
#######################################################
#                                                     #
#                        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   77 (   77),  selected   77 , name T0320TS599_5-D2
# Molecule2: number of CA atoms   73 (  604),  selected   73 , name T0320_D2.pdb
# PARAMETERS: T0320TS599_5-D2.T0320_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      N     228           -
LGA    -       -      N     229           -
LGA    -       -      S     230           -
LGA    -       -      L     231           -
LGA    -       -      P     232           -
LGA    N     228      N     233          3.344
LGA    N     229      P     234          1.012
LGA    S     230      H     235          2.880
LGA    L     231      L     236          1.800
LGA    P     232      R     237          1.455
LGA    N     233      K     238          2.194
LGA    P     234      D     239          2.288
LGA    H     235      S     240           -
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      N     241          3.541
LGA    I     251      N     242          0.574
LGA    I     252      -       -           -
LGA    H     253      -       -           -
LGA    A     254      -       -           -
LGA    F     255      P     243          3.179
LGA    G     256      A     244          0.788
LGA    K     257      L     245          5.308
LGA    D     258      -       -           -
LGA    A     259      H     246          1.463
LGA    E     260      -       -           -
LGA    G     261      -       -           -
LGA    E     262      F     247          3.658
LGA    R     263      E     248          2.275
LGA    S     264      W     249          2.586
LGA    S     265      -       -           -
LGA    A     266      -       -           -
LGA    I     267      E     250          4.151
LGA    N     268      I     251          2.855
LGA    -       -      I     252           -
LGA    -       -      H     253           -
LGA    T     269      A     254          1.294
LGA    -       -      F     255           -
LGA    -       -      G     256           -
LGA    S     270      K     257          2.227
LGA    P     271      D     258          5.236
LGA    -       -      R     263           -
LGA    I     272      S     264          0.714
LGA    S     273      S     265          3.176
LGA    V     274      A     266          1.611
LGA    V     275      I     267          1.709
LGA    D     276      N     268          2.632
LGA    K     277      T     269          2.595
LGA    E     278      S     270          1.797
LGA    R     279      P     271           -
LGA    F     280      -       -           -
LGA    S     281      I     272           #
LGA    K     282      S     273           -
LGA    Y     283      V     274           -
LGA    H     284      V     275           -
LGA    D     285      D     276           -
LGA    N     286      K     277           -
LGA    Y     287      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     288      Y     287           #
LGA    P     289      Y     288          3.367
LGA    G     290      P     289          2.028
LGA    W     291      G     290           -
LGA    Y     292      W     291           -
LGA    L     293      Y     292           -
LGA    V     294      L     293           -
LGA    D     295      V     294           -
LGA    D     296      D     295           -
LGA    T     297      D     296           -
LGA    L     298      T     297           -
LGA    E     299      L     298           -
LGA    R     300      E     299           -
LGA    A     301      R     300           -
LGA    G     302      A     301           -
LGA    R     303      G     302           -
LGA    I     304      R     303           -
LGA    -       -      I     304           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   77   73    5.0     30    2.73    10.00     25.925     1.062

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.440408 * X  +  -0.856529 * Y  +   0.269070 * Z  +   4.575899
  Y_new =  -0.736271 * X  +  -0.516071 * Y  +  -0.437693 * Z  +  19.894308
  Z_new =   0.513756 * X  +  -0.005345 * Y  +  -0.857920 * Z  +   0.961603 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -3.135363    0.006230  [ DEG:  -179.6431      0.3569 ]
  Theta =  -0.539557   -2.602036  [ DEG:   -30.9143   -149.0857 ]
  Phi   =  -1.031731    2.109862  [ DEG:   -59.1138    120.8862 ]
 
# 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-D2                               
REMARK     2: T0320_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0320TS599_5-D2.T0320_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   77   73   5.0   30   2.73   10.00  25.925
REMARK  ---------------------------------------------------------- 
MOLECULE T0320TS599_5-D2
PFRMAT TS                                                                       
TARGET T0320                                                                    
MODEL  5                                                                        
PARENT N/A                                                                      
ATOM    228  CA  ASN   228      19.608  15.259   2.213  1.00  0.00              
ATOM    229  CA  ASN   229      18.609  11.687   3.256  1.00  0.00              
ATOM    230  CA  SER   230      15.016  12.568   4.127  1.00  0.00              
ATOM    231  CA  LEU   231      13.967  14.000   0.853  1.00  0.00              
ATOM    232  CA  PRO   232      14.878  11.529  -1.914  1.00  0.00              
ATOM    233  CA  ASN   233      11.549  10.850  -3.893  1.00  0.00              
ATOM    234  CA  PRO   234      12.181  12.652  -7.295  1.00  0.00              
ATOM    235  CA  HIS   235       8.446  13.290  -8.210  1.00  0.00              
ATOM    236  CA  LEU   236       7.808  15.986 -10.368  1.00  0.00              
ATOM    237  CA  ARG   237       4.682  15.574 -13.120  1.00  0.00              
ATOM    238  CA  LYS   238       4.487  17.253 -15.786  1.00  0.00              
ATOM    239  CA  ASP   239       1.314  17.335 -17.988  1.00  0.00              
ATOM    240  CA  SER   240       0.540  20.540 -19.749  1.00  0.00              
ATOM    241  CA  ASN   241       3.093  22.009 -22.146  1.00  0.00              
ATOM    242  CA  ASN   242       4.147  25.103 -20.130  1.00  0.00              
ATOM    243  CA  PRO   243       3.771  23.589 -16.795  1.00  0.00              
ATOM    244  CA  ALA   244       7.346  23.270 -15.627  1.00  0.00              
ATOM    245  CA  LEU   245       8.123  23.583 -12.047  1.00  0.00              
ATOM    246  CA  HIS   246      10.288  20.897 -10.464  1.00  0.00              
ATOM    247  CA  PHE   247       9.246  19.944  -6.924  1.00  0.00              
ATOM    248  CA  GLU   248      10.866  16.959  -5.592  1.00  0.00              
ATOM    249  CA  TRP   249       8.973  14.847  -2.777  1.00  0.00              
ATOM    250  CA  GLU   250      10.040  11.515  -1.792  1.00  0.00              
ATOM    251  CA  ILE   251       7.204   9.286  -0.262  1.00  0.00              
ATOM    252  CA  ILE   252       8.971   6.595   1.782  1.00  0.00              
ATOM    253  CA  HIS   253       6.052   4.810   3.409  1.00  0.00              
ATOM    254  CA  ALA   254       6.712   5.999   6.972  1.00  0.00              
ATOM    255  CA  PHE   255       7.097   9.715   6.246  1.00  0.00              
ATOM    256  CA  GLY   256       3.982  10.416   4.212  1.00  0.00              
ATOM    257  CA  LYS   257       1.810   8.372   6.439  1.00  0.00              
ATOM    258  CA  ASP   258       2.651   9.644   9.900  1.00  0.00              
ATOM    259  CA  ALA   259       2.901  13.364   9.363  1.00  0.00              
ATOM    260  CA  GLU   260      -0.191  13.912   7.181  1.00  0.00              
ATOM    261  CA  GLY   261      -2.587  12.039   9.483  1.00  0.00              
ATOM    262  CA  GLU   262      -1.361  14.001  12.480  1.00  0.00              
ATOM    263  CA  ARG   263      -1.801  17.405  10.839  1.00  0.00              
ATOM    264  CA  SER   264      -5.345  16.742   9.599  1.00  0.00              
ATOM    265  CA  SER   265      -6.307  15.611  13.138  1.00  0.00              
ATOM    266  CA  ALA   266      -4.757  18.473  15.078  1.00  0.00              
ATOM    267  CA  ILE   267      -5.838  21.451  12.987  1.00  0.00              
ATOM    268  CA  ASN   268      -2.580  23.260  12.386  1.00  0.00              
ATOM    269  CA  THR   269      -3.312  26.739  13.645  1.00  0.00              
ATOM    270  CA  SER   270      -3.678  28.866  10.580  1.00  0.00              
ATOM    271  CA  PRO   271      -6.232  26.541   8.868  1.00  0.00              
ATOM    272  CA  ILE   272      -3.968  26.599   5.818  1.00  0.00              
ATOM    273  CA  SER   273      -0.542  26.132   7.248  1.00  0.00              
ATOM    274  CA  VAL   274       2.215  28.077   5.721  1.00  0.00              
ATOM    275  CA  VAL   275       5.538  27.345   7.254  1.00  0.00              
ATOM    276  CA  ASP   276       7.940  30.297   7.550  1.00  0.00              
ATOM    277  CA  LYS   277      11.185  29.672   5.856  1.00  0.00              
ATOM    278  CA  GLU   278      13.332  30.806   8.748  1.00  0.00              
ATOM    279  CA  ARG   279      11.871  28.272  11.214  1.00  0.00              
ATOM    280  CA  PHE   280      12.304  25.268   8.920  1.00  0.00              
ATOM    281  CA  SER   281      15.888  25.966   8.056  1.00  0.00              
ATOM    282  CA  LYS   282      17.046  26.115  11.490  1.00  0.00              
ATOM    283  CA  TYR   283      15.656  22.946  13.137  1.00  0.00              
ATOM    284  CA  HIS   284      16.510  20.447  10.600  1.00  0.00              
ATOM    285  CA  ASP   285      17.714  17.550  12.456  1.00  0.00              
ATOM    286  CA  ASN   286      15.165  14.869  11.625  1.00  0.00              
ATOM    287  CA  TYR   287      14.068  15.763   8.028  1.00  0.00              
ATOM    288  CA  TYR   288      10.953  15.342   7.732  1.00  0.00              
ATOM    289  CA  PRO   289       9.249  16.636   4.323  1.00  0.00              
ATOM    290  CA  GLY   290       8.705  20.094   3.903  1.00  0.00              
ATOM    291  CA  TRP   291       4.728  20.462   3.167  1.00  0.00              
ATOM    292  CA  TYR   292       3.677  23.383   3.329  1.00  0.00              
ATOM    293  CA  LEU   293      -0.393  23.556   3.014  1.00  0.00              
ATOM    294  CA  VAL   294      -1.866  26.414   1.443  1.00  0.00              
ATOM    295  CA  ASP   295      -5.778  27.072   1.512  1.00  0.00              
ATOM    296  CA  ASP   296      -6.346  26.051  -1.875  1.00  0.00              
ATOM    297  CA  THR   297      -4.917  22.730  -1.364  1.00  0.00              
ATOM    298  CA  LEU   298      -6.990  22.166   1.770  1.00  0.00              
ATOM    299  CA  GLU   299     -10.125  23.100  -0.039  1.00  0.00              
ATOM    300  CA  ARG   300      -9.482  20.652  -2.902  1.00  0.00              
ATOM    301  CA  ALA   301      -8.771  17.949  -0.367  1.00  0.00              
ATOM    302  CA  GLY   302     -12.011  18.672   1.511  1.00  0.00              
ATOM    303  CA  ARG   303     -10.636  19.498   4.902  1.00  0.00              
ATOM    304  CA  ILE   304     -12.334  17.015   7.035  1.00  0.00              
TER                                                                             
END
