
#######################################################
#                                                     #
#                        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   19 (   76),  selected   19 , name T0386TS383_2-D2
# Molecule2: number of CA atoms   81 (  636),  selected   81 , name T0386_D2.pdb
# PARAMETERS: T0386TS383_2-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    N     219      K     222          3.563
LGA    P     220      I     223          1.968
LGA    K     222      R     224          2.049
LGA    I     223      L     225          3.651
LGA    R     224      L     226          2.086
LGA    -       -      K     227           -
LGA    L     225      E     228          0.692
LGA    -       -      F     229           -
LGA    -       -      M     230           -
LGA    L     226      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    K     227      G     262          2.321
LGA    -       -      L     263           -
LGA    E     228      E     264          2.031
LGA    F     229      G     265          1.718
LGA    M     230      F     266          2.460
LGA    H     231      A     267           -
LGA    -       -      L     268           -
LGA    -       -      N     269           -
LGA    -       -      V     270           -
LGA    -       -      K     271           -
LGA    -       -      G     272           -
LGA    -       -      A     273           -
LGA    -       -      Y     274           -
LGA    -       -      I     275           -
LGA    -       -      I     276           -
LGA    T     232      G     277          4.673
LGA    M     233      N     278          4.293
LGA    K     234      I     279          3.468
LGA    N     235      D     280          1.992
LGA    T     236      H     281          1.760
LGA    G     237      L     282          2.131
LGA    R     238      P     283          2.167
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           -
LGA    -       -      T     299           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   19   81    5.0     17    2.72     5.88     13.661     0.602

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.974496 * X  +   0.094532 * Y  +   0.203524 * Z  +  23.104782
  Y_new =   0.174469 * X  +   0.251237 * Y  +  -0.952072 * Z  +  48.776073
  Z_new =  -0.141134 * X  +   0.963298 * Y  +   0.228336 * Z  +  31.472588 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.338056   -1.803536  [ DEG:    76.6650   -103.3350 ]
  Theta =   0.141607    2.999985  [ DEG:     8.1135    171.8865 ]
  Phi   =   0.177159   -2.964434  [ DEG:    10.1504   -169.8496 ]
 
# 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: T0386TS383_2-D2                               
REMARK     2: T0386_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0386TS383_2-D2.T0386_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   19   81   5.0   17   2.72    5.88  13.661
REMARK  ---------------------------------------------------------- 
MOLECULE T0386TS383_2-D2
PFRMAT TS
TARGET T0386
MODEL 2
PARENT 2f6sA
ATOM    621  N   ASN   219       3.240  58.270  77.927  1.00  0.00
ATOM    622  CA  ASN   219       3.069  59.662  77.515  1.00  0.00
ATOM    623  C   ASN   219       3.815  59.938  76.220  1.00  0.00
ATOM    624  O   ASN   219       4.892  59.366  75.986  1.00  0.00
ATOM    625  N   PRO   220       3.239  60.814  75.392  1.00  0.00
ATOM    626  CA  PRO   220       3.895  61.322  74.179  1.00  0.00
ATOM    627  C   PRO   220       4.875  62.461  74.471  1.00  0.00
ATOM    628  O   PRO   220       5.672  62.839  73.620  1.00  0.00
ATOM    629  N   LYS   222       4.817  62.980  75.688  1.00  0.00
ATOM    630  CA  LYS   222       5.628  64.104  76.092  1.00  0.00
ATOM    631  C   LYS   222       7.041  63.677  76.496  1.00  0.00
ATOM    632  O   LYS   222       7.468  63.864  77.642  1.00  0.00
ATOM    633  N   ILE   223       7.774  63.134  75.536  1.00  0.00
ATOM    634  CA  ILE   223       9.000  62.393  75.836  1.00  0.00
ATOM    635  C   ILE   223      10.189  63.271  76.201  1.00  0.00
ATOM    636  O   ILE   223      11.257  62.761  76.564  1.00  0.00
ATOM    637  N   ARG   224      10.010  64.583  76.090  1.00  0.00
ATOM    638  CA  ARG   224      11.129  65.507  76.174  1.00  0.00
ATOM    639  C   ARG   224      11.016  66.524  77.299  1.00  0.00
ATOM    640  O   ARG   224      11.990  67.214  77.597  1.00  0.00
ATOM    641  N   LEU   225       9.836  66.629  77.911  1.00  0.00
ATOM    642  CA  LEU   225       9.650  67.524  79.042  1.00  0.00
ATOM    643  C   LEU   225      10.562  67.138  80.228  1.00  0.00
ATOM    644  O   LEU   225      10.395  66.051  80.820  1.00  0.00
ATOM    645  N   LEU   226      11.538  68.012  80.587  1.00  0.00
ATOM    646  CA  LEU   226      12.445  67.511  81.635  1.00  0.00
ATOM    647  C   LEU   226      11.785  67.468  83.032  1.00  0.00
ATOM    648  O   LEU   226      12.217  66.663  83.868  1.00  0.00
ATOM    649  N   LYS   227      10.738  68.270  83.271  1.00  0.00
ATOM    650  CA  LYS   227       9.972  68.145  84.528  1.00  0.00
ATOM    651  C   LYS   227       9.359  66.735  84.650  1.00  0.00
ATOM    652  O   LYS   227       9.535  66.047  85.668  1.00  0.00
ATOM    653  N   GLU   228       8.662  66.311  83.594  1.00  0.00
ATOM    654  CA  GLU   228       8.080  64.976  83.497  1.00  0.00
ATOM    655  C   GLU   228       9.140  63.885  83.707  1.00  0.00
ATOM    656  O   GLU   228       8.907  62.910  84.416  1.00  0.00
ATOM    657  N   PHE   229      10.303  64.079  83.098  1.00  0.00
ATOM    658  CA  PHE   229      11.381  63.112  83.161  1.00  0.00
ATOM    659  C   PHE   229      11.967  63.019  84.570  1.00  0.00
ATOM    660  O   PHE   229      12.225  61.923  85.066  1.00  0.00
ATOM    661  N   MET   230      12.146  64.164  85.219  1.00  0.00
ATOM    662  CA  MET   230      12.666  64.205  86.583  1.00  0.00
ATOM    663  C   MET   230      11.679  63.568  87.573  1.00  0.00
ATOM    664  O   MET   230      12.087  62.772  88.417  1.00  0.00
ATOM    665  N   HIS   231      10.395  63.904  87.455  1.00  0.00
ATOM    666  CA  HIS   231       9.355  63.236  88.237  1.00  0.00
ATOM    667  C   HIS   231       9.403  61.721  88.063  1.00  0.00
ATOM    668  O   HIS   231       9.274  60.972  89.034  1.00  0.00
ATOM    669  N   THR   232       9.610  61.285  86.824  1.00  0.00
ATOM    670  CA  THR   232       9.751  59.888  86.504  1.00  0.00
ATOM    671  C   THR   232      10.928  59.237  87.205  1.00  0.00
ATOM    672  O   THR   232      10.785  58.165  87.820  1.00  0.00
ATOM    673  N   MET   233      12.093  59.871  87.127  1.00  0.00
ATOM    674  CA  MET   233      13.297  59.280  87.694  1.00  0.00
ATOM    675  C   MET   233      13.258  59.304  89.213  1.00  0.00
ATOM    676  O   MET   233      13.740  58.384  89.847  1.00  0.00
ATOM    677  N   LYS   234      12.663  60.345  89.795  1.00  0.00
ATOM    678  CA  LYS   234      12.479  60.414  91.235  1.00  0.00
ATOM    679  C   LYS   234      11.647  59.211  91.698  1.00  0.00
ATOM    680  O   LYS   234      11.933  58.614  92.726  1.00  0.00
ATOM    681  N   ASN   235      10.627  58.842  90.933  1.00  0.00
ATOM    682  CA  ASN   235       9.781  57.724  91.303  1.00  0.00
ATOM    683  C   ASN   235      10.550  56.414  91.157  1.00  0.00
ATOM    684  O   ASN   235      10.440  55.524  92.010  1.00  0.00
ATOM    685  N   THR   236      11.343  56.311  90.088  1.00  0.00
ATOM    686  CA  THR   236      12.177  55.149  89.874  1.00  0.00
ATOM    687  C   THR   236      13.059  54.900  91.107  1.00  0.00
ATOM    688  O   THR   236      13.169  53.767  91.579  1.00  0.00
ATOM    689  N   GLY   237      13.679  55.961  91.626  1.00  0.00
ATOM    690  CA  GLY   237      14.521  55.861  92.825  1.00  0.00
ATOM    691  C   GLY   237      13.701  55.573  94.078  1.00  0.00
ATOM    692  O   GLY   237      14.168  54.897  95.002  1.00  0.00
ATOM    693  N   ARG   238      12.468  56.071  94.085  1.00  0.00
ATOM    694  CA  ARG   238      11.553  55.779  95.159  1.00  0.00
ATOM    695  C   ARG   238      11.211  54.293  95.237  1.00  0.00
ATOM    696  O   ARG   238      10.968  53.779  96.334  1.00  0.00
TER
END
