
#######################################################
#                                                     #
#                        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   64 (   64),  selected   64 , name T0316TS168_3-D2
# Molecule2: number of CA atoms   60 (  457),  selected   60 , name T0316_D2.pdb
# PARAMETERS: T0316TS168_3-D2.T0316_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    G     220      G     220           -
LGA    R     221      R     221           -
LGA    M     222      -       -           -
LGA    M     223      -       -           -
LGA    T     224      M     222           #
LGA    -       -      M     223           -
LGA    V     225      T     224          3.339
LGA    -       -      V     225           -
LGA    -       -      D     226           -
LGA    -       -      G     227           -
LGA    -       -      R     228           -
LGA    D     226      D     229          2.181
LGA    G     227      M     230          3.957
LGA    R     228      G     231          3.591
LGA    D     229      E     232          1.420
LGA    M     230      H     233          1.946
LGA    G     231      A     234          4.422
LGA    -       -      G     235           -
LGA    -       -      L     236           -
LGA    -       -      M     237           -
LGA    -       -      Y     238           -
LGA    -       -      Y     239           -
LGA    -       -      T     240           -
LGA    -       -      I     241           -
LGA    -       -      G     242           -
LGA    -       -      Q     243           -
LGA    -       -      R     244           -
LGA    -       -      G     245           -
LGA    E     232      G     246          1.574
LGA    H     233      L     247          3.978
LGA    A     234      G     248          4.488
LGA    -       -      I     249           -
LGA    G     235      G     250          4.671
LGA    -       -      G     251           -
LGA    -       -      D     256           -
LGA    L     236      N     257           #
LGA    M     237      A     258          4.639
LGA    Y     238      P     259          2.541
LGA    Y     239      W     260          1.523
LGA    T     240      F     261          2.831
LGA    I     241      V     262          2.907
LGA    G     242      V     263          4.911
LGA    Q     243      G     264          4.671
LGA    R     244      K     265          2.984
LGA    G     245      D     266          1.402
LGA    G     246      L     267          4.363
LGA    L     247      -       -           -
LGA    G     248      -       -           -
LGA    I     249      -       -           -
LGA    G     250      -       -           -
LGA    G     251      -       -           -
LGA    Q     252      -       -           -
LGA    H     253      -       -           -
LGA    G     254      -       -           -
LGA    G     255      -       -           -
LGA    D     256      S     268          2.243
LGA    N     257      K     269          1.835
LGA    A     258      N     270           #
LGA    P     259      I     271          4.780
LGA    W     260      L     272          3.634
LGA    F     261      Y     273          2.423
LGA    V     262      V     274          2.021
LGA    V     263      G     275          2.855
LGA    -       -      Q     276           -
LGA    -       -      G     277           -
LGA    -       -      F     278           -
LGA    -       -      Y     279           -
LGA    G     264      H     280          3.102
LGA    -       -      D     281           -
LGA    K     265      S     282          2.390
LGA    D     266      L     283          1.033
LGA    L     267      -       -           -
LGA    S     268      -       -           -
LGA    K     269      -       -           -
LGA    N     270      -       -           -
LGA    I     271      -       -           -
LGA    L     272      -       -           -
LGA    Y     273      -       -           -
LGA    V     274      -       -           -
LGA    G     275      -       -           -
LGA    Q     276      -       -           -
LGA    G     277      -       -           -
LGA    F     278      -       -           -
LGA    Y     279      -       -           -
LGA    H     280      -       -           -
LGA    D     281      -       -           -
LGA    S     282      -       -           -
LGA    L     283      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   64   60    5.0     31    3.27     9.68     29.132     0.920

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.031045 * X  +  -0.969256 * Y  +  -0.244089 * Z  +  27.283951
  Y_new =  -0.994360 * X  +  -0.054728 * Y  +   0.090850 * Z  +  24.069193
  Z_new =  -0.101415 * X  +   0.239892 * Y  +  -0.965488 * Z  + -17.136011 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.898057   -0.243536  [ DEG:   166.0464    -13.9536 ]
  Theta =   0.101590    3.040003  [ DEG:     5.8207    174.1793 ]
  Phi   =  -1.539586    1.602007  [ DEG:   -88.2118     91.7882 ]
 
# 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: T0316TS168_3-D2                               
REMARK     2: T0316_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0316TS168_3-D2.T0316_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   64   60   5.0   31   3.27    9.68  29.132
REMARK  ---------------------------------------------------------- 
MOLECULE T0316TS168_3-D2
PFRMAT TS
TARGET T0316
MODEL 3
PARENT N/A
ATOM    220  CA  GLY   220      28.446  24.637 -33.265  1.00 25.00           C
ATOM    221  CA  ARG   221      26.570  27.607 -31.704  1.00 25.00           C
ATOM    222  CA  MET   222      26.357  25.451 -28.568  1.00 25.00           C
ATOM    223  CA  MET   223      29.281  23.421 -27.222  1.00 25.00           C
ATOM    224  CA  THR   224      30.510  19.965 -26.276  1.00 25.00           C
ATOM    225  CA  VAL   225      33.427  19.033 -28.542  1.00 25.00           C
ATOM    226  CA  ASP   226      36.899  18.719 -29.953  1.00 25.00           C
ATOM    227  CA  GLY   227      37.990  18.849 -26.370  1.00 25.00           C
ATOM    228  CA  ARG   228      40.730  21.370 -25.628  1.00 25.00           C
ATOM    229  CA  ASP   229      41.602  24.235 -23.213  1.00 25.00           C
ATOM    230  CA  MET   230      39.133  24.065 -20.347  1.00 25.00           C
ATOM    231  CA  GLY   231      37.968  26.753 -17.905  1.00 25.00           C
ATOM    232  CA  GLU   232      34.636  28.529 -18.344  1.00 25.00           C
ATOM    233  CA  HIS   233      33.107  31.584 -20.019  1.00 25.00           C
ATOM    234  CA  ALA   234      34.235  33.055 -23.278  1.00 25.00           C
ATOM    235  CA  GLY   235      31.184  34.118 -25.295  1.00 25.00           C
ATOM    236  CA  LEU   236      27.542  32.894 -25.058  1.00 25.00           C
ATOM    237  CA  MET   237      26.093  29.442 -25.401  1.00 25.00           C
ATOM    238  CA  TYR   238      27.653  26.337 -23.901  1.00 25.00           C
ATOM    239  CA  TYR   239      27.584  22.616 -23.132  1.00 25.00           C
ATOM    240  CA  THR   240      29.524  20.151 -21.023  1.00 25.00           C
ATOM    241  CA  ILE   241      31.858  18.049 -19.004  1.00 25.00           C
ATOM    242  CA  GLY   242      35.123  16.520 -17.887  1.00 25.00           C
ATOM    243  CA  GLN   243      36.222  18.358 -14.743  1.00 25.00           C
ATOM    244  CA  ARG   244      37.116  14.982 -13.179  1.00 25.00           C
ATOM    245  CA  GLY   245      38.932  13.203 -16.063  1.00 25.00           C
ATOM    246  CA  GLY   246      39.990  16.754 -16.915  1.00 25.00           C
ATOM    247  CA  LEU   247      39.111  20.348 -17.808  1.00 25.00           C
ATOM    248  CA  GLY   248      40.430  22.982 -15.411  1.00 25.00           C
ATOM    249  CA  ILE   249      37.185  23.377 -13.426  1.00 25.00           C
ATOM    250  CA  GLY   250      36.147  21.916 -10.105  1.00 25.00           C
ATOM    251  CA  GLY   251      37.762  18.524  -9.582  1.00 25.00           C
ATOM    252  CA  GLN   252      40.476  19.068 -12.198  1.00 25.00           C
ATOM    253  CA  HIS   253      43.901  19.106 -13.935  1.00 25.00           C
ATOM    254  CA  GLY   254      45.437  17.019 -11.202  1.00 25.00           C
ATOM    255  CA  GLY   255      43.481  13.774 -11.468  1.00 25.00           C
ATOM    256  CA  ASP   256      44.226  14.238 -15.208  1.00 25.00           C
ATOM    257  CA  ASN   257      43.520  13.190 -18.795  1.00 25.00           C
ATOM    258  CA  ALA   258      40.438  12.615 -20.992  1.00 25.00           C
ATOM    259  CA  PRO   259      37.837  14.906 -22.559  1.00 25.00           C
ATOM    260  CA  TRP   260      40.264  17.788 -21.946  1.00 25.00           C
ATOM    261  CA  PHE   261      36.688  18.857 -21.473  1.00 25.00           C
ATOM    262  CA  VAL   262      33.320  17.993 -22.963  1.00 25.00           C
ATOM    263  CA  VAL   263      29.813  16.457 -22.779  1.00 25.00           C
ATOM    264  CA  GLY   264      26.303  17.067 -21.640  1.00 25.00           C
ATOM    265  CA  LYS   265      26.396  14.323 -19.019  1.00 25.00           C
ATOM    266  CA  ASP   266      26.057  13.976 -15.259  1.00 25.00           C
ATOM    267  CA  LEU   267      27.595  14.311 -11.783  1.00 25.00           C
ATOM    268  CA  SER   268      24.737  12.016 -10.815  1.00 25.00           C
ATOM    269  CA  LYS   269      22.107  14.066 -12.638  1.00 25.00           C
ATOM    270  CA  ASN   270      20.653  17.482 -11.936  1.00 25.00           C
ATOM    271  CA  ILE   271      24.343  18.255 -11.694  1.00 25.00           C
ATOM    272  CA  LEU   272      24.597  19.854 -15.102  1.00 25.00           C
ATOM    273  CA  TYR   273      26.004  20.609 -18.573  1.00 25.00           C
ATOM    274  CA  VAL   274      24.072  20.733 -21.860  1.00 25.00           C
ATOM    275  CA  GLY   275      23.868  22.075 -25.429  1.00 25.00           C
ATOM    276  CA  GLN   276      20.433  22.177 -23.748  1.00 25.00           C
ATOM    277  CA  GLY   277      17.228  20.669 -25.169  1.00 25.00           C
ATOM    278  CA  PHE   278      16.001  17.237 -23.998  1.00 25.00           C
ATOM    279  CA  TYR   279      14.622  16.172 -27.423  1.00 25.00           C
ATOM    280  CA  HIS   280      16.821  13.086 -27.040  1.00 25.00           C
ATOM    281  CA  ASP   281      18.474  14.427 -30.184  1.00 25.00           C
ATOM    282  CA  SER   282      20.861  15.604 -27.431  1.00 25.00           C
ATOM    283  CA  LEU   283      23.645  16.086 -30.017  1.00 25.00           C
TER
END
