
#######################################################
#                                                     #
#                        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 T0386TS168_3-D2
# Molecule2: number of CA atoms   81 (  636),  selected   81 , name T0386_D2.pdb
# PARAMETERS: T0386TS168_3-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      -       -           -
LGA    R     224      -       -           -
LGA    L     225      -       -           -
LGA    L     226      -       -           -
LGA    K     227      -       -           -
LGA    E     228      -       -           -
LGA    F     229      -       -           -
LGA    M     230      -       -           -
LGA    H     231      -       -           -
LGA    T     232      -       -           -
LGA    M     233      -       -           -
LGA    K     234      -       -           -
LGA    N     235      -       -           -
LGA    T     236      N     219          2.983
LGA    G     237      P     220          1.940
LGA    R     238      E     221          1.588
LGA    N     239      K     222          4.570
LGA    -       -      I     223           -
LGA    V     240      R     224          1.894
LGA    N     241      L     225          4.853
LGA    -       -      L     226           -
LGA    D     242      K     227          1.570
LGA    R     243      E     228          2.597
LGA    P     244      F     229          2.912
LGA    -       -      M     230           -
LGA    -       -      H     231           -
LGA    -       -      T     232           -
LGA    -       -      M     233           -
LGA    -       -      K     234           -
LGA    -       -      N     235           -
LGA    -       -      T     236           -
LGA    -       -      G     237           -
LGA    -       -      R     238           -
LGA    -       -      N     239           -
LGA    -       -      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    -       -      G     256           -
LGA    -       -      T     257           -
LGA    -       -      Y     258           -
LGA    -       -      R     259           -
LGA    -       -      G     260           -
LGA    -       -      A     261           -
LGA    -       -      G     262           -
LGA    -       -      L     263           -
LGA    -       -      E     264           -
LGA    -       -      G     265           -
LGA    V     245      F     266          3.244
LGA    M     246      A     267          1.034
LGA    V     247      L     268          1.543
LGA    A     248      N     269          0.809
LGA    K     249      V     270          5.140
LGA    E     250      K     271          5.353
LGA    G     251      G     272          2.169
LGA    E     252      A     273          1.468
LGA    T     253      Y     274           #
LGA    Y     254      I     275          4.224
LGA    T     255      I     276           #
LGA    G     256      G     277           #
LGA    T     257      N     278           #
LGA    Y     258      -       -           -
LGA    R     259      I     279           #
LGA    G     260      D     280           -
LGA    A     261      H     281           -
LGA    G     262      L     282           -
LGA    L     263      P     283           -
LGA    E     264      P     284           -
LGA    G     265      E     285           #
LGA    F     266      Q     286           #
LGA    -       -      L     287           -
LGA    -       -      K     288           -
LGA    A     267      I     289          4.333
LGA    L     268      L     290          2.206
LGA    N     269      K     291          4.725
LGA    V     270      P     292          2.083
LGA    K     271      G     293          1.579
LGA    G     272      D     294          3.745
LGA    A     273      K     295          3.570
LGA    Y     274      I     296          4.569
LGA    I     275      T     297          2.853
LGA    I     276      F     298          4.712
LGA    G     277      -       -           -
LGA    N     278      -       -           -
LGA    I     279      -       -           -
LGA    D     280      -       -           -
LGA    H     281      -       -           -
LGA    L     282      -       -           -
LGA    P     283      -       -           -
LGA    P     284      -       -           -
LGA    E     285      -       -           -
LGA    Q     286      -       -           -
LGA    L     287      -       -           -
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      T     299          4.744
LGA    T     299      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   81   81    5.0     29    3.37     6.90     21.061     0.837

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.684340 * X  +  -0.190994 * Y  +   0.703704 * Z  +  15.621507
  Y_new =   0.704135 * X  +   0.077582 * Y  +   0.705816 * Z  +  46.745750
  Z_new =  -0.189401 * X  +   0.978521 * Y  +   0.081393 * Z  +  95.305527 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.487807   -1.653785  [ DEG:    85.2451    -94.7549 ]
  Theta =   0.190552    2.951041  [ DEG:    10.9178    169.0822 ]
  Phi   =   2.341939   -0.799653  [ DEG:   134.1832    -45.8168 ]
 
# 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: T0386TS168_3-D2                               
REMARK     2: T0386_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0386TS168_3-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   29   3.37    6.90  21.061
REMARK  ---------------------------------------------------------- 
MOLECULE T0386TS168_3-D2
PFRMAT TS
TARGET T0386
MODEL 3
PARENT N/A
ATOM    219  CA  ASN   219       1.050  64.066 101.588  1.00 25.00           C
ATOM    220  CA  PRO   220       0.405  61.371  98.980  1.00 25.00           C
ATOM    221  CA  GLU   221       2.518  63.091  96.290  1.00 25.00           C
ATOM    222  CA  LYS   222       4.952  60.134  96.276  1.00 25.00           C
ATOM    223  CA  ILE   223       2.022  57.693  95.915  1.00 25.00           C
ATOM    224  CA  ARG   224       0.635  59.752  92.998  1.00 25.00           C
ATOM    225  CA  LEU   225       4.075  59.730  91.315  1.00 25.00           C
ATOM    226  CA  LEU   226       4.295  55.932  91.759  1.00 25.00           C
ATOM    227  CA  LYS   227       0.807  55.525  90.231  1.00 25.00           C
ATOM    228  CA  GLU   228       1.827  57.717  87.261  1.00 25.00           C
ATOM    229  CA  PHE   229       4.989  55.615  86.764  1.00 25.00           C
ATOM    230  CA  MET   230       2.900  52.406  86.851  1.00 25.00           C
ATOM    231  CA  HIS   231       0.492  53.876  84.261  1.00 25.00           C
ATOM    232  CA  THR   232       3.446  54.827  82.017  1.00 25.00           C
ATOM    233  CA  MET   233       4.858  51.281  82.329  1.00 25.00           C
ATOM    234  CA  LYS   234       1.442  49.814  81.408  1.00 25.00           C
ATOM    235  CA  ASN   235       1.246  52.122  78.359  1.00 25.00           C
ATOM    236  CA  THR   236       0.375  54.457  75.498  1.00 25.00           C
ATOM    237  CA  GLY   237      -0.199  58.152  75.386  1.00 25.00           C
ATOM    238  CA  ARG   238       2.685  58.330  77.840  1.00 25.00           C
ATOM    239  CA  ASN   239       3.441  61.876  76.819  1.00 25.00           C
ATOM    240  CA  VAL   240       6.127  63.041  79.343  1.00 25.00           C
ATOM    241  CA  ASN   241       5.465  66.536  78.084  1.00 25.00           C
ATOM    242  CA  ASP   242       8.241  68.178  76.177  1.00 25.00           C
ATOM    243  CA  ARG   243      10.897  66.150  78.086  1.00 25.00           C
ATOM    244  CA  PRO   244      12.994  67.284  81.069  1.00 25.00           C
ATOM    245  CA  VAL   245      14.918  64.062  81.912  1.00 25.00           C
ATOM    246  CA  MET   246      18.124  62.203  82.551  1.00 25.00           C
ATOM    247  CA  VAL   247      21.147  60.851  84.328  1.00 25.00           C
ATOM    248  CA  ALA   248      23.628  60.792  81.392  1.00 25.00           C
ATOM    249  CA  LYS   249      26.796  62.422  80.035  1.00 25.00           C
ATOM    250  CA  GLU   250      26.270  62.468  76.268  1.00 25.00           C
ATOM    251  CA  GLY   251      27.117  58.782  76.490  1.00 25.00           C
ATOM    252  CA  GLU   252      23.503  58.196  75.441  1.00 25.00           C
ATOM    253  CA  THR   253      21.158  55.973  77.367  1.00 25.00           C
ATOM    254  CA  TYR   254      19.601  54.869  80.591  1.00 25.00           C
ATOM    255  CA  THR   255      18.454  56.098  83.996  1.00 25.00           C
ATOM    256  CA  GLY   256      18.329  57.831  87.427  1.00 25.00           C
ATOM    257  CA  THR   257      17.236  61.433  87.845  1.00 25.00           C
ATOM    258  CA  TYR   258      14.725  61.430  90.716  1.00 25.00           C
ATOM    259  CA  ARG   259      14.428  65.217  90.620  1.00 25.00           C
ATOM    260  CA  GLY   260      15.061  68.871  89.771  1.00 25.00           C
ATOM    261  CA  ALA   261      13.762  71.968  91.440  1.00 25.00           C
ATOM    262  CA  GLY   262      11.284  73.556  93.858  1.00 25.00           C
ATOM    263  CA  LEU   263      12.191  70.446  95.938  1.00 25.00           C
ATOM    264  CA  GLU   264      15.457  72.244  96.429  1.00 25.00           C
ATOM    265  CA  GLY   265      16.636  68.941  97.850  1.00 25.00           C
ATOM    266  CA  PHE   266      19.020  65.980  97.876  1.00 25.00           C
ATOM    267  CA  ALA   267      16.865  64.452  95.171  1.00 25.00           C
ATOM    268  CA  LEU   268      19.474  65.415  92.679  1.00 25.00           C
ATOM    269  CA  ASN   269      20.521  65.574  89.057  1.00 25.00           C
ATOM    270  CA  VAL   270      24.318  65.595  88.829  1.00 25.00           C
ATOM    271  CA  LYS   271      28.075  64.957  88.484  1.00 25.00           C
ATOM    272  CA  GLY   272      28.652  61.156  88.542  1.00 25.00           C
ATOM    273  CA  ALA   273      28.620  59.494  91.963  1.00 25.00           C
ATOM    274  CA  TYR   274      26.295  56.556  92.631  1.00 25.00           C
ATOM    275  CA  ILE   275      25.029  54.584  89.642  1.00 25.00           C
ATOM    276  CA  ILE   276      23.170  52.049  87.462  1.00 25.00           C
ATOM    277  CA  GLY   277      22.923  50.129  84.224  1.00 25.00           C
ATOM    278  CA  ASN   278      23.941  52.318  81.298  1.00 25.00           C
ATOM    279  CA  ILE   279      22.795  51.161  77.854  1.00 25.00           C
ATOM    280  CA  ASP   280      20.142  49.819  75.423  1.00 25.00           C
ATOM    281  CA  HIS   281      17.316  48.159  73.567  1.00 25.00           C
ATOM    282  CA  LEU   282      15.207  51.154  74.572  1.00 25.00           C
ATOM    283  CA  PRO   283      11.804  51.581  72.842  1.00 25.00           C
ATOM    284  CA  PRO   284      10.109  54.974  73.131  1.00 25.00           C
ATOM    285  CA  GLU   285       6.997  56.570  74.690  1.00 25.00           C
ATOM    286  CA  GLN   286       8.394  55.926  78.197  1.00 25.00           C
ATOM    287  CA  LEU   287      11.728  57.517  77.188  1.00 25.00           C
ATOM    288  CA  LYS   288       9.880  60.569  75.799  1.00 25.00           C
ATOM    289  CA  ILE   289      11.051  63.126  73.201  1.00 25.00           C
ATOM    290  CA  LEU   290      14.326  64.207  74.805  1.00 25.00           C
ATOM    291  CA  LYS   291      15.606  61.018  73.144  1.00 25.00           C
ATOM    292  CA  PRO   292      18.963  62.662  73.564  1.00 25.00           C
ATOM    293  CA  GLY   293      18.790  62.670  77.342  1.00 25.00           C
ATOM    294  CA  ASP   294      15.815  60.393  78.156  1.00 25.00           C
ATOM    295  CA  LYS   295      14.686  58.438  81.138  1.00 25.00           C
ATOM    296  CA  ILE   296      12.054  57.076  83.510  1.00 25.00           C
ATOM    297  CA  THR   297      10.974  53.788  85.060  1.00 25.00           C
ATOM    298  CA  PHE   298      12.006  51.377  87.830  1.00 25.00           C
ATOM    299  CA  THR   299      10.716  48.789  90.246  1.00 25.00           C
TER
END
