
#######################################################
#                                                     #
#                        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   15 (  129),  selected   15 , name T0347TS249_5_2-D1
# Molecule2: number of CA atoms   89 (  730),  selected   89 , name T0347_D1.pdb
# PARAMETERS: T0347TS249_5_2-D1.T0347_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

# WARNING! The change of the parameter DIST cutoff may give you better result.

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      P       7           -
LGA    -       -      R       8           -
LGA    -       -      L       9           -
LGA    -       -      S      10           -
LGA    L      94      R      11          4.635
LGA    -       -      I      12           -
LGA    -       -      A      13           -
LGA    -       -      I      14           -
LGA    -       -      D      15           -
LGA    -       -      K      16           -
LGA    -       -      L      17           -
LGA    -       -      R      18           -
LGA    -       -      P      19           -
LGA    -       -      T      20           -
LGA    -       -      Q      21           -
LGA    -       -      I      22           -
LGA    -       -      A      23           -
LGA    -       -      V      24           -
LGA    -       -      G      25           -
LGA    -       -      F      26           -
LGA    -       -      R      27           -
LGA    -       -      E      28           -
LGA    -       -      V      29           -
LGA    -       -      E      30           -
LGA    -       -      L      31           -
LGA    -       -      K      32           -
LGA    -       -      R      33           -
LGA    -       -      K      34           -
LGA    -       -      E      35           -
LGA    -       -      W      36           -
LGA    -       -      R      37           -
LGA    G      95      H      51          3.388
LGA    K      96      I      52          1.637
LGA    D      97      V      53          4.261
LGA    E      98      -       -           -
LGA    F      99      P      54          0.592
LGA    W     100      -       -           -
LGA    S     101      V      55          2.344
LGA    V     102      V      56          2.418
LGA    M     103      -       -           -
LGA    D     104      -       -           -
LGA    H     105      A      57          1.916
LGA    R     106      G      58          2.688
LGA    -       -      P      59           -
LGA    -       -      K      60           -
LGA    -       -      D      61           -
LGA    -       -      R      62           -
LGA    -       -      A      63           -
LGA    -       -      Y      64           -
LGA    -       -      L      65           -
LGA    -       -      I      66           -
LGA    -       -      D      67           -
LGA    -       -      H      68           -
LGA    -       -      H      69           -
LGA    -       -      H      70           -
LGA    -       -      L      71           -
LGA    -       -      V      72           -
LGA    -       -      L      73           -
LGA    -       -      A      74           -
LGA    -       -      L      75           -
LGA    -       -      S      76           -
LGA    -       -      K      77           -
LGA    -       -      E      78           -
LGA    -       -      G      79           -
LGA    -       -      V      80           -
LGA    -       -      E      81           -
LGA    -       -      H      82           -
LGA    -       -      V      83           -
LGA    -       -      L      84           -
LGA    -       -      T      85           -
LGA    -       -      S      86           -
LGA    -       -      E      87           -
LGA    -       -      V      88           -
LGA    N     107      A      89          4.233
LGA    L     108      K      90          1.159
LGA    -       -      F      91           -
LGA    -       -      S      92           -
LGA    -       -      H      93           -
LGA    -       -      L      94           -
LGA    -       -      G      95           -
LGA    -       -      K      96           -
LGA    -       -      D      97           -
LGA    -       -      E      98           -
LGA    -       -      F      99           -
LGA    -       -      W     100           -
LGA    -       -      S     101           -
LGA    -       -      V     102           -
LGA    -       -      M     103           -
LGA    -       -      D     104           -
LGA    -       -      H     105           -
LGA    -       -      R     106           -
LGA    -       -      N     107           -
LGA    -       -      L     108           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   15   89    5.0     11    2.95     9.09      8.154     0.361

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.476331 * X  +  -0.706233 * Y  +   0.523779 * Z  +   3.602339
  Y_new =  -0.798399 * X  +  -0.596948 * Y  +  -0.078816 * Z  +  16.707266
  Z_new =   0.368332 * X  +  -0.380642 * Y  +  -0.848200 * Z  +   2.692554 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.719767    0.421826  [ DEG:  -155.8311     24.1689 ]
  Theta =  -0.377214   -2.764379  [ DEG:   -21.6128   -158.3872 ]
  Phi   =  -1.032875    2.108717  [ DEG:   -59.1794    120.8206 ]
 
# 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: T0347TS249_5_2-D1                             
REMARK     2: T0347_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0347TS249_5_2-D1.T0347_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   15   89   5.0   11   2.95    9.09   8.154
REMARK  ---------------------------------------------------------- 
MOLECULE T0347TS249_5_2-D1
REMARK PARENT number 2
PFRMAT TS
TARGET T0347
PARENT 1oe8_A
ATOM    760  N   LEU    94       7.722  32.366 -14.023  1.00  9.99
ATOM    761  CA  LEU    94       7.557  33.676 -13.471  1.00  9.99
ATOM    762  CB  LEU    94       7.030  33.670 -12.026  1.00  9.99
ATOM    763  CG  LEU    94       5.609  33.093 -11.887  1.00  9.99
ATOM    764  CD1 LEU    94       5.143  33.115 -10.420  1.00  9.99
ATOM    765  CD2 LEU    94       4.628  33.804 -12.837  1.00  9.99
ATOM    766  C   LEU    94       8.982  34.192 -13.485  1.00  9.99
ATOM    767  O   LEU    94       9.849  33.530 -14.053  1.00  9.99
ATOM    768  N   GLY    95       9.280  35.393 -12.936  1.00  9.99
ATOM    769  CA  GLY    95      10.616  35.943 -13.070  1.00  9.99
ATOM    770  C   GLY    95      11.721  35.139 -12.436  1.00  9.99
ATOM    771  O   GLY    95      12.562  34.588 -13.138  1.00  9.99
ATOM    772  N   LYS    96      11.778  34.956 -11.104  1.00  9.99
ATOM    773  CA  LYS    96      12.723  33.977 -10.636  1.00  9.99
ATOM    774  CB  LYS    96      12.978  34.120  -9.137  1.00  9.99
ATOM    775  CG  LYS    96      13.180  35.608  -8.827  1.00  9.99
ATOM    776  CD  LYS    96      14.289  36.247  -9.671  1.00  9.99
ATOM    777  CE  LYS    96      14.600  37.696  -9.292  1.00  9.99
ATOM    778  NZ  LYS    96      15.800  38.167 -10.015  1.00  9.99
ATOM    779  C   LYS    96      11.851  32.807 -11.000  1.00  9.99
ATOM    780  O   LYS    96      11.620  32.466 -12.156  1.00  9.99
ATOM    781  N   ASP    97      11.243  32.159 -10.030  1.00  9.99
ATOM    782  CA  ASP    97      10.002  31.586 -10.456  1.00  9.99
ATOM    783  CB  ASP    97       9.502  30.443  -9.566  1.00  9.99
ATOM    784  CG  ASP    97      10.620  29.412  -9.553  1.00  9.99
ATOM    785  OD1 ASP    97      10.995  28.916 -10.648  1.00  9.99
ATOM    786  OD2 ASP    97      11.144  29.138  -8.441  1.00  9.99
ATOM    787  C   ASP    97       9.252  32.857 -10.144  1.00  9.99
ATOM    788  O   ASP    97       9.449  33.897 -10.768  1.00  9.99
ATOM    789  N   GLU    98       8.272  32.894  -9.261  1.00  9.99
ATOM    790  CA  GLU    98       8.171  34.271  -8.873  1.00  9.99
ATOM    791  CB  GLU    98       6.989  34.527  -7.927  1.00  9.99
ATOM    792  CG  GLU    98       6.547  35.987  -7.895  1.00  9.99
ATOM    793  CD  GLU    98       5.230  36.059  -7.141  1.00  9.99
ATOM    794  OE1 GLU    98       5.032  35.229  -6.214  1.00  9.99
ATOM    795  OE2 GLU    98       4.400  36.942  -7.487  1.00  9.99
ATOM    796  C   GLU    98       9.482  34.428  -8.122  1.00  9.99
ATOM    797  O   GLU    98      10.440  34.942  -8.668  1.00  9.99
ATOM    798  N   PHE    99       9.611  33.771  -6.956  1.00  9.99
ATOM    799  CA  PHE    99      10.771  33.579  -6.104  1.00  9.99
ATOM    800  CB  PHE    99      10.437  34.049  -4.660  1.00  9.99
ATOM    801  CG  PHE    99      11.237  33.873  -3.397  1.00  9.99
ATOM    802  CD1 PHE    99      12.378  34.539  -3.101  1.00  9.99
ATOM    803  CD2 PHE    99      10.777  33.122  -2.365  1.00  9.99
ATOM    804  CE1 PHE    99      13.092  34.433  -1.934  1.00  9.99
ATOM    805  CE2 PHE    99      11.458  32.978  -1.177  1.00  9.99
ATOM    806  CZ  PHE    99      12.630  33.637  -0.933  1.00  9.99
ATOM    807  C   PHE    99      10.670  32.146  -6.376  1.00  9.99
ATOM    808  O   PHE    99      10.701  31.805  -7.548  1.00  9.99
ATOM    809  N   TRP   100      10.413  31.223  -5.460  1.00  9.99
ATOM    810  CA  TRP   100       9.932  30.078  -6.171  1.00  9.99
ATOM    811  CB  TRP   100       9.877  28.871  -5.341  1.00  9.99
ATOM    812  CG  TRP   100      10.095  27.707  -6.202  1.00  9.99
ATOM    813  CD2 TRP   100      11.420  27.267  -6.350  1.00  9.99
ATOM    814  CD1 TRP   100       9.316  26.924  -6.984  1.00  9.99
ATOM    815  NE1 TRP   100      10.114  26.039  -7.659  1.00  9.99
ATOM    816  CE2 TRP   100      11.421  26.250  -7.260  1.00  9.99
ATOM    817  CE3 TRP   100      12.548  27.707  -5.791  1.00  9.99
ATOM    818  CZ2 TRP   100      12.603  25.681  -7.620  1.00  9.99
ATOM    819  CZ3 TRP   100      13.712  27.095  -6.139  1.00  9.99
ATOM    820  CH2 TRP   100      13.765  26.084  -7.047  1.00  9.99
ATOM    821  C   TRP   100       8.530  30.596  -6.317  1.00  9.99
ATOM    822  O   TRP   100       8.246  31.506  -7.090  1.00  9.99
ATOM    823  N   SER   101       7.507  30.092  -5.640  1.00  9.99
ATOM    824  CA  SER   101       6.554  31.180  -5.570  1.00  9.99
ATOM    825  CB  SER   101       5.238  30.784  -4.893  1.00  9.99
ATOM    826  OG  SER   101       4.358  31.899  -4.857  1.00  9.99
ATOM    827  C   SER   101       7.371  31.930  -4.602  1.00  9.99
ATOM    828  O   SER   101       8.139  32.799  -4.905  1.00  9.99
ATOM    829  N   VAL   102       7.302  31.464  -3.394  1.00  9.99
ATOM    830  CA  VAL   102       8.357  31.523  -2.489  1.00  9.99
ATOM    831  CB  VAL   102       7.834  32.088  -1.199  1.00  9.99
ATOM    832  CG1 VAL   102       8.899  32.045  -0.096  1.00  9.99
ATOM    833  CG2 VAL   102       7.389  33.525  -1.525  1.00  9.99
ATOM    834  C   VAL   102       8.163  30.054  -2.709  1.00  9.99
ATOM    835  O   VAL   102       7.039  29.728  -3.063  1.00  9.99
ATOM    836  N   MET   103       9.051  29.087  -2.707  1.00  9.99
ATOM    837  CA  MET   103       8.524  27.742  -2.855  1.00  9.99
ATOM    838  CB  MET   103       9.179  26.647  -3.649  1.00  9.99
ATOM    839  CG  MET   103       7.988  25.954  -4.299  1.00  9.99
ATOM    840  SD  MET   103       6.882  27.142  -5.146  1.00  9.99
ATOM    841  CE  MET   103       5.779  25.922  -5.914  1.00  9.99
ATOM    842  C   MET   103       8.443  27.251  -1.515  1.00  9.99
ATOM    843  O   MET   103       8.134  26.102  -1.195  1.00  9.99
ATOM    844  N   ASP   104       8.845  28.127  -0.664  1.00  9.99
ATOM    845  CA  ASP   104       7.943  28.096   0.330  1.00  9.99
ATOM    846  CB  ASP   104       8.184  29.435   1.050  1.00  9.99
ATOM    847  CG  ASP   104       9.428  29.438   1.885  1.00  9.99
ATOM    848  OD1 ASP   104      10.283  28.536   1.696  1.00  9.99
ATOM    849  OD2 ASP   104       9.526  30.362   2.735  1.00  9.99
ATOM    850  C   ASP   104       6.810  28.414  -0.666  1.00  9.99
ATOM    851  O   ASP   104       6.705  29.612  -0.670  1.00  9.99
ATOM    852  N   HIS   105       5.959  27.493  -1.389  1.00  9.99
ATOM    853  CA  HIS   105       5.212  27.776  -2.583  1.00  9.99
ATOM    854  ND1 HIS   105       3.671  24.648  -1.925  1.00  9.99
ATOM    855  CG  HIS   105       4.420  25.404  -2.782  1.00  9.99
ATOM    856  CB  HIS   105       4.095  26.826  -2.982  1.00  9.99
ATOM    857  NE2 HIS   105       5.250  23.319  -2.744  1.00  9.99
ATOM    858  CD2 HIS   105       5.386  24.583  -3.276  1.00  9.99
ATOM    859  CE1 HIS   105       4.202  23.417  -1.946  1.00  9.99
ATOM    860  C   HIS   105       4.502  28.890  -1.970  1.00  9.99
ATOM    861  O   HIS   105       4.686  30.057  -2.302  1.00  9.99
ATOM    862  N   ARG   106       3.734  28.550  -0.933  1.00  9.99
ATOM    863  CA  ARG   106       3.346  29.620  -0.075  1.00  9.99
ATOM    864  CB  ARG   106       2.186  29.268   0.877  1.00  9.99
ATOM    865  CG  ARG   106       1.049  28.456   0.244  1.00  9.99
ATOM    866  CD  ARG   106      -0.204  29.247  -0.130  1.00  9.99
ATOM    867  NE  ARG   106      -1.219  28.255  -0.592  1.00  9.99
ATOM    868  CZ  ARG   106      -1.310  27.922  -1.913  1.00  9.99
ATOM    869  NH1 ARG   106      -0.527  28.555  -2.834  1.00  9.99
ATOM    870  NH2 ARG   106      -2.186  26.953  -2.308  1.00  9.99
ATOM    871  C   ARG   106       4.528  29.890   0.823  1.00  9.99
ATOM    872  O   ARG   106       5.201  30.911   0.732  1.00  9.99
ATOM    873  N   ASN   107       4.904  28.822   1.558  1.00  9.99
ATOM    874  CA  ASN   107       5.972  28.474   2.483  1.00  9.99
ATOM    875  CB  ASN   107       5.531  28.314   3.934  1.00  9.99
ATOM    876  CG  ASN   107       5.185  29.705   4.428  1.00  9.99
ATOM    877  OD1 ASN   107       5.943  30.657   4.245  1.00  9.99
ATOM    878  ND2 ASN   107       3.991  29.828   5.063  1.00  9.99
ATOM    879  C   ASN   107       6.075  27.145   1.904  1.00  9.99
ATOM    880  O   ASN   107       5.309  27.116   0.975  1.00  9.99
ATOM    881  N   LEU   108       7.109  26.260   2.154  1.00  9.99
ATOM    882  CA  LEU   108       7.413  25.073   1.341  1.00  9.99
ATOM    883  CB  LEU   108       7.845  23.906   2.236  1.00  9.99
ATOM    884  CG  LEU   108       9.140  24.242   3.009  1.00  9.99
ATOM    885  CD1 LEU   108       9.517  23.157   4.035  1.00  9.99
ATOM    886  CD2 LEU   108      10.292  24.550   2.039  1.00  9.99
ATOM    887  C   LEU   108       6.130  24.749   0.666  1.00  9.99
ATOM    888  O   LEU   108       5.941  25.072  -0.491  1.00  9.99
TER
END
