
#######################################################
#                                                     #
#                        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    8 (   61),  selected    8 , name T0385TS009_1_3
# Molecule2: number of CA atoms  142 ( 1050),  selected  142 , name T0385.pdb
# PARAMETERS: T0385TS009_1_3.T0385.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      S      17           -
LGA    -       -      E      18           -
LGA    -       -      G      19           -
LGA    -       -      S      20           -
LGA    -       -      A      21           -
LGA    -       -      D      22           -
LGA    -       -      N      23           -
LGA    -       -      A      24           -
LGA    -       -      A      25           -
LGA    -       -      L      26           -
LGA    -       -      C      27           -
LGA    -       -      D      28           -
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    E     119      V     104          1.124
LGA    H     120      R     105          0.661
LGA    A     121      M     106          1.128
LGA    E     122      E     107          0.837
LGA    T     123      N     108          2.556
LGA    -       -      D     109           -
LGA    A     124      G     110          1.293
LGA    -       -      A     111           -
LGA    -       -      T     112           -
LGA    -       -      A     113           -
LGA    -       -      W     114           -
LGA    D     125      R     115          4.825
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    D     126      L     134          1.543
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)    8  142    5.0      8    2.17    12.50      4.530     0.353

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.333498 * X  +  -0.924977 * Y  +  -0.182198 * Z  +  71.192680
  Y_new =   0.485220 * X  +  -0.334110 * Y  +   0.808042 * Z  +  14.672171
  Z_new =  -0.808295 * X  +   0.181074 * Y  +   0.560242 * Z  +  -1.350342 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.312609   -2.828983  [ DEG:    17.9112   -162.0888 ]
  Theta =   0.941250    2.200343  [ DEG:    53.9297    126.0703 ]
  Phi   =   2.172957   -0.968635  [ DEG:   124.5013    -55.4987 ]
 
# 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_1_3                                
REMARK     2: T0385.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0385TS009_1_3.T0385.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:    8  142   5.0    8   2.17   12.50   4.530
REMARK  ---------------------------------------------------------- 
MOLECULE T0385TS009_1_3
REMARK PARENT number 3
PFRMAT TS                                                                       
TARGET T0385                                                                    
PARENT N/A                                                                      
ATOM    858  N   GLU   119      20.082  19.878  16.981  1.00  0.00              
ATOM    859  CA  GLU   119      20.551  18.609  16.436  1.00  0.00              
ATOM    860  C   GLU   119      19.845  17.431  17.098  1.00  0.00              
ATOM    861  O   GLU   119      20.492  16.514  17.605  1.00  0.00              
ATOM    862  CB  GLU   119      20.338  18.567  14.922  1.00  0.00              
ATOM    863  CG  GLU   119      21.515  19.089  14.114  1.00  0.00              
ATOM    864  CD  GLU   119      21.656  18.396  12.773  1.00  0.00              
ATOM    865  OE1 GLU   119      20.695  17.718  12.351  1.00  0.00              
ATOM    866  OE2 GLU   119      22.727  18.530  12.145  1.00  0.00              
ATOM    867  N   HIS   120      18.517  17.461  17.090  1.00  0.00              
ATOM    868  CA  HIS   120      17.723  16.396  17.689  1.00  0.00              
ATOM    869  C   HIS   120      18.270  16.002  19.057  1.00  0.00              
ATOM    870  O   HIS   120      17.856  16.544  20.081  1.00  0.00              
ATOM    871  CB  HIS   120      16.258  16.824  17.812  1.00  0.00              
ATOM    872  CG  HIS   120      15.603  16.377  19.082  1.00  0.00              
ATOM    873  ND1 HIS   120      16.312  16.120  20.235  1.00  0.00              
ATOM    874  CD2 HIS   120      14.303  16.142  19.379  1.00  0.00              
ATOM    875  CE1 HIS   120      15.477  15.747  21.187  1.00  0.00              
ATOM    876  NE2 HIS   120      14.253  15.751  20.696  1.00  0.00              
ATOM    877  N   ALA   121      19.203  15.056  19.065  1.00  0.00              
ATOM    878  CA  ALA   121      19.809  14.588  20.306  1.00  0.00              
ATOM    879  C   ALA   121      20.702  15.659  20.922  1.00  0.00              
ATOM    880  O   ALA   121      21.194  15.503  22.039  1.00  0.00              
ATOM    881  CB  ALA   121      18.733  14.169  21.296  1.00  0.00              
ATOM    882  N   GLU   122      20.907  16.747  20.187  1.00  0.00              
ATOM    883  CA  GLU   122      21.739  17.847  20.659  1.00  0.00              
ATOM    884  C   GLU   122      21.421  18.197  22.109  1.00  0.00              
ATOM    885  O   GLU   122      22.234  18.807  22.803  1.00  0.00              
ATOM    886  CB  GLU   122      23.222  17.494  20.516  1.00  0.00              
ATOM    887  CG  GLU   122      23.495  16.323  19.586  1.00  0.00              
ATOM    888  CD  GLU   122      23.599  16.744  18.133  1.00  0.00              
ATOM    889  OE1 GLU   122      22.732  17.519  17.677  1.00  0.00              
ATOM    890  OE2 GLU   122      24.545  16.298  17.452  1.00  0.00              
ATOM    891  N   THR   123      20.233  17.805  22.559  1.00  0.00              
ATOM    892  CA  THR   123      19.796  18.083  23.957  1.00  0.00              
ATOM    893  C   THR   123      20.993  18.239  24.889  1.00  0.00              
ATOM    894  O   THR   123      20.848  18.664  26.035  1.00  0.00              
ATOM    895  CB  THR   123      18.928  19.352  24.035  1.00  0.00              
ATOM    896  OG1 THR   123      19.315  20.263  23.000  1.00  0.00              
ATOM    897  CG2 THR   123      17.456  19.001  23.871  1.00  0.00              
ATOM    898  N   ALA   124      22.175  17.895  24.389  1.00  0.00              
ATOM    899  CA  ALA   124      23.398  17.997  25.175  1.00  0.00              
ATOM    900  C   ALA   124      23.332  19.167  26.150  1.00  0.00              
ATOM    901  O   ALA   124      24.175  19.296  27.038  1.00  0.00              
ATOM    902  CB  ALA   124      23.654  16.700  25.928  1.00  0.00              
ATOM    903  N   ASP   125      22.325  20.017  25.978  1.00  0.00              
ATOM    904  CA  ASP   125      22.147  21.179  26.842  1.00  0.00              
ATOM    905  C   ASP   125      23.404  22.040  26.874  1.00  0.00              
ATOM    906  O   ASP   125      24.000  22.326  25.835  1.00  0.00              
ATOM    907  CB  ASP   125      20.949  22.011  26.380  1.00  0.00              
ATOM    908  CG  ASP   125      19.624  21.412  26.806  1.00  0.00              
ATOM    909  OD1 ASP   125      19.205  21.655  27.957  1.00  0.00              
ATOM    910  OD2 ASP   125      19.004  20.699  25.988  1.00  0.00              
ATOM    911  N   ASP   126      23.804  22.453  28.073  1.00  0.00              
ATOM    912  CA  ASP   126      24.990  23.282  28.242  1.00  0.00              
ATOM    913  C   ASP   126      25.701  22.967  29.553  1.00  0.00              
ATOM    914  O   ASP   126      25.126  22.349  30.449  1.00  0.00              
ATOM    915  CB  ASP   126      25.950  23.091  27.066  1.00  0.00              
ATOM    916  CG  ASP   126      26.223  24.383  26.321  1.00  0.00              
ATOM    917  OD1 ASP   126      27.403  24.656  26.017  1.00  0.00              
ATOM    918  OD2 ASP   126      25.256  25.123  26.040  1.00  0.00              
TER
END
