
#######################################################
#                                                     #
#                        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   18 (   72),  selected   18 , name T0298TS550_3_2-D1
# Molecule2: number of CA atoms  148 ( 1074),  selected  148 , name T0298_D1.pdb
# PARAMETERS: T0298TS550_3_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     316      V      16          2.071
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    -       -      S      79           -
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    -       -      D      95           -
LGA    -       -      L      96           -
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    -       -      S     128           -
LGA    -       -      P     129           -
LGA    R     317      V     316          3.148
LGA    -       -      R     317           -
LGA    -       -      K     318           -
LGA    -       -      G     319           -
LGA    K     318      A     320          1.181
LGA    G     319      A     321          1.012
LGA    A     320      L     322          0.506
LGA    A     321      N     323          0.585
LGA    L     322      A     324          0.850
LGA    N     323      V     325          1.005
LGA    A     324      L     326          0.609
LGA    V     325      L     327          0.829
LGA    L     326      G     328          0.699
LGA    L     327      E     329          0.223
LGA    G     328      L     330          0.635
LGA    E     329      L     331          0.833
LGA    L     330      I     332          0.681
LGA    L     331      K     333          0.605
LGA    I     332      H     334          1.347
LGA    K     333      Y     335          1.666
LGA    -       -      L     336           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   18  148    5.0     18    1.23     5.56     11.759     1.357

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.773480 * X  +   0.631281 * Y  +   0.056677 * Z  +  32.552151
  Y_new =   0.626887 * X  +   0.748764 * Y  +   0.215326 * Z  + -57.464775
  Z_new =   0.093493 * X  +   0.202080 * Y  +  -0.974896 * Z  +  58.178501 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.937203   -0.204389  [ DEG:   168.2894    -11.7106 ]
  Theta =  -0.093630   -3.047963  [ DEG:    -5.3646   -174.6354 ]
  Phi   =   2.460496   -0.681096  [ DEG:   140.9761    -39.0239 ]
 
# 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_3_2-D1                             
REMARK     2: T0298_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0298TS550_3_2-D1.T0298_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   18  148   5.0   18   1.23    5.56  11.759
REMARK  ---------------------------------------------------------- 
MOLECULE T0298TS550_3_2-D1
REMARK PARENT number 2
PFRMAT TS
TARGET T0298
PARENT 1f2k_B
ATOM    545  N   VAL   316     -13.103  62.064   0.155  1.00  0.00
ATOM    546  CA  VAL   316     -13.449  63.201  -0.687  1.00  0.00
ATOM    547  C   VAL   316     -13.653  64.420   0.213  1.00  0.00
ATOM    548  O   VAL   316     -13.860  64.264   1.408  1.00  0.00
ATOM    549  N   ARG   317     -13.491  65.593  -0.360  1.00  0.00
ATOM    550  CA  ARG   317     -13.663  66.835   0.373  1.00  0.00
ATOM    551  C   ARG   317     -15.044  67.419   0.031  1.00  0.00
ATOM    552  O   ARG   317     -15.387  67.627  -1.136  1.00  0.00
ATOM    553  N   LYS   318     -16.144  68.374   1.801  1.00  0.00
ATOM    554  CA  LYS   318     -16.334  69.064   0.531  1.00  0.00
ATOM    555  C   LYS   318     -17.717  68.882  -0.053  1.00  0.00
ATOM    556  O   LYS   318     -18.327  69.826  -0.555  1.00  0.00
ATOM    557  N   GLY   319     -18.234  67.673   0.036  1.00  0.00
ATOM    558  CA  GLY   319     -19.534  67.416  -0.557  1.00  0.00
ATOM    559  C   GLY   319     -20.658  68.136   0.137  1.00  0.00
ATOM    560  O   GLY   319     -21.644  68.486  -0.506  1.00  0.00
ATOM    561  N   ALA   320     -20.510  68.369   1.441  1.00  0.00
ATOM    562  CA  ALA   320     -21.551  69.040   2.208  1.00  0.00
ATOM    563  C   ALA   320     -21.624  70.481   1.723  1.00  0.00
ATOM    564  O   ALA   320     -22.723  71.044   1.487  1.00  0.00
ATOM    565  N   ALA   321     -20.441  71.071   1.569  1.00  0.00
ATOM    566  CA  ALA   321     -20.347  72.434   1.081  1.00  0.00
ATOM    567  C   ALA   321     -21.078  72.561  -0.280  1.00  0.00
ATOM    568  O   ALA   321     -21.963  73.391  -0.418  1.00  0.00
ATOM    569  N   LEU   322     -20.742  71.715  -1.248  1.00  0.00
ATOM    570  CA  LEU   322     -21.357  71.748  -2.571  1.00  0.00
ATOM    571  C   LEU   322     -22.877  71.643  -2.492  1.00  0.00
ATOM    572  O   LEU   322     -23.587  72.356  -3.167  1.00  0.00
ATOM    573  N   ASN   323     -23.373  70.737  -1.671  1.00  0.00
ATOM    574  CA  ASN   323     -24.806  70.557  -1.529  1.00  0.00
ATOM    575  C   ASN   323     -25.435  71.860  -1.036  1.00  0.00
ATOM    576  O   ASN   323     -26.475  72.287  -1.548  1.00  0.00
ATOM    577  N   ALA   324     -24.821  72.509  -0.058  1.00  0.00
ATOM    578  CA  ALA   324     -25.422  73.737   0.429  1.00  0.00
ATOM    579  C   ALA   324     -25.505  74.792  -0.654  1.00  0.00
ATOM    580  O   ALA   324     -26.599  75.224  -0.991  1.00  0.00
ATOM    581  N   VAL   325     -24.358  75.160  -1.223  1.00  0.00
ATOM    582  CA  VAL   325     -24.295  76.140  -2.306  1.00  0.00
ATOM    583  C   VAL   325     -25.144  75.763  -3.530  1.00  0.00
ATOM    584  O   VAL   325     -25.857  76.598  -4.074  1.00  0.00
ATOM    585  N   LEU   326     -25.055  74.519  -3.978  1.00  0.00
ATOM    586  CA  LEU   326     -25.826  74.101  -5.137  1.00  0.00
ATOM    587  C   LEU   326     -27.319  74.154  -4.857  1.00  0.00
ATOM    588  O   LEU   326     -28.107  74.365  -5.762  1.00  0.00
ATOM    589  N   LEU   327     -27.705  73.978  -3.600  1.00  0.00
ATOM    590  CA  LEU   327     -29.122  74.000  -3.230  1.00  0.00
ATOM    591  C   LEU   327     -29.634  75.395  -3.393  1.00  0.00
ATOM    592  O   LEU   327     -30.682  75.635  -4.007  1.00  0.00
ATOM    593  N   GLY   328     -28.899  76.315  -2.792  1.00  0.00
ATOM    594  CA  GLY   328     -29.255  77.713  -2.845  1.00  0.00
ATOM    595  C   GLY   328     -29.356  78.100  -4.320  1.00  0.00
ATOM    596  O   GLY   328     -30.370  78.618  -4.748  1.00  0.00
ATOM    597  N   GLU   329     -28.333  77.800  -5.115  1.00  0.00
ATOM    598  CA  GLU   329     -28.410  78.120  -6.546  1.00  0.00
ATOM    599  C   GLU   329     -29.702  77.580  -7.153  1.00  0.00
ATOM    600  O   GLU   329     -30.477  78.331  -7.759  1.00  0.00
ATOM    601  N   LEU   330     -29.963  76.287  -6.974  1.00  0.00
ATOM    602  CA  LEU   330     -31.184  75.725  -7.539  1.00  0.00
ATOM    603  C   LEU   330     -32.395  76.541  -7.074  1.00  0.00
ATOM    604  O   LEU   330     -33.355  76.727  -7.815  1.00  0.00
ATOM    605  N   LEU   331     -32.365  77.004  -5.836  1.00  0.00
ATOM    606  CA  LEU   331     -33.505  77.755  -5.338  1.00  0.00
ATOM    607  C   LEU   331     -33.618  79.087  -6.119  1.00  0.00
ATOM    608  O   LEU   331     -34.669  79.449  -6.708  1.00  0.00
ATOM    609  N   ILE   332     -32.504  79.807  -6.144  1.00  0.00
ATOM    610  CA  ILE   332     -32.497  81.070  -6.820  1.00  0.00
ATOM    611  C   ILE   332     -32.913  80.931  -8.272  1.00  0.00
ATOM    612  O   ILE   332     -33.852  81.611  -8.684  1.00  0.00
ATOM    613  N   LYS   333     -32.257  80.060  -9.042  1.00  0.00
ATOM    614  CA  LYS   333     -32.635  79.911 -10.445  1.00  0.00
ATOM    615  C   LYS   333     -34.177  79.691 -10.558  1.00  0.00
ATOM    616  O   LYS   333     -34.822  80.144 -11.509  1.00  0.00
TER
END
