
#######################################################
#                                                     #
#                        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 T0320TS393_2-D2
# Molecule2: number of CA atoms   73 (  604),  selected   73 , name T0320_D2.pdb
# PARAMETERS: T0320TS393_2-D2.T0320_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    N     228      N     228           -
LGA    N     229      N     229           -
LGA    S     230      S     230           -
LGA    L     231      L     231           -
LGA    P     232      P     232           -
LGA    N     233      N     233           -
LGA    P     234      P     234           -
LGA    H     235      H     235           -
LGA    L     236      L     236           -
LGA    R     237      R     237           -
LGA    K     238      K     238           -
LGA    D     239      D     239           -
LGA    S     240      S     240           -
LGA    N     241      N     241           -
LGA    N     242      N     242           -
LGA    P     243      P     243           -
LGA    A     244      A     244           -
LGA    L     245      L     245           -
LGA    H     246      H     246           -
LGA    F     247      F     247           -
LGA    E     248      E     248           -
LGA    -       -      W     249           -
LGA    -       -      E     250           -
LGA    -       -      I     251           -
LGA    -       -      I     252           -
LGA    -       -      H     253           -
LGA    -       -      A     254           -
LGA    -       -      F     255           -
LGA    -       -      G     256           -
LGA    -       -      K     257           -
LGA    -       -      D     258           -
LGA    W     249      R     263           #
LGA    E     250      -       -           -
LGA    I     251      -       -           -
LGA    I     252      S     264          4.329
LGA    H     253      S     265          2.599
LGA    A     254      A     266          2.020
LGA    F     255      I     267          5.026
LGA    G     256      -       -           -
LGA    K     257      N     268          4.057
LGA    D     258      T     269          2.700
LGA    A     259      -       -           -
LGA    E     260      S     270          4.668
LGA    G     261      P     271          3.251
LGA    E     262      I     272          4.220
LGA    R     263      S     273          2.816
LGA    S     264      V     274          2.618
LGA    -       -      V     275           -
LGA    S     265      D     276          1.406
LGA    A     266      K     277          2.856
LGA    -       -      E     278           -
LGA    -       -      R     279           -
LGA    -       -      F     280           -
LGA    I     267      S     281          1.207
LGA    -       -      K     282           -
LGA    N     268      Y     283          3.898
LGA    T     269      H     284          1.651
LGA    -       -      D     285           -
LGA    S     270      N     286          0.826
LGA    P     271      Y     287          0.769
LGA    I     272      Y     288          2.274
LGA    -       -      P     289           -
LGA    S     273      G     290          5.073
LGA    V     274      W     291          3.343
LGA    V     275      Y     292          4.075
LGA    D     276      L     293          2.115
LGA    K     277      V     294           #
LGA    -       -      D     295           -
LGA    -       -      D     296           -
LGA    -       -      T     297           -
LGA    -       -      L     298           -
LGA    E     278      E     299          0.765
LGA    R     279      R     300           #
LGA    F     280      A     301           -
LGA    S     281      G     302           -
LGA    K     282      R     303           -
LGA    Y     283      I     304           -
LGA    H     284      -       -           -
LGA    D     285      -       -           -
LGA    N     286      -       -           -
LGA    Y     287      -       -           -
LGA    Y     288      -       -           -
LGA    P     289      -       -           -
LGA    G     290      -       -           -
LGA    W     291      -       -           -
LGA    Y     292      -       -           -
LGA    L     293      -       -           -
LGA    V     294      -       -           -
LGA    D     295      -       -           -
LGA    D     296      -       -           -
LGA    T     297      -       -           -
LGA    L     298      -       -           -
LGA    E     299      -       -           -
LGA    R     300      -       -           -
LGA    A     301      -       -           -
LGA    G     302      -       -           -
LGA    R     303      -       -           -
LGA    I     304      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   77   73    5.0     24    3.15     8.33     19.836     0.739

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.484796 * X  +   0.738602 * Y  +  -0.468443 * Z  +  -5.965724
  Y_new =   0.445393 * X  +  -0.252463 * Y  +  -0.859004 * Z  +  15.900211
  Z_new =  -0.752727 * X  +  -0.625083 * Y  +  -0.206576 * Z  +   1.930572 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.889974    1.251619  [ DEG:  -108.2875     71.7125 ]
  Theta =   0.852194    2.289398  [ DEG:    48.8271    131.1729 ]
  Phi   =   2.398529   -0.743064  [ DEG:   137.4256    -42.5744 ]
 
# 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: T0320TS393_2-D2                               
REMARK     2: T0320_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0320TS393_2-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   24   3.15    8.33  19.836
REMARK  ---------------------------------------------------------- 
MOLECULE T0320TS393_2-D2
PFRMAT TS
TARGET T0320
MODEL 2
PARENT N/A
ATOM    228  CA  ASN   228      -6.305  44.446   7.249  1.00 25.00           C
ATOM    229  CA  ASN   229      -3.580  44.041   4.613  1.00 25.00           C
ATOM    230  CA  SER   230      -0.058  43.913   3.188  1.00 25.00           C
ATOM    231  CA  LEU   231      -0.019  43.311  -0.569  1.00 25.00           C
ATOM    232  CA  PRO   232       1.954  43.265  -3.757  1.00 25.00           C
ATOM    233  CA  ASN   233      -0.942  41.127  -5.004  1.00 25.00           C
ATOM    234  CA  PRO   234      -2.796  41.978  -8.268  1.00 25.00           C
ATOM    235  CA  HIS   235      -5.674  39.652  -7.602  1.00 25.00           C
ATOM    236  CA  LEU   236      -3.693  36.577  -8.575  1.00 25.00           C
ATOM    237  CA  ARG   237      -4.903  36.703 -12.175  1.00 25.00           C
ATOM    238  CA  LYS   238      -6.517  38.421 -15.130  1.00 25.00           C
ATOM    239  CA  ASP   239      -8.231  37.266 -18.240  1.00 25.00           C
ATOM    240  CA  SER   240      -6.472  35.012 -20.703  1.00 25.00           C
ATOM    241  CA  ASN   241      -3.981  34.286 -17.921  1.00 25.00           C
ATOM    242  CA  ASN   242      -0.261  33.418 -18.133  1.00 25.00           C
ATOM    243  CA  PRO   243       0.367  29.680 -17.490  1.00 25.00           C
ATOM    244  CA  ALA   244       1.966  26.304 -16.777  1.00 25.00           C
ATOM    245  CA  LEU   245       1.565  24.872 -13.274  1.00 25.00           C
ATOM    246  CA  HIS   246      -1.131  26.883 -11.509  1.00 25.00           C
ATOM    247  CA  PHE   247       0.173  27.108  -7.920  1.00 25.00           C
ATOM    248  CA  GLU   248      -0.478  29.883  -5.449  1.00 25.00           C
ATOM    249  CA  TRP   249      -2.684  27.934  -3.057  1.00 25.00           C
ATOM    250  CA  GLU   250       0.451  26.121  -1.878  1.00 25.00           C
ATOM    251  CA  ILE   251      -1.078  23.218   0.118  1.00 25.00           C
ATOM    252  CA  ILE   252      -2.095  25.582   2.867  1.00 25.00           C
ATOM    253  CA  HIS   253      -1.508  26.509   6.537  1.00 25.00           C
ATOM    254  CA  ALA   254       2.280  26.305   6.006  1.00 25.00           C
ATOM    255  CA  PHE   255       1.994  28.550   2.917  1.00 25.00           C
ATOM    256  CA  GLY   256       4.691  30.446   4.805  1.00 25.00           C
ATOM    257  CA  LYS   257       8.399  30.372   5.804  1.00 25.00           C
ATOM    258  CA  ASP   258       8.517  30.552   9.601  1.00 25.00           C
ATOM    259  CA  ALA   259      11.306  31.494  12.049  1.00 25.00           C
ATOM    260  CA  GLU   260      13.681  34.384  11.363  1.00 25.00           C
ATOM    261  CA  GLY   261      14.312  32.657   8.018  1.00 25.00           C
ATOM    262  CA  GLU   262      15.277  34.837   5.108  1.00 25.00           C
ATOM    263  CA  ARG   263      17.223  33.622   2.101  1.00 25.00           C
ATOM    264  CA  SER   264      19.881  31.926  -0.079  1.00 25.00           C
ATOM    265  CA  SER   265      22.327  29.114   0.224  1.00 25.00           C
ATOM    266  CA  ALA   266      21.969  27.950  -3.372  1.00 25.00           C
ATOM    267  CA  ILE   267      21.624  25.581  -6.312  1.00 25.00           C
ATOM    268  CA  ASN   268      18.803  23.390  -4.972  1.00 25.00           C
ATOM    269  CA  THR   269      17.410  19.894  -4.508  1.00 25.00           C
ATOM    270  CA  SER   270      14.724  17.255  -4.009  1.00 25.00           C
ATOM    271  CA  PRO   271      13.134  17.379  -0.584  1.00 25.00           C
ATOM    272  CA  ILE   272      11.712  15.056   2.033  1.00 25.00           C
ATOM    273  CA  SER   273      10.243  13.686   5.226  1.00 25.00           C
ATOM    274  CA  VAL   274       7.190  14.965   7.133  1.00 25.00           C
ATOM    275  CA  VAL   275       8.767  15.008  10.607  1.00 25.00           C
ATOM    276  CA  ASP   276      11.661  12.516  10.570  1.00 25.00           C
ATOM    277  CA  LYS   277      15.139  12.526   8.975  1.00 25.00           C
ATOM    278  CA  GLU   278      16.651  11.502  12.327  1.00 25.00           C
ATOM    279  CA  ARG   279      15.224  13.709  15.110  1.00 25.00           C
ATOM    280  CA  PHE   280      13.893  12.069  18.319  1.00 25.00           C
ATOM    281  CA  SER   281      16.474   9.304  18.771  1.00 25.00           C
ATOM    282  CA  LYS   282      17.228   8.102  22.294  1.00 25.00           C
ATOM    283  CA  TYR   283      14.719  10.103  24.374  1.00 25.00           C
ATOM    284  CA  HIS   284      12.637  11.797  27.034  1.00 25.00           C
ATOM    285  CA  ASP   285       9.362  12.570  28.801  1.00 25.00           C
ATOM    286  CA  ASN   286       7.518   9.245  29.035  1.00 25.00           C
ATOM    287  CA  TYR   287       4.601  10.873  27.187  1.00 25.00           C
ATOM    288  CA  TYR   288       2.818  10.557  23.871  1.00 25.00           C
ATOM    289  CA  PRO   289       0.811   7.411  24.310  1.00 25.00           C
ATOM    290  CA  GLY   290      -0.715   8.679  21.106  1.00 25.00           C
ATOM    291  CA  TRP   291      -3.487   8.522  18.540  1.00 25.00           C
ATOM    292  CA  TYR   292      -5.794   5.667  19.454  1.00 25.00           C
ATOM    293  CA  LEU   293      -8.840   3.345  19.605  1.00 25.00           C
ATOM    294  CA  VAL   294      -8.865   1.333  22.786  1.00 25.00           C
ATOM    295  CA  ASP   295      -9.134  -1.742  24.938  1.00 25.00           C
ATOM    296  CA  ASP   296     -10.060  -3.850  21.958  1.00 25.00           C
ATOM    297  CA  THR   297     -13.351  -5.567  21.107  1.00 25.00           C
ATOM    298  CA  LEU   298     -15.207  -3.155  23.430  1.00 25.00           C
ATOM    299  CA  GLU   299     -14.042  -0.182  21.315  1.00 25.00           C
ATOM    300  CA  ARG   300     -15.242  -1.944  18.134  1.00 25.00           C
ATOM    301  CA  ALA   301     -17.816  -0.711  15.613  1.00 25.00           C
ATOM    302  CA  GLY   302     -18.267   2.847  16.770  1.00 25.00           C
ATOM    303  CA  ARG   303     -21.224   5.101  16.321  1.00 25.00           C
ATOM    304  CA  ILE   304     -20.927   7.314  13.278  1.00 25.00           C
TER
END
