
#######################################################
#                                                     #
#                        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 T0316TS393_1-D2
# Molecule2: number of CA atoms   60 (  457),  selected   60 , name T0316_D2.pdb
# PARAMETERS: T0316TS393_1-D2.T0316_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    G     220      -       -           -
LGA    R     221      -       -           -
LGA    M     222      -       -           -
LGA    M     223      -       -           -
LGA    T     224      -       -           -
LGA    V     225      -       -           -
LGA    D     226      G     220          2.578
LGA    G     227      R     221          1.172
LGA    R     228      -       -           -
LGA    D     229      -       -           -
LGA    M     230      M     222          1.393
LGA    G     231      M     223           #
LGA    -       -      T     224           -
LGA    -       -      V     225           -
LGA    -       -      D     226           -
LGA    -       -      G     227           -
LGA    -       -      R     228           -
LGA    -       -      D     229           -
LGA    E     232      M     230          3.943
LGA    H     233      G     231           #
LGA    A     234      E     232          4.574
LGA    G     235      H     233           #
LGA    L     236      A     234           #
LGA    M     237      G     235          3.870
LGA    Y     238      L     236          3.524
LGA    Y     239      M     237          2.652
LGA    T     240      Y     238          3.733
LGA    I     241      Y     239          3.118
LGA    G     242      T     240          3.510
LGA    Q     243      I     241          3.485
LGA    R     244      G     242           #
LGA    G     245      Q     243          4.704
LGA    G     246      R     244          4.229
LGA    L     247      G     245          1.508
LGA    G     248      G     246          4.485
LGA    I     249      -       -           -
LGA    G     250      L     247          3.539
LGA    G     251      G     248          3.086
LGA    Q     252      I     249          3.747
LGA    H     253      G     250          4.176
LGA    G     254      G     251           #
LGA    G     255      D     256          3.299
LGA    D     256      N     257          1.322
LGA    N     257      A     258          3.099
LGA    A     258      P     259          2.830
LGA    P     259      W     260           #
LGA    W     260      F     261          3.904
LGA    F     261      V     262          4.896
LGA    V     262      V     263          2.761
LGA    V     263      G     264          3.517
LGA    G     264      -       -           -
LGA    K     265      K     265          3.200
LGA    D     266      D     266          2.988
LGA    L     267      L     267          4.393
LGA    S     268      S     268           #
LGA    K     269      K     269          3.363
LGA    N     270      N     270          2.397
LGA    I     271      I     271          4.290
LGA    L     272      L     272          2.156
LGA    Y     273      Y     273          4.810
LGA    V     274      V     274          3.760
LGA    G     275      -       -           -
LGA    Q     276      G     275          5.244
LGA    G     277      Q     276           -
LGA    F     278      G     277           -
LGA    Y     279      F     278           -
LGA    H     280      Y     279           -
LGA    D     281      H     280           -
LGA    S     282      D     281           -
LGA    L     283      S     282           -
LGA    -       -      L     283           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   64   60    5.0     38    3.55    34.21     34.440     1.042

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.245576 * X  +   0.763427 * Y  +  -0.597387 * Z  +  37.928608
  Y_new =   0.825705 * X  +   0.487586 * Y  +   0.283674 * Z  +  20.457245
  Z_new =   0.507842 * X  +  -0.423603 * Y  +  -0.750105 * Z  + -13.053392 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.627515    0.514078  [ DEG:  -150.5455     29.4545 ]
  Theta =  -0.532677   -2.608915  [ DEG:   -30.5202   -149.4798 ]
  Phi   =   1.859878   -1.281715  [ DEG:   106.5632    -73.4368 ]
 
# 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: T0316TS393_1-D2                               
REMARK     2: T0316_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0316TS393_1-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   38   3.55   34.21  34.440
REMARK  ---------------------------------------------------------- 
MOLECULE T0316TS393_1-D2
PFRMAT TS
TARGET T0316
MODEL 1
PARENT N/A
ATOM    220  CA  GLY   220      27.789  31.305 -15.572  1.00 25.00           C
ATOM    221  CA  ARG   221      30.952  29.345 -14.989  1.00 25.00           C
ATOM    222  CA  MET   222      33.044  27.849 -12.194  1.00 25.00           C
ATOM    223  CA  MET   223      34.597  25.473 -14.783  1.00 25.00           C
ATOM    224  CA  THR   224      37.754  23.607 -15.792  1.00 25.00           C
ATOM    225  CA  VAL   225      39.947  24.797 -18.695  1.00 25.00           C
ATOM    226  CA  ASP   226      42.744  22.459 -19.787  1.00 25.00           C
ATOM    227  CA  GLY   227      42.458  19.880 -22.586  1.00 25.00           C
ATOM    228  CA  ARG   228      41.206  16.632 -24.013  1.00 25.00           C
ATOM    229  CA  ASP   229      37.972  17.495 -22.252  1.00 25.00           C
ATOM    230  CA  MET   230      37.682  20.508 -24.607  1.00 25.00           C
ATOM    231  CA  GLY   231      37.385  22.950 -27.422  1.00 25.00           C
ATOM    232  CA  GLU   232      41.005  22.150 -28.240  1.00 25.00           C
ATOM    233  CA  HIS   233      44.275  20.408 -27.435  1.00 25.00           C
ATOM    234  CA  ALA   234      45.919  22.887 -25.047  1.00 25.00           C
ATOM    235  CA  GLY   235      46.890  25.455 -22.432  1.00 25.00           C
ATOM    236  CA  LEU   236      49.139  26.400 -19.520  1.00 25.00           C
ATOM    237  CA  MET   237      46.459  24.838 -17.363  1.00 25.00           C
ATOM    238  CA  TYR   238      43.363  23.874 -15.426  1.00 25.00           C
ATOM    239  CA  TYR   239      40.751  22.451 -13.105  1.00 25.00           C
ATOM    240  CA  THR   240      37.415  23.076 -11.353  1.00 25.00           C
ATOM    241  CA  ILE   241      33.756  22.168 -11.945  1.00 25.00           C
ATOM    242  CA  GLY   242      32.643  18.659 -10.928  1.00 25.00           C
ATOM    243  CA  GLN   243      33.611  17.556 -14.462  1.00 25.00           C
ATOM    244  CA  ARG   244      33.894  21.011 -16.058  1.00 25.00           C
ATOM    245  CA  GLY   245      30.917  21.963 -18.268  1.00 25.00           C
ATOM    246  CA  GLY   246      29.452  24.369 -20.881  1.00 25.00           C
ATOM    247  CA  LEU   247      31.237  27.354 -19.327  1.00 25.00           C
ATOM    248  CA  GLY   248      30.267  30.647 -20.950  1.00 25.00           C
ATOM    249  CA  ILE   249      31.920  33.668 -19.285  1.00 25.00           C
ATOM    250  CA  GLY   250      34.670  31.932 -21.209  1.00 25.00           C
ATOM    251  CA  GLY   251      34.227  29.019 -23.609  1.00 25.00           C
ATOM    252  CA  GLN   252      31.055  28.226 -25.564  1.00 25.00           C
ATOM    253  CA  HIS   253      29.219  29.443 -28.681  1.00 25.00           C
ATOM    254  CA  GLY   254      28.409  26.265 -30.558  1.00 25.00           C
ATOM    255  CA  GLY   255      25.094  24.688 -29.760  1.00 25.00           C
ATOM    256  CA  ASP   256      23.410  28.027 -29.299  1.00 25.00           C
ATOM    257  CA  ASN   257      25.051  28.419 -25.915  1.00 25.00           C
ATOM    258  CA  ALA   258      26.656  28.247 -22.494  1.00 25.00           C
ATOM    259  CA  PRO   259      26.232  27.592 -18.742  1.00 25.00           C
ATOM    260  CA  TRP   260      26.055  24.167 -17.189  1.00 25.00           C
ATOM    261  CA  PHE   261      26.629  20.521 -16.458  1.00 25.00           C
ATOM    262  CA  VAL   262      29.205  17.843 -15.841  1.00 25.00           C
ATOM    263  CA  VAL   263      30.729  14.515 -14.789  1.00 25.00           C
ATOM    264  CA  GLY   264      32.897  13.564 -11.808  1.00 25.00           C
ATOM    265  CA  LYS   265      36.094  13.701 -13.799  1.00 25.00           C
ATOM    266  CA  ASP   266      38.162  11.532 -16.047  1.00 25.00           C
ATOM    267  CA  LEU   267      40.067  14.425 -17.543  1.00 25.00           C
ATOM    268  CA  SER   268      42.544  15.218 -20.338  1.00 25.00           C
ATOM    269  CA  LYS   269      45.775  17.027 -19.742  1.00 25.00           C
ATOM    270  CA  ASN   270      45.422  16.114 -16.059  1.00 25.00           C
ATOM    271  CA  ILE   271      42.628  18.642 -16.184  1.00 25.00           C
ATOM    272  CA  LEU   272      39.813  19.455 -18.538  1.00 25.00           C
ATOM    273  CA  TYR   273      36.703  21.431 -19.427  1.00 25.00           C
ATOM    274  CA  VAL   274      33.740  22.795 -21.417  1.00 25.00           C
ATOM    275  CA  GLY   275      34.074  24.072 -25.030  1.00 25.00           C
ATOM    276  CA  GLN   276      30.846  22.881 -26.586  1.00 25.00           C
ATOM    277  CA  GLY   277      32.075  22.480 -30.133  1.00 25.00           C
ATOM    278  CA  PHE   278      34.558  19.789 -31.191  1.00 25.00           C
ATOM    279  CA  TYR   279      37.546  18.025 -32.710  1.00 25.00           C
ATOM    280  CA  HIS   280      39.662  17.652 -29.602  1.00 25.00           C
ATOM    281  CA  ASP   281      39.581  14.094 -28.177  1.00 25.00           C
ATOM    282  CA  SER   282      36.754  11.550 -27.722  1.00 25.00           C
ATOM    283  CA  LEU   283      35.590  13.372 -24.561  1.00 25.00           C
TER
END
