
#######################################################
#                                                     #
#                        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   12 (   97),  selected   12 , name T0385TS009_2_1
# Molecule2: number of CA atoms  142 ( 1050),  selected  142 , name T0385.pdb
# PARAMETERS: T0385TS009_2_1.T0385.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    H      64      S      17          3.957
LGA    R      65      E      18          1.174
LGA    R      66      G      19          1.794
LGA    D      67      S      20          1.160
LGA    D      68      A      21          2.496
LGA    -       -      D      22           -
LGA    V      69      N      23          0.284
LGA    I      70      A      24          0.483
LGA    V      71      A      25          0.669
LGA    M      72      L      26          0.681
LGA    L      73      C      27          1.430
LGA    S      74      D      28          1.509
LGA    -       -      A      29           -
LGA    -       -      L      30           -
LGA    -       -      A      31           -
LGA    -       -      V      32           -
LGA    -       -      E      33           -
LGA    -       -      H      34           -
LGA    -       -      A      35           -
LGA    -       -      T      36           -
LGA    -       -      I      37           -
LGA    -       -      Y      38           -
LGA    -       -      G      39           -
LGA    -       -      Y      40           -
LGA    -       -      G      41           -
LGA    -       -      I      42           -
LGA    -       -      V      43           -
LGA    -       -      S      44           -
LGA    -       -      A      45           -
LGA    -       -      L      46           -
LGA    -       -      S      47           -
LGA    -       -      P      48           -
LGA    -       -      P      49           -
LGA    -       -      G      50           -
LGA    -       -      V      51           -
LGA    -       -      N      52           -
LGA    -       -      F      53           -
LGA    -       -      L      54           -
LGA    -       -      V      55           -
LGA    -       -      A      56           -
LGA    -       -      D      57           -
LGA    -       -      A      58           -
LGA    -       -      L      59           -
LGA    -       -      K      60           -
LGA    -       -      Q      61           -
LGA    -       -      H      62           -
LGA    -       -      R      63           -
LGA    -       -      H      64           -
LGA    -       -      R      65           -
LGA    -       -      R      66           -
LGA    -       -      D      67           -
LGA    -       -      D      68           -
LGA    -       -      V      69           -
LGA    -       -      I      70           -
LGA    -       -      V      71           -
LGA    -       -      M      72           -
LGA    -       -      L      73           -
LGA    -       -      S      74           -
LGA    -       -      A      75           -
LGA    -       -      R      76           -
LGA    -       -      G      77           -
LGA    -       -      V      78           -
LGA    -       -      T      79           -
LGA    -       -      A      80           -
LGA    -       -      P      81           -
LGA    -       -      I      82           -
LGA    -       -      A      83           -
LGA    -       -      A      84           -
LGA    -       -      A      85           -
LGA    -       -      G      86           -
LGA    -       -      Y      87           -
LGA    -       -      Q      88           -
LGA    -       -      L      89           -
LGA    -       -      P      90           -
LGA    -       -      M      91           -
LGA    -       -      Q      92           -
LGA    -       -      V      93           -
LGA    -       -      S      94           -
LGA    -       -      S      95           -
LGA    -       -      A      96           -
LGA    -       -      A      97           -
LGA    -       -      D      98           -
LGA    -       -      A      99           -
LGA    -       -      A     100           -
LGA    -       -      R     101           -
LGA    -       -      L     102           -
LGA    -       -      A     103           -
LGA    -       -      V     104           -
LGA    -       -      R     105           -
LGA    -       -      M     106           -
LGA    -       -      E     107           -
LGA    -       -      N     108           -
LGA    -       -      D     109           -
LGA    -       -      G     110           -
LGA    -       -      A     111           -
LGA    -       -      T     112           -
LGA    A      75      A     113          3.297
LGA    -       -      W     114           -
LGA    -       -      R     115           -
LGA    -       -      A     116           -
LGA    -       -      V     117           -
LGA    -       -      V     118           -
LGA    -       -      E     119           -
LGA    -       -      H     120           -
LGA    -       -      A     121           -
LGA    -       -      E     122           -
LGA    -       -      T     123           -
LGA    -       -      A     124           -
LGA    -       -      D     125           -
LGA    -       -      D     126           -
LGA    -       -      R     127           -
LGA    -       -      V     128           -
LGA    -       -      F     129           -
LGA    -       -      A     130           -
LGA    -       -      S     131           -
LGA    -       -      T     132           -
LGA    -       -      A     133           -
LGA    -       -      L     134           -
LGA    -       -      T     135           -
LGA    -       -      E     136           -
LGA    -       -      S     137           -
LGA    -       -      A     138           -
LGA    -       -      V     139           -
LGA    -       -      M     140           -
LGA    -       -      A     141           -
LGA    -       -      T     142           -
LGA    -       -      R     143           -
LGA    -       -      W     144           -
LGA    -       -      N     145           -
LGA    -       -      R     146           -
LGA    -       -      V     147           -
LGA    -       -      L     148           -
LGA    -       -      G     149           -
LGA    -       -      A     150           -
LGA    -       -      W     151           -
LGA    -       -      P     152           -
LGA    -       -      I     153           -
LGA    -       -      T     154           -
LGA    -       -      A     155           -
LGA    -       -      A     156           -
LGA    -       -      F     157           -
LGA    -       -      P     158           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   12  142    5.0     12    1.92     8.33      7.694     0.594

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.597532 * X  +  -0.184337 * Y  +   0.780369 * Z  +  26.184853
  Y_new =   0.791216 * X  +  -0.293486 * Y  +   0.536511 * Z  + -23.382959
  Z_new =   0.130129 * X  +   0.938022 * Y  +   0.321218 * Z  + 103.064117 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.240871   -1.900721  [ DEG:    71.0967   -108.9033 ]
  Theta =  -0.130499   -3.011094  [ DEG:    -7.4770   -172.5230 ]
  Phi   =   2.217622   -0.923971  [ DEG:   127.0604    -52.9396 ]
 
# 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: T0385TS009_2_1                                
REMARK     2: T0385.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0385TS009_2_1.T0385.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   12  142   5.0   12   1.92    8.33   7.694
REMARK  ---------------------------------------------------------- 
MOLECULE T0385TS009_2_1
REMARK PARENT number 1
PFRMAT TS                                                                       
TARGET T0385                                                                    
PARENT N/A                                                                      
ATOM    453  N   HIS    64      20.530  14.251  45.904  1.00  0.00              
ATOM    454  CA  HIS    64      20.541  15.345  44.939  1.00  0.00              
ATOM    455  C   HIS    64      21.477  16.462  45.386  1.00  0.00              
ATOM    456  O   HIS    64      22.294  16.950  44.604  1.00  0.00              
ATOM    457  CB  HIS    64      20.951  14.835  43.557  1.00  0.00              
ATOM    458  CG  HIS    64      20.031  15.267  42.457  1.00  0.00              
ATOM    459  ND1 HIS    64      18.793  15.823  42.698  1.00  0.00              
ATOM    460  CD2 HIS    64      20.169  15.225  41.110  1.00  0.00              
ATOM    461  CE1 HIS    64      18.209  16.104  41.546  1.00  0.00              
ATOM    462  NE2 HIS    64      19.020  15.751  40.568  1.00  0.00              
ATOM    463  N   ARG    65      21.352  16.865  46.646  1.00  0.00              
ATOM    464  CA  ARG    65      22.186  17.926  47.197  1.00  0.00              
ATOM    465  C   ARG    65      23.655  17.708  46.854  1.00  0.00              
ATOM    466  O   ARG    65      24.186  18.330  45.934  1.00  0.00              
ATOM    467  CB  ARG    65      21.723  19.292  46.686  1.00  0.00              
ATOM    468  CG  ARG    65      21.643  20.363  47.762  1.00  0.00              
ATOM    469  CD  ARG    65      20.936  21.608  47.251  1.00  0.00              
ATOM    470  NE  ARG    65      20.409  22.424  48.340  1.00  0.00              
ATOM    471  CZ  ARG    65      20.997  23.520  48.806  1.00  0.00              
ATOM    472  NH1 ARG    65      22.139  23.936  48.274  1.00  0.00              
ATOM    473  NH2 ARG    65      20.444  24.199  49.800  1.00  0.00              
ATOM    474  N   ARG    66      24.307  16.821  47.599  1.00  0.00              
ATOM    475  CA  ARG    66      25.715  16.519  47.374  1.00  0.00              
ATOM    476  C   ARG    66      25.889  15.502  46.250  1.00  0.00              
ATOM    477  O   ARG    66      26.629  15.740  45.296  1.00  0.00              
ATOM    478  CB  ARG    66      26.493  17.798  47.052  1.00  0.00              
ATOM    479  CG  ARG    66      27.606  18.111  48.038  1.00  0.00              
ATOM    480  CD  ARG    66      28.568  19.143  47.474  1.00  0.00              
ATOM    481  NE  ARG    66      29.634  19.470  48.416  1.00  0.00              
ATOM    482  CZ  ARG    66      30.807  18.846  48.465  1.00  0.00              
ATOM    483  NH1 ARG    66      31.067  17.857  47.621  1.00  0.00              
ATOM    484  NH2 ARG    66      31.716  19.213  49.357  1.00  0.00              
ATOM    485  N   ASP    67      25.203  14.371  46.372  1.00  0.00              
ATOM    486  CA  ASP    67      25.280  13.317  45.367  1.00  0.00              
ATOM    487  C   ASP    67      25.278  13.897  43.957  1.00  0.00              
ATOM    488  O   ASP    67      25.802  13.290  43.024  1.00  0.00              
ATOM    489  CB  ASP    67      26.532  12.463  45.582  1.00  0.00              
ATOM    490  CG  ASP    67      26.208  10.994  45.780  1.00  0.00              
ATOM    491  OD1 ASP    67      27.120  10.157  45.613  1.00  0.00              
ATOM    492  OD2 ASP    67      25.043  10.682  46.103  1.00  0.00              
ATOM    493  N   ASP    68      24.685  15.077  43.810  1.00  0.00              
ATOM    494  CA  ASP    68      24.612  15.742  42.514  1.00  0.00              
ATOM    495  C   ASP    68      25.255  14.894  41.422  1.00  0.00              
ATOM    496  O   ASP    68      24.920  15.022  40.245  1.00  0.00              
ATOM    497  CB  ASP    68      23.160  16.054  42.151  1.00  0.00              
ATOM    498  CG  ASP    68      23.024  17.312  41.316  1.00  0.00              
ATOM    499  OD1 ASP    68      22.168  17.331  40.406  1.00  0.00              
ATOM    500  OD2 ASP    68      23.773  18.278  41.572  1.00  0.00              
ATOM    501  N   VAL    69      26.180  14.026  41.821  1.00  0.00              
ATOM    502  CA  VAL    69      26.886  13.136  40.857  1.00  0.00              
ATOM    503  C   VAL    69      25.951  12.676  39.743  1.00  0.00              
ATOM    504  O   VAL    69      26.251  12.840  38.561  1.00  0.00              
ATOM    505  CB  VAL    69      28.108  13.836  40.232  1.00  0.00              
ATOM    506  CG1 VAL    69      29.398  13.236  40.768  1.00  0.00              
ATOM    507  CG2 VAL    69      28.057  15.333  40.497  1.00  0.00              
ATOM    508  N   ILE    70      24.817  12.100  40.129  1.00  0.00              
ATOM    509  CA  ILE    70      23.815  11.606  39.143  1.00  0.00              
ATOM    510  C   ILE    70      23.794  12.477  37.893  1.00  0.00              
ATOM    511  O   ILE    70      23.675  11.973  36.775  1.00  0.00              
ATOM    512  CB  ILE    70      24.095  10.147  38.736  1.00  0.00              
ATOM    513  CG2 ILE    70      23.255   9.191  39.570  1.00  0.00              
ATOM    514  CG1 ILE    70      25.584   9.828  38.887  1.00  0.00              
ATOM    515  CD1 ILE    70      25.861   8.433  39.400  1.00  0.00              
ATOM    516  N   VAL    71      23.912  13.787  38.088  1.00  0.00              
ATOM    517  CA  VAL    71      23.908  14.752  36.951  1.00  0.00              
ATOM    518  C   VAL    71      24.903  14.337  35.872  1.00  0.00              
ATOM    519  O   VAL    71      24.561  14.267  34.692  1.00  0.00              
ATOM    520  CB  VAL    71      22.507  14.877  36.322  1.00  0.00              
ATOM    521  CG1 VAL    71      21.785  16.098  36.871  1.00  0.00              
ATOM    522  CG2 VAL    71      21.697  13.614  36.570  1.00  0.00              
ATOM    523  N   MET    72      26.137  14.066  36.285  1.00  0.00              
ATOM    524  CA  MET    72      27.184  13.659  35.356  1.00  0.00              
ATOM    525  C   MET    72      26.729  12.489  34.490  1.00  0.00              
ATOM    526  O   MET    72      27.258  12.268  33.402  1.00  0.00              
ATOM    527  CB  MET    72      27.603  14.836  34.473  1.00  0.00              
ATOM    528  CG  MET    72      28.943  15.449  34.849  1.00  0.00              
ATOM    529  SD  MET    72      29.934  15.894  33.410  1.00  0.00              
ATOM    530  CE  MET    72      31.052  17.094  34.128  1.00  0.00              
ATOM    531  N   LEU    73      25.744  11.744  34.982  1.00  0.00              
ATOM    532  CA  LEU    73      25.216  10.596  34.253  1.00  0.00              
ATOM    533  C   LEU    73      24.260  11.036  33.150  1.00  0.00              
ATOM    534  O   LEU    73      24.507  10.794  31.969  1.00  0.00              
ATOM    535  CB  LEU    73      26.357   9.766  33.662  1.00  0.00              
ATOM    536  CG  LEU    73      26.755   8.509  34.439  1.00  0.00              
ATOM    537  CD1 LEU    73      27.190   7.404  33.489  1.00  0.00              
ATOM    538  CD2 LEU    73      25.611   8.041  35.326  1.00  0.00              
ATOM    539  N   SER    74      23.168  11.682  33.543  1.00  0.00              
ATOM    540  CA  SER    74      22.173  12.156  32.589  1.00  0.00              
ATOM    541  C   SER    74      22.234  13.672  32.435  1.00  0.00              
ATOM    542  O   SER    74      23.053  14.196  31.678  1.00  0.00              
ATOM    543  CB  SER    74      22.369  11.480  31.229  1.00  0.00              
ATOM    544  OG  SER    74      21.129  11.283  30.574  1.00  0.00              
ATOM    545  N   ALA    75      21.364  14.371  33.155  1.00  0.00              
ATOM    546  CA  ALA    75      21.318  15.826  33.099  1.00  0.00              
ATOM    547  C   ALA    75      22.080  16.448  34.265  1.00  0.00              
ATOM    548  O   ALA    75      21.844  17.600  34.630  1.00  0.00              
ATOM    549  CB  ALA    75      21.883  16.326  31.778  1.00  0.00              
TER
END
