
#######################################################
#                                                     #
#                        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   81 (   81),  selected   81 , name T0386TS393_5-D2
# Molecule2: number of CA atoms   81 (  636),  selected   81 , name T0386_D2.pdb
# PARAMETERS: T0386TS393_5-D2.T0386_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    N     219      -       -           -
LGA    P     220      -       -           -
LGA    E     221      -       -           -
LGA    K     222      -       -           -
LGA    I     223      N     219          0.901
LGA    R     224      P     220          0.865
LGA    L     225      E     221          1.583
LGA    L     226      K     222          1.067
LGA    K     227      I     223          1.469
LGA    E     228      R     224          1.664
LGA    F     229      L     225          1.582
LGA    M     230      L     226          1.947
LGA    H     231      K     227          1.845
LGA    T     232      E     228          1.959
LGA    M     233      F     229          2.315
LGA    K     234      M     230          2.095
LGA    N     235      H     231          1.900
LGA    T     236      -       -           -
LGA    G     237      -       -           -
LGA    R     238      -       -           -
LGA    N     239      T     232           #
LGA    V     240      M     233          4.092
LGA    -       -      K     234           -
LGA    -       -      N     235           -
LGA    N     241      T     236          4.292
LGA    D     242      G     237           #
LGA    R     243      R     238          4.912
LGA    P     244      N     239           -
LGA    V     245      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    M     246      G     256           #
LGA    V     247      T     257          0.652
LGA    A     248      Y     258          5.331
LGA    K     249      R     259           -
LGA    E     250      G     260           -
LGA    G     251      -       -           -
LGA    E     252      -       -           -
LGA    T     253      -       -           -
LGA    Y     254      -       -           -
LGA    T     255      -       -           -
LGA    G     256      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    T     257      N     278          6.449
LGA    Y     258      I     279          1.373
LGA    R     259      D     280          3.760
LGA    G     260      -       -           -
LGA    A     261      -       -           -
LGA    G     262      -       -           -
LGA    L     263      -       -           -
LGA    E     264      -       -           -
LGA    G     265      -       -           -
LGA    F     266      H     281           #
LGA    A     267      L     282          4.056
LGA    L     268      P     283          2.066
LGA    N     269      P     284          4.599
LGA    V     270      E     285          1.669
LGA    K     271      Q     286           #
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      L     287           #
LGA    -       -      K     288           -
LGA    -       -      I     289           -
LGA    -       -      L     290           -
LGA    H     281      K     291          2.307
LGA    L     282      P     292          2.046
LGA    P     283      G     293           #
LGA    P     284      D     294           -
LGA    E     285      K     295           -
LGA    Q     286      I     296           -
LGA    L     287      T     297           -
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      F     298           #
LGA    T     299      T     299           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   81   81    5.0     27    2.96     3.70     24.021     0.882

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.835272 * X  +  -0.524400 * Y  +  -0.165306 * Z  +  19.583845
  Y_new =   0.226755 * X  +   0.054645 * Y  +   0.972418 * Z  +  46.714165
  Z_new =  -0.500903 * X  +  -0.849717 * Y  +   0.164554 * Z  +  78.054169 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.379506    1.762086  [ DEG:   -79.0399    100.9601 ]
  Theta =   0.524641    2.616951  [ DEG:    30.0597    149.9403 ]
  Phi   =   0.265086   -2.876507  [ DEG:    15.1883   -164.8117 ]
 
# 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: T0386TS393_5-D2                               
REMARK     2: T0386_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0386TS393_5-D2.T0386_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   81   81   5.0   27   2.96    3.70  24.021
REMARK  ---------------------------------------------------------- 
MOLECULE T0386TS393_5-D2
PFRMAT TS
TARGET T0386
MODEL 5
PARENT N/A
ATOM    219  CA  ASN   219      -5.639  52.842  77.335  1.00 25.00           C
ATOM    220  CA  PRO   220      -2.668  54.158  75.286  1.00 25.00           C
ATOM    221  CA  GLU   221      -2.128  56.290  78.420  1.00 25.00           C
ATOM    222  CA  LYS   222       1.455  54.973  78.728  1.00 25.00           C
ATOM    223  CA  ILE   223       2.104  55.804  75.047  1.00 25.00           C
ATOM    224  CA  ARG   224       0.729  59.339  75.578  1.00 25.00           C
ATOM    225  CA  LEU   225       2.991  59.787  78.635  1.00 25.00           C
ATOM    226  CA  LEU   226       6.013  58.604  76.602  1.00 25.00           C
ATOM    227  CA  LYS   227       5.134  61.074  73.811  1.00 25.00           C
ATOM    228  CA  GLU   228       4.850  63.907  76.372  1.00 25.00           C
ATOM    229  CA  PHE   229       8.261  62.960  77.835  1.00 25.00           C
ATOM    230  CA  MET   230       9.794  62.963  74.325  1.00 25.00           C
ATOM    231  CA  HIS   231       8.283  66.415  73.642  1.00 25.00           C
ATOM    232  CA  THR   232       9.708  67.720  76.949  1.00 25.00           C
ATOM    233  CA  MET   233      13.156  66.320  76.043  1.00 25.00           C
ATOM    234  CA  LYS   234      12.967  68.008  72.611  1.00 25.00           C
ATOM    235  CA  ASN   235      12.017  71.328  74.268  1.00 25.00           C
ATOM    236  CA  THR   236       9.940  73.595  76.582  1.00 25.00           C
ATOM    237  CA  GLY   237       8.016  75.290  79.389  1.00 25.00           C
ATOM    238  CA  ARG   238      11.479  75.665  80.908  1.00 25.00           C
ATOM    239  CA  ASN   239      13.304  78.074  78.646  1.00 25.00           C
ATOM    240  CA  VAL   240      15.263  75.011  77.559  1.00 25.00           C
ATOM    241  CA  ASN   241      18.744  75.851  78.838  1.00 25.00           C
ATOM    242  CA  ASP   242      22.454  75.080  78.719  1.00 25.00           C
ATOM    243  CA  ARG   243      21.820  72.135  76.413  1.00 25.00           C
ATOM    244  CA  PRO   244      23.705  69.457  78.432  1.00 25.00           C
ATOM    245  CA  VAL   245      23.450  65.731  79.152  1.00 25.00           C
ATOM    246  CA  MET   246      24.505  63.518  82.075  1.00 25.00           C
ATOM    247  CA  VAL   247      25.880  61.977  85.245  1.00 25.00           C
ATOM    248  CA  ALA   248      27.590  62.462  88.639  1.00 25.00           C
ATOM    249  CA  LYS   249      29.499  65.307  90.292  1.00 25.00           C
ATOM    250  CA  GLU   250      28.778  68.465  92.268  1.00 25.00           C
ATOM    251  CA  GLY   251      26.238  68.825  94.990  1.00 25.00           C
ATOM    252  CA  GLU   252      25.489  65.574  96.788  1.00 25.00           C
ATOM    253  CA  THR   253      23.694  62.523  95.500  1.00 25.00           C
ATOM    254  CA  TYR   254      24.098  59.627  92.970  1.00 25.00           C
ATOM    255  CA  THR   255      20.352  59.688  92.533  1.00 25.00           C
ATOM    256  CA  GLY   256      17.074  59.996  90.740  1.00 25.00           C
ATOM    257  CA  THR   257      13.244  59.629  90.669  1.00 25.00           C
ATOM    258  CA  TYR   258       9.723  60.475  89.459  1.00 25.00           C
ATOM    259  CA  ARG   259       6.871  62.088  91.473  1.00 25.00           C
ATOM    260  CA  GLY   260       7.153  64.129  94.620  1.00 25.00           C
ATOM    261  CA  ALA   261       4.562  62.508  96.807  1.00 25.00           C
ATOM    262  CA  GLY   262       1.647  61.491  94.517  1.00 25.00           C
ATOM    263  CA  LEU   263       2.325  58.767  91.937  1.00 25.00           C
ATOM    264  CA  GLU   264       1.075  56.228  94.479  1.00 25.00           C
ATOM    265  CA  GLY   265       3.240  53.771  92.575  1.00 25.00           C
ATOM    266  CA  PHE   266       6.433  55.196  94.085  1.00 25.00           C
ATOM    267  CA  ALA   267       9.688  57.022  93.615  1.00 25.00           C
ATOM    268  CA  LEU   268      12.080  57.211  96.494  1.00 25.00           C
ATOM    269  CA  ASN   269      15.832  57.336  95.919  1.00 25.00           C
ATOM    270  CA  VAL   270      16.575  59.094  99.259  1.00 25.00           C
ATOM    271  CA  LYS   271      17.178  57.866 102.790  1.00 25.00           C
ATOM    272  CA  GLY   272      15.875  54.382 101.945  1.00 25.00           C
ATOM    273  CA  ALA   273      18.505  52.939  99.610  1.00 25.00           C
ATOM    274  CA  TYR   274      17.280  52.538  96.030  1.00 25.00           C
ATOM    275  CA  ILE   275      18.039  53.861  92.604  1.00 25.00           C
ATOM    276  CA  ILE   276      19.655  54.516  89.218  1.00 25.00           C
ATOM    277  CA  GLY   277      22.961  54.923  87.288  1.00 25.00           C
ATOM    278  CA  ASN   278      23.269  58.575  88.131  1.00 25.00           C
ATOM    279  CA  ILE   279      21.611  61.974  87.983  1.00 25.00           C
ATOM    280  CA  ASP   280      21.637  64.726  90.604  1.00 25.00           C
ATOM    281  CA  HIS   281      24.008  67.670  90.543  1.00 25.00           C
ATOM    282  CA  LEU   282      22.971  67.885  86.963  1.00 25.00           C
ATOM    283  CA  PRO   283      22.387  68.095  83.240  1.00 25.00           C
ATOM    284  CA  PRO   284      18.906  67.219  81.979  1.00 25.00           C
ATOM    285  CA  GLU   285      17.663  70.171  79.878  1.00 25.00           C
ATOM    286  CA  GLN   286      15.248  71.176  82.675  1.00 25.00           C
ATOM    287  CA  LEU   287      18.096  71.002  85.230  1.00 25.00           C
ATOM    288  CA  LYS   288      20.288  73.184  82.972  1.00 25.00           C
ATOM    289  CA  ILE   289      20.572  75.513  85.994  1.00 25.00           C
ATOM    290  CA  LEU   290      22.113  73.061  88.524  1.00 25.00           C
ATOM    291  CA  LYS   291      18.797  73.280  90.371  1.00 25.00           C
ATOM    292  CA  PRO   292      15.560  73.063  92.362  1.00 25.00           C
ATOM    293  CA  GLY   293      16.749  69.463  92.589  1.00 25.00           C
ATOM    294  CA  ASP   294      15.227  68.605  89.187  1.00 25.00           C
ATOM    295  CA  LYS   295      16.014  66.089  86.487  1.00 25.00           C
ATOM    296  CA  ILE   296      14.865  63.448  84.017  1.00 25.00           C
ATOM    297  CA  THR   297      15.344  62.626  80.330  1.00 25.00           C
ATOM    298  CA  PHE   298      17.179  59.486  79.095  1.00 25.00           C
ATOM    299  CA  THR   299      17.160  58.284  75.457  1.00 25.00           C
TER
END
