
#######################################################
#                                                     #
#                        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    9 (   75),  selected    9 , name T0356TS013_1_2-D1
# Molecule2: number of CA atoms  124 (  963),  selected  124 , name T0356_D1.pdb
# PARAMETERS: T0356TS013_1_2-D1.T0356_D1.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    -       -      N       7           -
LGA    -       -      D       8           -
LGA    -       -      L       9           -
LGA    -       -      R      10           -
LGA    -       -      D      11           -
LGA    -       -      F      12           -
LGA    -       -      L      13           -
LGA    -       -      T      14           -
LGA    -       -      L      15           -
LGA    -       -      L      16           -
LGA    -       -      E      17           -
LGA    -       -      Q      18           -
LGA    -       -      Q      19           -
LGA    -       -      G      20           -
LGA    -       -      E      21           -
LGA    -       -      L      22           -
LGA    -       -      K      23           -
LGA    -       -      R      24           -
LGA    -       -      I      25           -
LGA    -       -      T      26           -
LGA    -       -      L      27           -
LGA    -       -      P      28           -
LGA    -       -      V      29           -
LGA    -       -      D      30           -
LGA    -       -      P      31           -
LGA    -       -      H      32           -
LGA    -       -      L      33           -
LGA    -       -      E      34           -
LGA    -       -      I      35           -
LGA    -       -      T      36           -
LGA    -       -      E      37           -
LGA    -       -      I      38           -
LGA    -       -      A      39           -
LGA    -       -      D      40           -
LGA    -       -      R      41           -
LGA    -       -      T      42           -
LGA    -       -      L      43           -
LGA    -       -      R      44           -
LGA    -       -      A      45           -
LGA    -       -      G      46           -
LGA    -       -      G      47           -
LGA    -       -      P      48           -
LGA    -       -      A      49           -
LGA    -       -      L      50           -
LGA    -       -      L      51           -
LGA    -       -      F      52           -
LGA    -       -      E      53           -
LGA    -       -      N      54           -
LGA    -       -      P      55           -
LGA    -       -      K      56           -
LGA    -       -      G      57           -
LGA    -       -      Y      58           -
LGA    -       -      S      59           -
LGA    -       -      M      60           -
LGA    -       -      P      61           -
LGA    -       -      V      62           -
LGA    -       -      L      63           -
LGA    -       -      C      64           -
LGA    -       -      N      65           -
LGA    -       -      L      66           -
LGA    -       -      F      67           -
LGA    -       -      G      68           -
LGA    -       -      T      69           -
LGA    -       -      P      70           -
LGA    -       -      K      71           -
LGA    -       -      R      72           -
LGA    -       -      V      73           -
LGA    -       -      A      74           -
LGA    -       -      M      75           -
LGA    -       -      G      76           -
LGA    -       -      M      77           -
LGA    -       -      G      78           -
LGA    -       -      Q      79           -
LGA    -       -      E      80           -
LGA    -       -      D      81           -
LGA    -       -      V      82           -
LGA    -       -      S      83           -
LGA    -       -      A      84           -
LGA    -       -      L      85           -
LGA    -       -      R      86           -
LGA    -       -      E      87           -
LGA    -       -      V      88           -
LGA    -       -      G      89           -
LGA    -       -      K      90           -
LGA    -       -      L      91           -
LGA    -       -      L      92           -
LGA    -       -      A      93           -
LGA    -       -      F      94           -
LGA    -       -      L      95           -
LGA    -       -      K      96           -
LGA    -       -      D     314           -
LGA    -       -      A     315           -
LGA    -       -      I     316           -
LGA    -       -      Y     317           -
LGA    -       -      H     318           -
LGA    -       -      S     319           -
LGA    -       -      T     320           -
LGA    -       -      Y     321           -
LGA    -       -      T     322           -
LGA    -       -      G     323           -
LGA    -       -      R     324           -
LGA    -       -      P     325           -
LGA    -       -      P     326           -
LGA    -       -      D     327           -
LGA    -       -      E     328           -
LGA    -       -      P     329           -
LGA    -       -      A     330           -
LGA    D     314      V     331          1.453
LGA    A     315      L     332          0.360
LGA    -       -      G     333           -
LGA    -       -      V     334           -
LGA    I     316      A     335          1.252
LGA    Y     317      L     336          0.686
LGA    -       -      N     337           -
LGA    -       -      E     338           -
LGA    H     318      V     339          1.407
LGA    S     319      F     340          0.800
LGA    T     320      V     341          2.835
LGA    -       -      P     342           -
LGA    -       -      I     343           -
LGA    Y     321      L     344          1.561
LGA    T     322      Q     345          2.145
LGA    -       -      K     346           -
LGA    -       -      Q     347           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)    9  124    5.0      9    1.56     0.00      6.844     0.541

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.627272 * X  +   0.139658 * Y  +   0.766176 * Z  +  63.196846
  Y_new =   0.437245 * X  +   0.877261 * Y  +   0.198068 * Z  +  76.523750
  Z_new =  -0.644474 * X  +   0.459249 * Y  +  -0.611345 * Z  +  61.900387 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.497317   -0.644275  [ DEG:   143.0857    -36.9143 ]
  Theta =   0.700336    2.441257  [ DEG:    40.1263    139.8737 ]
  Phi   =   2.532844   -0.608749  [ DEG:   145.1213    -34.8787 ]
 
# 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: T0356TS013_1_2-D1                             
REMARK     2: T0356_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0356TS013_1_2-D1.T0356_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:    9  124   5.0    9   1.56    0.00   6.844
REMARK  ---------------------------------------------------------- 
MOLECULE T0356TS013_1_2-D1
REMARK PARENT number 2
PFRMAT TS
TARGET T0356
PARENT N/A
ATOM   2449  N   ASP   314      57.630  67.694  78.497  1.00  8.97
ATOM   2450  CA  ASP   314      57.554  69.158  78.474  1.00  8.97
ATOM   2451  C   ASP   314      58.679  69.802  77.658  1.00  8.97
ATOM   2452  O   ASP   314      58.791  71.032  77.574  1.00  8.97
ATOM   2453  CB  ASP   314      57.508  69.706  79.921  1.00  8.97
ATOM   2454  CG  ASP   314      56.145  69.913  80.572  1.00  8.97
ATOM   2455  OD1 ASP   314      55.193  70.360  79.934  1.00  8.97
ATOM   2456  OD2 ASP   314      56.052  69.645  81.769  1.00  8.97
ATOM   2457  N   ALA   315      59.530  68.999  76.996  1.00  9.42
ATOM   2458  CA  ALA   315      60.472  69.643  76.079  1.00  9.42
ATOM   2459  C   ALA   315      59.745  70.259  74.884  1.00  9.42
ATOM   2460  O   ALA   315      58.719  69.761  74.459  1.00  9.42
ATOM   2461  CB  ALA   315      61.537  68.634  75.655  1.00  9.42
ATOM   2462  N   ILE   316      60.303  71.350  74.379  1.00  0.10
ATOM   2463  CA  ILE   316      59.766  72.074  73.218  1.00  0.10
ATOM   2464  C   ILE   316      60.864  72.020  72.156  1.00  0.10
ATOM   2465  O   ILE   316      61.965  72.558  72.405  1.00  0.10
ATOM   2466  CB  ILE   316      59.433  73.512  73.580  1.00  0.10
ATOM   2467  CG1 ILE   316      58.431  73.580  74.741  1.00  0.10
ATOM   2468  CG2 ILE   316      58.822  74.257  72.390  1.00  0.10
ATOM   2469  CD1 ILE   316      58.176  74.996  75.277  1.00  0.10
ATOM   2470  N   TYR   317      60.569  71.380  71.039  1.00  4.60
ATOM   2471  CA  TYR   317      61.580  71.164  70.006  1.00  4.60
ATOM   2472  C   TYR   317      61.150  71.798  68.702  1.00  4.60
ATOM   2473  O   TYR   317      59.962  71.734  68.350  1.00  4.60
ATOM   2474  CB  TYR   317      61.844  69.664  69.833  1.00  4.60
ATOM   2475  CG  TYR   317      62.397  69.027  71.106  1.00  4.60
ATOM   2476  CD1 TYR   317      63.695  69.323  71.524  1.00  4.60
ATOM   2477  CD2 TYR   317      61.605  68.143  71.825  1.00  4.60
ATOM   2478  CE1 TYR   317      64.190  68.724  72.669  1.00  4.60
ATOM   2479  CE2 TYR   317      62.099  67.544  72.961  1.00  4.60
ATOM   2480  CZ  TYR   317      63.386  67.837  73.374  1.00  4.60
ATOM   2481  OH  TYR   317      63.880  67.186  74.494  1.00  4.60
ATOM   2482  N   HIS   318      62.073  72.405  67.987  1.00  6.17
ATOM   2483  CA  HIS   318      61.770  72.978  66.666  1.00  6.17
ATOM   2484  C   HIS   318      62.063  71.989  65.561  1.00  6.17
ATOM   2485  O   HIS   318      63.205  71.456  65.508  1.00  6.17
ATOM   2486  CB  HIS   318      62.585  74.269  66.442  1.00  6.17
ATOM   2487  CG  HIS   318      62.318  75.409  67.351  1.00  6.17
ATOM   2488  ND1 HIS   318      61.116  76.062  67.391  1.00  6.17
ATOM   2489  CD2 HIS   318      63.140  76.105  68.166  1.00  6.17
ATOM   2490  CE1 HIS   318      61.255  77.114  68.220  1.00  6.17
ATOM   2491  NE2 HIS   318      62.488  77.177  68.719  1.00  6.17
ATOM   2492  N   SER   319      61.104  71.751  64.677  1.00  8.31
ATOM   2493  CA  SER   319      61.384  70.917  63.500  1.00  8.31
ATOM   2494  C   SER   319      60.861  71.658  62.278  1.00  8.31
ATOM   2495  O   SER   319      60.019  72.541  62.349  1.00  8.31
ATOM   2496  CB  SER   319      60.758  69.514  63.595  1.00  8.31
ATOM   2497  OG  SER   319      59.352  69.424  63.394  1.00  8.31
ATOM   2498  N   THR   320      61.421  71.263  61.109  1.00  9.25
ATOM   2499  CA  THR   320      61.111  71.965  59.866  1.00  9.25
ATOM   2500  C   THR   320      60.591  70.974  58.831  1.00  9.25
ATOM   2501  O   THR   320      61.229  69.915  58.651  1.00  9.25
ATOM   2502  CB  THR   320      62.354  72.645  59.284  1.00  9.25
ATOM   2503  OG1 THR   320      63.317  71.666  58.932  1.00  9.25
ATOM   2504  CG2 THR   320      62.995  73.642  60.275  1.00  9.25
ATOM   2505  N   TYR   321      59.481  71.274  58.182  1.00  6.58
ATOM   2506  CA  TYR   321      58.957  70.295  57.209  1.00  6.58
ATOM   2507  C   TYR   321      58.467  71.061  55.997  1.00  6.58
ATOM   2508  O   TYR   321      57.781  72.067  56.167  1.00  6.58
ATOM   2509  CB  TYR   321      57.788  69.485  57.795  1.00  6.58
ATOM   2510  CG  TYR   321      58.215  68.663  59.006  1.00  6.58
ATOM   2511  CD1 TYR   321      59.046  67.556  58.839  1.00  6.58
ATOM   2512  CD2 TYR   321      57.749  69.016  60.266  1.00  6.58
ATOM   2513  CE1 TYR   321      59.406  66.806  59.945  1.00  6.58
ATOM   2514  CE2 TYR   321      58.104  68.269  61.365  1.00  6.58
ATOM   2515  CZ  TYR   321      58.927  67.170  61.199  1.00  6.58
ATOM   2516  OH  TYR   321      59.232  66.403  62.312  1.00  6.58
ATOM   2517  N   THR   322      59.047  70.724  54.827  1.00  8.66
ATOM   2518  CA  THR   322      58.667  71.399  53.617  1.00  8.66
ATOM   2519  C   THR   322      57.438  70.767  52.974  1.00  8.66
ATOM   2520  O   THR   322      56.652  71.462  52.346  1.00  8.66
ATOM   2521  CB  THR   322      59.844  71.408  52.622  1.00  8.66
ATOM   2522  OG1 THR   322      60.934  72.098  53.261  1.00  8.66
ATOM   2523  CG2 THR   322      59.480  72.060  51.285  1.00  8.66
TER
END
