     40    2.85     7.50      9.261     1.354

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.439416 * X  +  -0.794112 * Y  +   0.419880 * Z  +   5.442026
  Y_new =  -0.830545 * X  +  -0.181094 * Y  +   0.526688 * Z  +  51.832970
  Z_new =  -0.342211 * X  +  -0.580164 * Y  +  -0.739122 * Z  +  55.438057 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.476104    0.665488  [ DEG:  -141.8703     38.1297 ]
  Theta =   0.349269    2.792323  [ DEG:    20.0117    159.9883 ]
  Phi   =  -1.084164    2.057428  [ DEG:   -62.1180    117.8820 ]
 
# 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_4                                  
REMARK     2: T0386.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0386TS599_4.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   40   2.85    7.50   9.261
REMARK  ---------------------------------------------------------- 
MOLECULE T0386TS599_4
PFRMAT TS                                                                       
TARGET T0386                                                                    
MODEL  4                                                                        
PARENT N/A                                                                      
ATOM    211  CA  GLN   211      24.051  59.275  32.639  1.00  0.00              
ATOM    212  CA  HIS   212      20.478  58.544  33.638  1.00  0.00              
ATOM    213  CA  LEU   213      17.105  58.633  36.145  1.00  0.00              
ATOM    214  CA  PHE   214      20.801  58.910  35.029  1.00  0.00              
ATOM    215  CA  GLU   215      22.090  58.520  38.528  1.00  0.00              
ATOM    216  CA  ASP   216      19.973  55.432  39.155  1.00  0.00              
ATOM    217  CA  ILE   217      21.154  53.857  35.861  1.00  0.00              
ATOM    218  CA  SER   218      24.819  54.408  36.482  1.00  0.00              
ATOM    219  CA  ASN   219      25.415  52.883  39.869  1.00  0.00              
ATOM    220  CA  PRO   220      23.905  49.393  39.551  1.00  0.00              
ATOM    221  CA  GLU   221      23.669  48.721  43.259  1.00  0.00              
ATOM    222  CA  LYS   222      21.848  52.012  44.034  1.00  0.00              
ATOM    223  CA  ILE   223      19.405  51.235  41.196  1.00  0.00              
ATOM    224  CA  ARG   224      18.614  47.589  42.034  1.00  0.00              
ATOM    225  CA  LEU   225      18.012  48.512  45.711  1.00  0.00              
ATOM    226  CA  LEU   226      15.808  51.491  44.871  1.00  0.00              
ATOM    227  CA  LYS   227      13.772  49.248  42.524  1.00  0.00              
ATOM    228  CA  GLU   228      13.206  46.704  45.252  1.00  0.00              
ATOM    229  CA  PHE   229      12.125  49.427  47.629  1.00  0.00              
ATOM    230  CA  MET   230       9.702  50.896  45.114  1.00  0.00              
ATOM    231  CA  HIS   231       8.154  47.440  44.443  1.00  0.00              
ATOM    232  CA  THR   232       7.792  46.935  48.169  1.00  0.00              
ATOM    233  CA  MET   233       6.149  50.382  48.566  1.00  0.00              
ATOM    234  CA  LYS   234       3.520  49.296  46.023  1.00  0.00              
ATOM    235  CA  ASN   235       2.915  46.037  47.915  1.00  0.00              
ATOM    236  CA  THR   236       2.503  48.065  51.148  1.00  0.00              
ATOM    237  CA  GLY   237      -0.154  50.164  49.352  1.00  0.00              
ATOM    238  CA  ARG   238      -2.043  46.947  48.539  1.00  0.00              
ATOM    239  CA  ASN   239      -1.687  45.746  52.141  1.00  0.00              
ATOM    240  CA  VAL   240      -2.968  49.080  53.519  1.00  0.00              
ATOM    241  CA  ASN   241      -6.091  48.528  51.448  1.00  0.00              
ATOM    242  CA  ASP   242      -6.672  45.165  53.182  1.00  0.00              
ATOM    243  CA  ARG   243      -6.485  45.543  56.810  1.00  0.00              
ATOM    244  CA  PRO   244      -4.814  47.884  59.241  1.00  0.00              
ATOM    245  CA  VAL   245      -1.779  47.009  61.301  1.00  0.00              
ATOM    246  CA  MET   246      -0.985  48.966  64.419  1.00  0.00              
ATOM    247  CA  VAL   247       2.594  49.275  65.646  1.00  0.00              
ATOM    248  CA  ALA   248       3.301  51.228  68.853  1.00  0.00              
ATOM    249  CA  LYS   249       6.298  53.497  69.706  1.00  0.00              
ATOM    250  CA  GLU   250       7.712  50.940  72.085  1.00  0.00              
ATOM    251  CA  GLY   251       7.558  47.968  69.778  1.00  0.00              
ATOM    252  CA  GLU   252       4.193  46.526  70.734  1.00  0.00              
ATOM    253  CA  THR   253       2.471  44.870  67.968  1.00  0.00              
ATOM    254  CA  TYR   254      -1.274  45.023  67.660  1.00  0.00              
ATOM    255  CA  THR   255      -3.048  43.474  64.713  1.00  0.00              
ATOM    256  CA  GLY   256      -6.228  45.378  64.271  1.00  0.00              
ATOM    257  CA  THR   257      -7.411  44.542  60.821  1.00  0.00              
ATOM    258  CA  TYR   258      -9.182  47.642  59.479  1.00  0.00              
ATOM    259  CA  ARG   259     -11.915  46.741  56.951  1.00  0.00              
ATOM    260  CA  GLY   260     -12.495  50.180  55.319  1.00  0.00              
ATOM    261  CA  ALA   261     -11.329  52.563  58.016  1.00  0.00              
ATOM    262  CA  GLY   262      -8.338  54.408  56.675  1.00  0.00              
ATOM    263  CA  LEU   263      -7.401  57.350  58.631  1.00  0.00              
ATOM    264  CA  GLU   264      -6.697  56.094  62.112  1.00  0.00              
ATOM    265  CA  GLY   265      -5.001  52.924  60.997  1.00  0.00              
ATOM    266  CA  PHE   266      -1.225  52.774  61.417  1.00  0.00              
ATOM    267  CA  ALA   267       0.765  50.368  59.322  1.00  0.00              
ATOM    268  CA  LEU   268       4.316  49.441  60.413  1.00  0.00              
ATOM    269  CA  ASN   269       6.335  47.308  58.199  1.00  0.00              
ATOM    270  CA  VAL   270       9.777  46.182  59.196  1.00  0.00              
ATOM    271  CA  LYS   271      12.308  45.172  56.543  1.00  0.00              
ATOM    272  CA  GLY   272      13.585  48.183  54.535  1.00  0.00              
ATOM    273  CA  ALA   273      11.704  50.486  56.940  1.00  0.00              
ATOM    274  CA  TYR   274       8.173  51.418  56.039  1.00  0.00              
ATOM    275  CA  ILE   275       6.024  53.522  58.163  1.00  0.00              
ATOM    276  CA  ILE   276       2.570  54.217  57.084  1.00  0.00              
ATOM    277  CA  GLY   277       0.511  56.652  59.004  1.00  0.00              
ATOM    278  CA  ASN   278      -2.994  57.423  57.860  1.00  0.00              
ATOM    279  CA  ILE   279      -2.666  61.111  57.205  1.00  0.00              
ATOM    280  CA  ASP   280      -5.807  62.522  58.512  1.00  0.00              
ATOM    281  CA  HIS   281      -5.882  60.963  61.931  1.00  0.00              
ATOM    282  CA  LEU   282      -2.361  61.212  63.164  1.00  0.00              
ATOM    283  CA  PRO   283      -1.664  63.450  66.092  1.00  0.00              
ATOM    284  CA  PRO   284       1.613  65.332  66.109  1.00  0.00              
ATOM    285  CA  GLU   285       2.835  63.152  68.968  1.00  0.00              
ATOM    286  CA  GLN   286       2.150  59.972  66.978  1.00  0.00              
ATOM    287  CA  LEU   287       3.748  61.215  63.765  1.00  0.00              
ATOM    288  CA  LYS   288       6.818  62.248  65.764  1.00  0.00              
ATOM    289  CA  ILE   289       7.131  58.829  67.438  1.00  0.00              
ATOM    290  CA  LEU   290       6.910  56.841  64.186  1.00  0.00              
ATOM    291  CA  LYS   291       8.949  58.554  61.531  1.00  0.00              
ATOM    292  CA  PRO   292       9.447  57.987  57.839  1.00  0.00              
ATOM    293  CA  GLY   293      11.966  55.183  57.240  1.00  0.00              
ATOM    294  CA  ASP   294      11.394  53.606  60.665  1.00  0.00              
ATOM    295  CA  LYS   295      10.686  49.936  60.939  1.00  0.00              
ATOM    296  CA  ILE   296       7.994  48.710  63.355  1.00  0.00              
ATOM    297  CA  THR   297       7.083  44.874  63.190  1.00  0.00              
ATOM    298  CA  PHE   298       3.020  43.974  63.875  1.00  0.00              
ATOM    299  CA  THR   299       2.012  40.819  65.372  1.00  0.00              
TER                                                                             
END
