
#######################################################
#                                                     #
#                        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   17 (   68),  selected   17 , name T0298TS550_2_2-D1
# Molecule2: number of CA atoms  148 ( 1074),  selected  148 , name T0298_D1.pdb
# PARAMETERS: T0298TS550_2_2-D1.T0298_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      Q       3           -
LGA    -       -      P       4           -
LGA    -       -      L       5           -
LGA    -       -      N       6           -
LGA    -       -      V       7           -
LGA    -       -      A       8           -
LGA    -       -      V       9           -
LGA    -       -      V      10           -
LGA    -       -      G      11           -
LGA    -       -      A      12           -
LGA    -       -      T      13           -
LGA    -       -      G      14           -
LGA    -       -      S      15           -
LGA    -       -      V      16           -
LGA    -       -      G      17           -
LGA    -       -      E      18           -
LGA    -       -      A      19           -
LGA    -       -      L      20           -
LGA    -       -      V      21           -
LGA    -       -      G      22           -
LGA    -       -      L      23           -
LGA    -       -      L      24           -
LGA    -       -      D      25           -
LGA    -       -      E      26           -
LGA    -       -      R      27           -
LGA    -       -      D      28           -
LGA    -       -      F      29           -
LGA    -       -      P      30           -
LGA    -       -      L      31           -
LGA    -       -      H      32           -
LGA    -       -      R      33           -
LGA    -       -      L      34           -
LGA    -       -      H      35           -
LGA    -       -      L      36           -
LGA    -       -      L      37           -
LGA    -       -      A      38           -
LGA    -       -      S      39           -
LGA    -       -      A      40           -
LGA    -       -      E      41           -
LGA    -       -      S      42           -
LGA    -       -      A      43           -
LGA    -       -      G      44           -
LGA    -       -      Q      45           -
LGA    -       -      R      46           -
LGA    -       -      M      47           -
LGA    -       -      G      48           -
LGA    -       -      F      49           -
LGA    -       -      A      50           -
LGA    -       -      E      51           -
LGA    -       -      S      52           -
LGA    -       -      S      53           -
LGA    -       -      L      54           -
LGA    -       -      R      55           -
LGA    -       -      V      56           -
LGA    -       -      G      57           -
LGA    -       -      D      58           -
LGA    -       -      V      59           -
LGA    -       -      D      60           -
LGA    -       -      S      61           -
LGA    -       -      F      62           -
LGA    -       -      D      63           -
LGA    -       -      F      64           -
LGA    -       -      S      65           -
LGA    -       -      S      66           -
LGA    -       -      V      67           -
LGA    -       -      G      68           -
LGA    -       -      L      69           -
LGA    -       -      A      70           -
LGA    -       -      F      71           -
LGA    -       -      F      72           -
LGA    -       -      A      73           -
LGA    -       -      A      74           -
LGA    -       -      A      75           -
LGA    -       -      A      76           -
LGA    -       -      E      77           -
LGA    -       -      V      78           -
LGA    V     316      S      79          3.584
LGA    -       -      R      80           -
LGA    -       -      A      81           -
LGA    -       -      H      82           -
LGA    -       -      A      83           -
LGA    -       -      E      84           -
LGA    -       -      R      85           -
LGA    -       -      A      86           -
LGA    -       -      R      87           -
LGA    -       -      A      88           -
LGA    -       -      A      89           -
LGA    -       -      G      90           -
LGA    -       -      C      91           -
LGA    -       -      S      92           -
LGA    -       -      V      93           -
LGA    -       -      I      94           -
LGA    R     317      D      95          1.084
LGA    K     318      L      96          1.577
LGA    -       -      S      97           -
LGA    -       -      G      98           -
LGA    -       -      A      99           -
LGA    -       -      L     100           -
LGA    -       -      E     101           -
LGA    -       -      P     102           -
LGA    -       -      S     103           -
LGA    -       -      V     104           -
LGA    -       -      A     105           -
LGA    -       -      P     106           -
LGA    -       -      P     107           -
LGA    -       -      V     108           -
LGA    -       -      M     109           -
LGA    -       -      V     110           -
LGA    -       -      S     111           -
LGA    -       -      V     112           -
LGA    -       -      N     113           -
LGA    -       -      A     114           -
LGA    -       -      E     115           -
LGA    -       -      R     116           -
LGA    -       -      L     117           -
LGA    -       -      A     118           -
LGA    -       -      S     119           -
LGA    -       -      Q     120           -
LGA    -       -      A     121           -
LGA    -       -      A     122           -
LGA    -       -      P     123           -
LGA    -       -      F     124           -
LGA    -       -      L     125           -
LGA    -       -      L     126           -
LGA    -       -      S     127           -
LGA    G     319      S     128          3.755
LGA    -       -      P     129           -
LGA    -       -      V     316           -
LGA    -       -      R     317           -
LGA    -       -      K     318           -
LGA    -       -      G     319           -
LGA    A     320      A     320          1.247
LGA    A     321      A     321          0.959
LGA    L     322      L     322          0.723
LGA    N     323      N     323          0.267
LGA    A     324      A     324          0.749
LGA    V     325      V     325          0.782
LGA    L     326      L     326          0.557
LGA    L     327      L     327          0.594
LGA    G     328      G     328          0.639
LGA    E     329      E     329          0.791
LGA    L     330      L     330          0.902
LGA    L     331      L     331          0.563
LGA    I     332      I     332          0.489
LGA    -       -      K     333           -
LGA    -       -      H     334           -
LGA    -       -      Y     335           -
LGA    -       -      L     336           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   17  148    5.0     17    1.49    76.47     11.042     1.067

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.057987 * X  +  -0.998309 * Y  +  -0.003978 * Z  + -44.946648
  Y_new =   0.366699 * X  +   0.025005 * Y  +  -0.930003 * Z  +  75.072708
  Z_new =   0.928531 * X  +   0.052469 * Y  +   0.367529 * Z  +  18.853148 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.141803   -2.999789  [ DEG:     8.1247   -171.8753 ]
  Theta =  -1.190435   -1.951157  [ DEG:   -68.2069   -111.7931 ]
  Phi   =   1.413964   -1.727629  [ DEG:    81.0142    -98.9858 ]
 
# 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: T0298TS550_2_2-D1                             
REMARK     2: T0298_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0298TS550_2_2-D1.T0298_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   17  148   5.0   17   1.49   76.47  11.042
REMARK  ---------------------------------------------------------- 
MOLECULE T0298TS550_2_2-D1
REMARK PARENT number 2
PFRMAT TS
TARGET T0298
PARENT 1u28_C
ATOM    661  N   VAL   316     -14.832  70.557 -13.607  1.00  0.00
ATOM    662  CA  VAL   316     -14.521  70.378 -12.177  1.00  0.00
ATOM    663  C   VAL   316     -15.323  71.362 -11.331  1.00  0.00
ATOM    664  O   VAL   316     -15.702  72.433 -11.806  1.00  0.00
ATOM    665  N   ARG   317     -15.588  70.961 -10.090  1.00  0.00
ATOM    666  CA  ARG   317     -16.195  71.844  -9.087  1.00  0.00
ATOM    667  C   ARG   317     -15.309  71.794  -7.841  1.00  0.00
ATOM    668  O   ARG   317     -15.373  70.827  -7.078  1.00  0.00
ATOM    669  N   LYS   318     -14.492  72.823  -7.652  1.00  0.00
ATOM    670  CA  LYS   318     -13.456  72.800  -6.609  1.00  0.00
ATOM    671  C   LYS   318     -13.903  73.362  -5.274  1.00  0.00
ATOM    672  O   LYS   318     -13.667  74.527  -4.963  1.00  0.00
ATOM    673  N   GLY   319     -13.598  72.534  -3.942  1.00  0.00
ATOM    674  CA  GLY   319     -13.961  72.953  -2.601  1.00  0.00
ATOM    675  C   GLY   319     -14.626  71.812  -1.839  1.00  0.00
ATOM    676  O   GLY   319     -14.697  70.677  -2.332  1.00  0.00
ATOM    677  N   ALA   320     -15.121  72.103  -0.643  1.00  0.00
ATOM    678  CA  ALA   320     -15.776  71.097   0.168  1.00  0.00
ATOM    679  C   ALA   320     -17.009  70.536  -0.535  1.00  0.00
ATOM    680  O   ALA   320     -17.881  71.284  -0.961  1.00  0.00
ATOM    681  N   ALA   321     -17.263  68.984  -0.417  1.00  0.00
ATOM    682  CA  ALA   321     -18.385  68.294  -1.033  1.00  0.00
ATOM    683  C   ALA   321     -19.704  68.682  -0.392  1.00  0.00
ATOM    684  O   ALA   321     -20.750  68.675  -1.046  1.00  0.00
ATOM    685  N   LEU   322     -19.658  68.999   0.901  1.00  0.00
ATOM    686  CA  LEU   322     -20.830  69.436   1.641  1.00  0.00
ATOM    687  C   LEU   322     -21.165  70.882   1.242  1.00  0.00
ATOM    688  O   LEU   322     -22.326  71.186   0.936  1.00  0.00
ATOM    689  N   ASN   323     -20.163  71.752   1.224  1.00  0.00
ATOM    690  CA  ASN   323     -20.347  73.168   0.859  1.00  0.00
ATOM    691  C   ASN   323     -20.828  73.366  -0.578  1.00  0.00
ATOM    692  O   ASN   323     -21.805  74.077  -0.830  1.00  0.00
ATOM    693  N   ALA   324     -20.132  72.731  -1.523  1.00  0.00
ATOM    694  CA  ALA   324     -20.476  72.797  -2.939  1.00  0.00
ATOM    695  C   ALA   324     -21.913  72.379  -3.222  1.00  0.00
ATOM    696  O   ALA   324     -22.599  73.029  -4.007  1.00  0.00
ATOM    697  N   VAL   325     -22.367  71.313  -2.579  1.00  0.00
ATOM    698  CA  VAL   325     -23.678  70.747  -2.855  1.00  0.00
ATOM    699  C   VAL   325     -24.786  71.601  -2.230  1.00  0.00
ATOM    700  O   VAL   325     -25.825  71.839  -2.862  1.00  0.00
ATOM    701  N   LEU   326     -24.559  72.057  -0.992  1.00  0.00
ATOM    702  CA  LEU   326     -25.431  73.031  -0.331  1.00  0.00
ATOM    703  C   LEU   326     -25.648  74.251  -1.219  1.00  0.00
ATOM    704  O   LEU   326     -26.780  74.676  -1.435  1.00  0.00
ATOM    705  N   LEU   327     -24.538  74.810  -1.725  1.00  0.00
ATOM    706  CA  LEU   327     -24.587  75.972  -2.622  1.00  0.00
ATOM    707  C   LEU   327     -25.412  75.698  -3.895  1.00  0.00
ATOM    708  O   LEU   327     -26.175  76.559  -4.338  1.00  0.00
ATOM    709  N   GLY   328     -25.241  74.516  -4.462  1.00  0.00
ATOM    710  CA  GLY   328     -25.936  74.128  -5.697  1.00  0.00
ATOM    711  C   GLY   328     -27.449  74.041  -5.472  1.00  0.00
ATOM    712  O   GLY   328     -28.227  74.418  -6.348  1.00  0.00
ATOM    713  N   GLU   329     -27.861  73.547  -4.303  1.00  0.00
ATOM    714  CA  GLU   329     -29.286  73.482  -3.941  1.00  0.00
ATOM    715  C   GLU   329     -29.940  74.880  -3.892  1.00  0.00
ATOM    716  O   GLU   329     -31.098  75.039  -4.292  1.00  0.00
ATOM    717  N   LEU   330     -29.207  75.855  -3.375  1.00  0.00
ATOM    718  CA  LEU   330     -29.697  77.229  -3.252  1.00  0.00
ATOM    719  C   LEU   330     -29.844  77.862  -4.645  1.00  0.00
ATOM    720  O   LEU   330     -30.801  78.604  -4.900  1.00  0.00
ATOM    721  N   LEU   331     -28.918  77.544  -5.546  1.00  0.00
ATOM    722  CA  LEU   331     -29.001  77.951  -6.940  1.00  0.00
ATOM    723  C   LEU   331     -30.092  77.216  -7.724  1.00  0.00
ATOM    724  O   LEU   331     -30.450  77.632  -8.824  1.00  0.00
ATOM    725  N   ILE   332     -30.602  76.123  -7.174  1.00  0.00
ATOM    726  CA  ILE   332     -31.657  75.339  -7.811  1.00  0.00
ATOM    727  C   ILE   332     -33.037  75.950  -7.503  1.00  0.00
ATOM    728  O   ILE   332     -33.994  75.743  -8.255  1.00  0.00
TER
END
