
#######################################################
#                                                     #
#                        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   31 (  153),  selected   31 , name T0386TS239_1_1-D2
# Molecule2: number of CA atoms   81 (  636),  selected   81 , name T0386_D2.pdb
# PARAMETERS: T0386TS239_1_1-D2.T0386_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    K     222      -       -           -
LGA    I     223      N     219          3.712
LGA    R     224      P     220          2.352
LGA    L     225      E     221          2.552
LGA    L     226      K     222          1.833
LGA    K     227      I     223          2.322
LGA    E     228      R     224          2.562
LGA    F     229      L     225          2.481
LGA    M     230      L     226          2.922
LGA    -       -      K     227           -
LGA    -       -      E     228           -
LGA    -       -      F     229           -
LGA    H     231      M     230           #
LGA    T     232      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    M     233      V     245          2.295
LGA    K     234      M     246          3.923
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    -       -      F     266           -
LGA    -       -      A     267           -
LGA    -       -      L     268           -
LGA    -       -      N     269           -
LGA    -       -      V     270           -
LGA    -       -      K     271           -
LGA    N     235      G     272          4.946
LGA    T     236      A     273          2.316
LGA    G     237      Y     274          4.662
LGA    R     238      -       -           -
LGA    N     239      -       -           -
LGA    V     240      I     275          2.708
LGA    N     241      -       -           -
LGA    D     242      -       -           -
LGA    R     243      I     276          3.394
LGA    P     244      G     277          5.212
LGA    V     245      N     278           -
LGA    M     246      I     279          3.482
LGA    V     247      D     280           #
LGA    -       -      H     281           -
LGA    A     248      L     282          1.660
LGA    K     249      P     283          3.333
LGA    E     250      P     284          1.445
LGA    G     251      E     285          2.681
LGA    E     252      Q     286          3.093
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           -
LGA    -       -      T     299           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   31   81    5.0     22    3.15     0.00     17.095     0.676

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.679583 * X  +   0.177131 * Y  +  -0.711892 * Z  +  18.815905
  Y_new =  -0.713897 * X  +   0.383066 * Y  +  -0.586184 * Z  +  25.518126
  Z_new =   0.168871 * X  +   0.906579 * Y  +   0.386778 * Z  +  37.750122 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.167542   -1.974051  [ DEG:    66.8952   -113.1048 ]
  Theta =  -0.169684   -2.971909  [ DEG:    -9.7222   -170.2778 ]
  Phi   =  -0.810018    2.331575  [ DEG:   -46.4106    133.5894 ]
 
# 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: T0386TS239_1_1-D2                             
REMARK     2: T0386_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0386TS239_1_1-D2.T0386_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   31   81   5.0   22   3.15    0.00  17.095
REMARK  ---------------------------------------------------------- 
MOLECULE T0386TS239_1_1-D2
REMARK PARENT number 1
PFRMAT TS
TARGET T0386
PARENT 2f6s_A
ATOM    724  N   LYS   222      -1.200  56.161  81.105  1.00  9.99
ATOM    725  CA  LYS   222       0.218  55.931  80.948  1.00  9.99
ATOM    726  C   LYS   222       0.643  56.146  79.499  1.00  9.99
ATOM    727  O   LYS   222       1.676  56.760  79.258  1.00  9.99
ATOM    728  CB  LYS   222       0.699  54.553  81.525  1.00  9.99
ATOM    729  N   ILE   223      -0.156  55.676  78.537  1.00  9.99
ATOM    730  CA  ILE   223       0.183  55.874  77.122  1.00  9.99
ATOM    731  C   ILE   223       0.297  57.357  76.806  1.00  9.99
ATOM    732  O   ILE   223       1.251  57.777  76.167  1.00  9.99
ATOM    733  CB  ILE   223      -0.848  55.248  76.186  1.00  9.99
ATOM    734  N   ARG   224      -0.664  58.152  77.271  1.00  9.99
ATOM    735  CA  ARG   224      -0.693  59.588  76.995  1.00  9.99
ATOM    736  C   ARG   224       0.471  60.293  77.673  1.00  9.99
ATOM    737  O   ARG   224       1.114  61.163  77.079  1.00  9.99
ATOM    738  CB  ARG   224      -2.033  60.207  77.481  1.00  9.99
ATOM    739  N   LEU   225       0.741  59.915  78.917  1.00  9.99
ATOM    740  CA  LEU   225       1.763  60.561  79.717  1.00  9.99
ATOM    741  C   LEU   225       3.134  60.348  79.096  1.00  9.99
ATOM    742  O   LEU   225       3.901  61.302  78.923  1.00  9.99
ATOM    743  CB  LEU   225       1.736  60.012  81.140  1.00  9.99
ATOM    744  N   LEU   226       3.435  59.095  78.756  1.00  9.99
ATOM    745  CA  LEU   226       4.704  58.757  78.111  1.00  9.99
ATOM    746  C   LEU   226       4.867  59.378  76.734  1.00  9.99
ATOM    747  O   LEU   226       5.942  59.878  76.420  1.00  9.99
ATOM    748  CB  LEU   226       4.896  57.240  78.029  1.00  9.99
ATOM    749  N   LYS   227       3.809  59.371  75.921  1.00  9.99
ATOM    750  CA  LYS   227       3.925  59.859  74.539  1.00  9.99
ATOM    751  C   LYS   227       4.347  61.321  74.476  1.00  9.99
ATOM    752  O   LYS   227       4.964  61.744  73.515  1.00  9.99
ATOM    753  CB  LYS   227       2.641  59.640  73.752  1.00  9.99
ATOM    754  N   GLU   228       4.040  62.072  75.526  1.00  9.99
ATOM    755  CA  GLU   228       4.315  63.508  75.580  1.00  9.99
ATOM    756  C   GLU   228       5.726  63.880  76.029  1.00  9.99
ATOM    757  O   GLU   228       6.076  65.046  76.003  1.00  9.99
ATOM    758  CB  GLU   228       3.311  64.196  76.505  1.00  9.99
ATOM    759  N   PHE   229       6.518  62.904  76.461  1.00  9.99
ATOM    760  CA  PHE   229       7.832  63.179  77.015  1.00  9.99
ATOM    761  C   PHE   229       8.853  62.218  76.458  1.00  9.99
ATOM    762  O   PHE   229       9.653  61.640  77.189  1.00  9.99
ATOM    763  CB  PHE   229       7.790  63.142  78.545  1.00  9.99
ATOM    764  N   MET   230       8.817  62.051  75.144  1.00  9.99
ATOM    765  CA  MET   230       9.810  61.261  74.436  1.00  9.99
ATOM    766  C   MET   230      10.897  62.160  73.855  1.00  9.99
ATOM    767  O   MET   230      10.640  63.320  73.535  1.00  9.99
ATOM    768  CB  MET   230       9.143  60.469  73.315  1.00  9.99
ATOM    769  N   HIS   231      12.109  61.623  73.725  1.00  9.99
ATOM    770  CA  HIS   231      13.224  62.356  73.129  1.00  9.99
ATOM    771  C   HIS   231      13.968  61.485  72.129  1.00  9.99
ATOM    772  O   HIS   231      14.083  60.265  72.327  1.00  9.99
ATOM    773  CB  HIS   231      14.193  62.819  74.211  1.00  9.99
ATOM    774  N   THR   232      14.470  62.120  71.065  1.00  9.99
ATOM    775  CA  THR   232      15.354  61.470  70.087  1.00  9.99
ATOM    776  C   THR   232      16.809  61.409  70.557  1.00  9.99
ATOM    777  O   THR   232      17.628  60.703  69.980  1.00  9.99
ATOM    778  CB  THR   232      15.272  62.173  68.736  1.00  9.99
ATOM    779  N   MET   233      17.107  62.138  71.621  1.00  9.99
ATOM    780  CA  MET   233      18.451  62.237  72.143  1.00  9.99
ATOM    781  C   MET   233      18.811  61.047  73.033  1.00  9.99
ATOM    782  O   MET   233      19.095  61.198  74.228  1.00  9.99
ATOM    783  CB  MET   233      18.575  63.546  72.916  1.00  9.99
ATOM    784  N   LYS   234      18.830  59.866  72.434  1.00  9.99
ATOM    785  CA  LYS   234      18.835  58.619  73.202  1.00  9.99
ATOM    786  C   LYS   234      20.177  58.281  73.838  1.00  9.99
ATOM    787  O   LYS   234      20.286  57.301  74.586  1.00  9.99
ATOM    788  CB  LYS   234      18.403  57.419  72.324  1.00  9.99
ATOM    789  N   ASN   235      21.194  59.078  73.529  1.00  9.99
ATOM    790  CA  ASN   235      22.561  58.724  73.874  1.00  9.99
ATOM    791  C   ASN   235      23.257  59.729  74.779  1.00  9.99
ATOM    792  O   ASN   235      24.331  59.435  75.302  1.00  9.99
ATOM    793  CB  ASN   235      23.397  58.493  72.604  1.00  9.99
ATOM    794  N   THR   236      22.661  60.909  74.952  1.00  9.99
ATOM    795  CA  THR   236      23.216  61.908  75.853  1.00  9.99
ATOM    796  C   THR   236      23.274  61.392  77.308  1.00  9.99
ATOM    797  O   THR   236      22.219  61.145  77.929  1.00  9.99
ATOM    798  CB  THR   236      22.414  63.193  75.793  1.00  9.99
ATOM    799  N   GLY   237      24.499  61.215  77.868  1.00  9.99
ATOM    800  CA  GLY   237      24.470  60.596  79.205  1.00  9.99
ATOM    801  C   GLY   237      23.958  61.556  80.303  1.00  9.99
ATOM    802  O   GLY   237      23.439  61.074  81.318  1.00  9.99
ATOM    803  N   ARG   238      24.052  62.877  80.094  1.00  9.99
ATOM    804  CA  ARG   238      23.427  63.829  81.034  1.00  9.99
ATOM    805  C   ARG   238      21.904  63.600  81.103  1.00  9.99
ATOM    806  O   ARG   238      21.330  63.441  82.193  1.00  9.99
ATOM    807  CB  ARG   238      23.746  65.292  80.682  1.00  9.99
ATOM    808  N   ASN   239      21.268  63.564  79.931  1.00  9.99
ATOM    809  CA  ASN   239      19.843  63.277  79.797  1.00  9.99
ATOM    810  C   ASN   239      19.473  61.945  80.463  1.00  9.99
ATOM    811  O   ASN   239      18.467  61.847  81.160  1.00  9.99
ATOM    812  CB  ASN   239      19.443  63.239  78.308  1.00  9.99
ATOM    813  N   VAL   240      20.312  60.936  80.253  1.00  9.99
ATOM    814  CA  VAL   240      20.068  59.607  80.774  1.00  9.99
ATOM    815  C   VAL   240      20.179  59.574  82.299  1.00  9.99
ATOM    816  O   VAL   240      19.353  58.959  82.971  1.00  9.99
ATOM    817  CB  VAL   240      21.026  58.610  80.119  1.00  9.99
ATOM    818  N   ASN   241      21.180  60.259  82.840  1.00  9.99
ATOM    819  CA  ASN   241      21.373  60.334  84.285  1.00  9.99
ATOM    820  C   ASN   241      20.224  61.098  84.960  1.00  9.99
ATOM    821  O   ASN   241      19.698  60.642  85.973  1.00  9.99
ATOM    822  CB  ASN   241      22.779  60.927  84.664  1.00  9.99
ATOM    823  N   ASP   242      19.831  62.236  84.389  1.00  9.99
ATOM    824  CA  ASP   242      18.645  62.955  84.854  1.00  9.99
ATOM    825  C   ASP   242      17.412  62.057  84.875  1.00  9.99
ATOM    826  O   ASP   242      16.628  62.086  85.826  1.00  9.99
ATOM    827  CB  ASP   242      18.360  64.169  83.989  1.00  9.99
ATOM    828  N   ARG   243      17.265  61.248  83.830  1.00  9.99
ATOM    829  CA  ARG   243      16.193  60.290  83.731  1.00  9.99
ATOM    830  C   ARG   243      16.213  59.265  84.848  1.00  9.99
ATOM    831  O   ARG   243      15.181  59.015  85.497  1.00  9.99
ATOM    832  CB  ARG   243      16.273  59.606  82.356  1.00  9.99
ATOM    833  N   PRO   244      17.376  58.667  85.087  1.00  9.99
ATOM    834  CA  PRO   244      17.471  57.607  86.081  1.00  9.99
ATOM    835  C   PRO   244      17.337  58.160  87.490  1.00  9.99
ATOM    836  O   PRO   244      16.765  57.509  88.345  1.00  9.99
ATOM    837  CB  PRO   244      18.757  56.782  85.914  1.00  9.99
ATOM    838  N   VAL   245      17.844  59.370  87.725  1.00  9.99
ATOM    839  CA  VAL   245      17.677  60.034  89.006  1.00  9.99
ATOM    840  C   VAL   245      16.180  60.200  89.300  1.00  9.99
ATOM    841  O   VAL   245      15.741  60.006  90.425  1.00  9.99
ATOM    842  CB  VAL   245      18.412  61.400  89.036  1.00  9.99
ATOM    843  N   MET   246      15.393  60.542  88.289  1.00  9.99
ATOM    844  CA  MET   246      13.968  60.733  88.482  1.00  9.99
ATOM    845  C   MET   246      13.290  59.391  88.743  1.00  9.99
ATOM    846  O   MET   246      12.408  59.291  89.606  1.00  9.99
ATOM    847  CB  MET   246      13.355  61.391  87.268  1.00  9.99
ATOM    848  N   VAL   247      13.721  58.360  88.013  1.00  9.99
ATOM    849  CA  VAL   247      13.208  57.023  88.216  1.00  9.99
ATOM    850  C   VAL   247      13.361  56.618  89.690  1.00  9.99
ATOM    851  O   VAL   247      12.427  56.091  90.294  1.00  9.99
ATOM    852  CB  VAL   247      13.931  56.031  87.298  1.00  9.99
ATOM    853  N   ALA   248      14.539  56.872  90.263  1.00  9.99
ATOM    854  CA  ALA   248      14.799  56.566  91.675  1.00  9.99
ATOM    855  C   ALA   248      14.009  57.473  92.612  1.00  9.99
ATOM    856  O   ALA   248      13.609  57.061  93.708  1.00  9.99
ATOM    857  CB  ALA   248      16.295  56.641  91.979  1.00  9.99
ATOM    858  N   LYS   249      10.567  56.245  93.569  1.00  9.99
ATOM    859  CA  LYS   249      10.571  55.275  94.643  1.00  9.99
ATOM    860  C   LYS   249      10.841  55.921  96.008  1.00  9.99
ATOM    861  O   LYS   249      10.974  55.211  97.008  1.00  9.99
ATOM    862  CB  LYS   249      11.628  54.209  94.365  1.00  9.99
ATOM    863  N   GLU   250      10.932  57.256  96.052  1.00  9.99
ATOM    864  CA  GLU   250      11.140  57.988  97.306  1.00  9.99
ATOM    865  C   GLU   250      12.571  58.388  97.655  1.00  9.99
ATOM    866  O   GLU   250      12.845  58.801  98.786  1.00  9.99
ATOM    867  CB  GLU   250      10.552  57.135  98.442  1.00  9.99
ATOM    868  N   GLY   251      13.495  58.267  96.704  1.00  9.99
ATOM    869  CA  GLY   251      14.871  58.719  96.925  1.00  9.99
ATOM    870  C   GLY   251      15.002  60.205  96.589  1.00  9.99
ATOM    871  O   GLY   251      14.800  60.603  95.440  1.00  9.99
ATOM    872  N   GLU   252      15.344  61.018  97.594  1.00  9.99
ATOM    873  CA  GLU   252      15.325  62.480  97.461  1.00  9.99
ATOM    874  C   GLU   252      16.707  63.103  97.542  1.00  9.99
ATOM    875  O   GLU   252      17.500  63.009  96.599  1.00  9.99
ATOM    876  CB  GLU   252      14.406  63.069  98.544  1.00  9.99
TER
END
