
#######################################################
#                                                     #
#                        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   16 (   78),  selected   16 , name T0301TS239_2_1-D1
# Molecule2: number of CA atoms  200 ( 1505),  selected  200 , name T0301_D1.pdb
# PARAMETERS: T0301TS239_2_1-D1.T0301_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    -       -      M       1           -
LGA    -       -      A       2           -
LGA    -       -      H       3           -
LGA    -       -      P       4           -
LGA    -       -      P       5           -
LGA    -       -      Q       6           -
LGA    -       -      I       7           -
LGA    -       -      R       8           -
LGA    -       -      I       9           -
LGA    -       -      P      10           -
LGA    -       -      A      11           -
LGA    -       -      T      12           -
LGA    -       -      Y      13           -
LGA    -       -      L      14           -
LGA    -       -      R      15           -
LGA    -       -      G      16           -
LGA    -       -      G      17           -
LGA    -       -      T      18           -
LGA    -       -      S      19           -
LGA    -       -      K      20           -
LGA    -       -      G      21           -
LGA    -       -      V      22           -
LGA    -       -      F      23           -
LGA    -       -      F      24           -
LGA    -       -      R      25           -
LGA    -       -      L      26           -
LGA    -       -      E      27           -
LGA    -       -      D      28           -
LGA    -       -      L      29           -
LGA    -       -      P      30           -
LGA    -       -      E      31           -
LGA    -       -      S      32           -
LGA    -       -      C      33           -
LGA    -       -      R      34           -
LGA    -       -      V      35           -
LGA    -       -      P      36           -
LGA    -       -      G      37           -
LGA    -       -      E      38           -
LGA    -       -      A      39           -
LGA    -       -      R      40           -
LGA    -       -      D      41           -
LGA    -       -      R      42           -
LGA    -       -      L      43           -
LGA    -       -      F      44           -
LGA    -       -      M      45           -
LGA    -       -      R      46           -
LGA    -       -      V      47           -
LGA    -       -      I      48           -
LGA    -       -      G      49           -
LGA    -       -      S      50           -
LGA    -       -      P      51           -
LGA    -       -      D      52           -
LGA    -       -      P      53           -
LGA    -       -      Y      54           -
LGA    -       -      A      55           -
LGA    -       -      A      56           -
LGA    -       -      H      57           -
LGA    -       -      I      58           -
LGA    -       -      D      59           -
LGA    -       -      G      60           -
LGA    -       -      M      61           -
LGA    -       -      G      62           -
LGA    -       -      G      63           -
LGA    -       -      A      64           -
LGA    -       -      T      65           -
LGA    -       -      S      66           -
LGA    -       -      S      67           -
LGA    -       -      T      68           -
LGA    -       -      S      69           -
LGA    -       -      K      70           -
LGA    -       -      C      71           -
LGA    -       -      V      72           -
LGA    -       -      I      73           -
LGA    -       -      L      74           -
LGA    -       -      S      75           -
LGA    -       -      K      76           -
LGA    -       -      S      77           -
LGA    -       -      S      78           -
LGA    -       -      Q      79           -
LGA    -       -      P      80           -
LGA    -       -      G      81           -
LGA    -       -      H      82           -
LGA    -       -      D      83           -
LGA    -       -      V      84           -
LGA    -       -      D      85           -
LGA    -       -      Y      86           -
LGA    -       -      L      87           -
LGA    -       -      Y      88           -
LGA    -       -      G      89           -
LGA    -       -      Q      90           -
LGA    -       -      V      91           -
LGA    -       -      S      92           -
LGA    -       -      I      93           -
LGA    -       -      D      94           -
LGA    -       -      K      95           -
LGA    -       -      P      96           -
LGA    -       -      F      97           -
LGA    -       -      V      98           -
LGA    R     378      D      99          2.618
LGA    S     379      W     100          1.724
LGA    A     380      S     101          1.990
LGA    R     381      G     102          3.784
LGA    I     382      N     103          1.424
LGA    L     383      C     104           #
LGA    -       -      G     105           -
LGA    -       -      N     106           -
LGA    -       -      L     107           -
LGA    -       -      S     108           -
LGA    -       -      T     109           -
LGA    -       -      G     110           -
LGA    -       -      A     111           -
LGA    -       -      G     112           -
LGA    -       -      A     113           -
LGA    -       -      F     114           -
LGA    -       -      A     115           -
LGA    -       -      L     116           -
LGA    -       -      H     117           -
LGA    -       -      A     118           -
LGA    -       -      G     119           -
LGA    -       -      L     120           -
LGA    -       -      V     121           -
LGA    -       -      D     122           -
LGA    -       -      P     123           -
LGA    -       -      A     124           -
LGA    -       -      R     125           -
LGA    -       -      I     126           -
LGA    -       -      P     127           -
LGA    -       -      E     128           -
LGA    -       -      D     129           -
LGA    -       -      G     130           -
LGA    -       -      I     131           -
LGA    -       -      C     132           -
LGA    -       -      E     133           -
LGA    -       -      V     134           -
LGA    -       -      R     135           -
LGA    -       -      I     136           -
LGA    -       -      W     137           -
LGA    -       -      Q     138           -
LGA    -       -      A     139           -
LGA    -       -      N     140           -
LGA    -       -      I     141           -
LGA    -       -      G     142           -
LGA    M     384      K     143          2.895
LGA    E     385      T     144          1.081
LGA    G     386      I     145          0.899
LGA    W     387      I     146          1.195
LGA    V     388      A     147          0.587
LGA    R     389      H     148          1.099
LGA    V     390      V     149          0.403
LGA    P     391      P     150          0.219
LGA    G     392      V     151          2.279
LGA    F     395      S     152           -
LGA    -       -      G     153           -
LGA    -       -      G     154           -
LGA    -       -      Q     155           -
LGA    -       -      V     156           -
LGA    -       -      Q     157           -
LGA    -       -      E     158           -
LGA    -       -      T     159           -
LGA    -       -      G     160           -
LGA    -       -      D     161           -
LGA    -       -      F     162           -
LGA    -       -      E     163           -
LGA    -       -      L     164           -
LGA    -       -      D     165           -
LGA    -       -      G     166           -
LGA    -       -      V     167           -
LGA    -       -      T     168           -
LGA    -       -      F     169           -
LGA    -       -      P     170           -
LGA    -       -      A     171           -
LGA    -       -      A     172           -
LGA    -       -      E     173           -
LGA    -       -      I     174           -
LGA    -       -      V     175           -
LGA    -       -      L     176           -
LGA    -       -      E     177           -
LGA    -       -      F     178           -
LGA    -       -      L     179           -
LGA    -       -      D     180           -
LGA    -       -      P     181           -
LGA    -       -      S     182           -
LGA    -       -      R     378           -
LGA    -       -      S     379           -
LGA    -       -      A     380           -
LGA    -       -      R     381           -
LGA    -       -      I     382           -
LGA    -       -      L     383           -
LGA    -       -      M     384           -
LGA    -       -      E     385           -
LGA    -       -      G     386           -
LGA    -       -      W     387           -
LGA    -       -      V     388           -
LGA    -       -      R     389           -
LGA    -       -      V     390           -
LGA    -       -      P     391           -
LGA    -       -      G     392           -
LGA    -       -      D     393           -
LGA    -       -      A     394           -
LGA    -       -      F     395           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   16  200    5.0     14    1.87    14.29      5.566     0.711

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.100697 * X  +   0.271087 * Y  +  -0.957273 * Z  + 118.987801
  Y_new =  -0.990046 * X  +   0.122399 * Y  +  -0.069482 * Z  +  88.367371
  Z_new =   0.098334 * X  +   0.954741 * Y  +   0.280713 * Z  + -55.702347 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.284834   -1.856758  [ DEG:    73.6156   -106.3844 ]
  Theta =  -0.098493   -3.043100  [ DEG:    -5.6432   -174.3568 ]
  Phi   =  -1.469436    1.672157  [ DEG:   -84.1925     95.8075 ]
 
# 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: T0301TS239_2_1-D1                             
REMARK     2: T0301_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0301TS239_2_1-D1.T0301_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   16  200   5.0   14   1.87   14.29   5.566
REMARK  ---------------------------------------------------------- 
MOLECULE T0301TS239_2_1-D1
REMARK PARENT number 1
PFRMAT TS
TARGET T0301
PARENT 1tm0_A
ATOM    669  N   ARG   378      84.990  31.868  -2.214  1.00  9.99
ATOM    670  CA  ARG   378      84.755  30.493  -2.653  1.00  9.99
ATOM    671  C   ARG   378      83.891  29.717  -1.649  1.00  9.99
ATOM    672  O   ARG   378      84.258  29.604  -0.479  1.00  9.99
ATOM    673  CB  ARG   378      86.175  29.931  -2.804  1.00  9.99
ATOM    674  N   SER   379      82.738  29.218  -2.112  1.00  9.99
ATOM    675  CA  SER   379      81.789  28.453  -1.287  1.00  9.99
ATOM    676  C   SER   379      81.968  26.962  -1.515  1.00  9.99
ATOM    677  O   SER   379      82.476  26.556  -2.552  1.00  9.99
ATOM    678  CB  SER   379      80.342  28.826  -1.622  1.00  9.99
ATOM    679  N   ALA   380      81.537  26.144  -0.560  1.00  9.99
ATOM    680  CA  ALA   380      81.700  24.703  -0.694  1.00  9.99
ATOM    681  C   ALA   380      80.818  23.938   0.277  1.00  9.99
ATOM    682  O   ALA   380      80.256  24.519   1.194  1.00  9.99
ATOM    683  CB  ALA   380      83.160  24.338  -0.455  1.00  9.99
ATOM    684  N   ARG   381      80.703  22.632   0.061  1.00  9.99
ATOM    685  CA  ARG   381      79.883  21.789   0.911  1.00  9.99
ATOM    686  C   ARG   381      80.782  20.807   1.621  1.00  9.99
ATOM    687  O   ARG   381      81.520  20.066   0.980  1.00  9.99
ATOM    688  CB  ARG   381      78.852  21.053   0.085  1.00  9.99
ATOM    689  N   ILE   382      80.726  20.808   2.950  1.00  9.99
ATOM    690  CA  ILE   382      81.555  19.921   3.748  1.00  9.99
ATOM    691  C   ILE   382      81.017  18.500   3.682  1.00  9.99
ATOM    692  O   ILE   382      81.497  17.688   2.893  1.00  9.99
ATOM    693  CB  ILE   382      81.606  20.420   5.194  1.00  9.99
ATOM    694  N   LEU   383      80.017  18.198   4.501  1.00  9.99
ATOM    695  CA  LEU   383      79.434  16.864   4.506  1.00  9.99
ATOM    696  C   LEU   383      78.176  16.827   3.645  1.00  9.99
ATOM    697  O   LEU   383      77.514  17.844   3.460  1.00  9.99
ATOM    698  CB  LEU   383      79.094  16.453   5.937  1.00  9.99
ATOM    699  N   MET   384      77.855  15.652   3.114  1.00  9.99
ATOM    700  CA  MET   384      76.671  15.470   2.279  1.00  9.99
ATOM    701  C   MET   384      75.961  14.183   2.680  1.00  9.99
ATOM    702  O   MET   384      76.594  13.139   2.803  1.00  9.99
ATOM    703  CB  MET   384      77.068  15.390   0.801  1.00  9.99
ATOM    704  N   GLU   385      74.648  14.253   2.876  1.00  9.99
ATOM    705  CA  GLU   385      73.878  13.072   3.263  1.00  9.99
ATOM    706  C   GLU   385      74.619  12.292   4.342  1.00  9.99
ATOM    707  O   GLU   385      75.138  11.206   4.086  1.00  9.99
ATOM    708  CB  GLU   385      73.646  12.159   2.052  1.00  9.99
ATOM    709  N   GLY   386      74.685  12.852   5.541  1.00  9.99
ATOM    710  CA  GLY   386      75.352  12.178   6.640  1.00  9.99
ATOM    711  C   GLY   386      74.350  12.003   7.767  1.00  9.99
ATOM    712  O   GLY   386      73.537  12.886   8.028  1.00  9.99
ATOM    713  N   TRP   387      74.382  10.847   8.441  1.00  9.99
ATOM    714  CA  TRP   387      73.447  10.603   9.540  1.00  9.99
ATOM    715  C   TRP   387      73.612  11.673  10.609  1.00  9.99
ATOM    716  O   TRP   387      74.662  12.307  10.696  1.00  9.99
ATOM    717  CB  TRP   387      73.848   9.216  10.032  1.00  9.99
ATOM    718  N   VAL   388      72.575  11.870  11.416  1.00  9.99
ATOM    719  CA  VAL   388      72.609  12.874  12.475  1.00  9.99
ATOM    720  C   VAL   388      71.728  12.469  13.658  1.00  9.99
ATOM    721  O   VAL   388      70.501  12.538  13.586  1.00  9.99
ATOM    722  CB  VAL   388      72.155  14.224  11.918  1.00  9.99
ATOM    723  N   ARG   389      72.365  12.047  14.747  1.00  9.99
ATOM    724  CA  ARG   389      71.656  11.625  15.954  1.00  9.99
ATOM    725  C   ARG   389      71.007  12.804  16.680  1.00  9.99
ATOM    726  O   ARG   389      71.617  13.431  17.548  1.00  9.99
ATOM    727  CB  ARG   389      72.624  10.896  16.898  1.00  9.99
ATOM    728  N   VAL   390      69.762  13.098  16.322  1.00  9.99
ATOM    729  CA  VAL   390      69.031  14.196  16.937  1.00  9.99
ATOM    730  C   VAL   390      68.166  13.702  18.094  1.00  9.99
ATOM    731  O   VAL   390      67.268  12.880  17.906  1.00  9.99
ATOM    732  CB  VAL   390      68.135  14.909  15.902  1.00  9.99
ATOM    733  N   PRO   391      68.439  14.208  19.292  1.00  9.99
ATOM    734  CA  PRO   391      67.677  13.808  20.467  1.00  9.99
ATOM    735  C   PRO   391      66.203  14.180  20.303  1.00  9.99
ATOM    736  O   PRO   391      65.362  13.770  21.103  1.00  9.99
ATOM    737  CB  PRO   391      68.217  14.476  21.755  1.00  9.99
ATOM    738  N   GLY   392      65.893  14.953  19.265  1.00  9.99
ATOM    739  CA  GLY   392      64.517  15.358  19.027  1.00  9.99
ATOM    740  C   GLY   392      63.599  14.182  18.742  1.00  9.99
ATOM    741  O   GLY   392      62.739  13.846  19.555  1.00  9.99
ATOM    742  N   PHE   395      63.776  13.565  17.577  1.00  9.99
ATOM    743  CA  PHE   395      62.975  12.411  17.188  1.00  9.99
ATOM    744  C   PHE   395      63.576  11.751  15.954  1.00  9.99
ATOM    745  O   PHE   395      63.856  12.413  14.957  1.00  9.99
ATOM    746  CB  PHE   395      61.525  12.817  16.900  1.00  9.99
TER
END
