
#######################################################
#                                                     #
#                        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   35 (   35),  selected   35 , name T0301TS464_3_1-D1
# Molecule2: number of CA atoms  200 ( 1505),  selected  200 , name T0301_D1.pdb
# PARAMETERS: T0301TS464_3_1-D1.T0301_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    G      60      M       1           -
LGA    M      61      A       2           -
LGA    G      62      H       3           -
LGA    G      63      P       4           -
LGA    A      64      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    -       -      D      99           -
LGA    -       -      W     100           -
LGA    -       -      S     101           -
LGA    -       -      G     102           -
LGA    -       -      N     103           -
LGA    -       -      C     104           -
LGA    -       -      G     105           -
LGA    G     166      N     106          3.694
LGA    V     167      L     107          1.620
LGA    T     168      S     108          1.560
LGA    F     169      T     109          1.172
LGA    P     170      G     110          0.997
LGA    A     171      A     111          0.384
LGA    A     172      G     112          0.469
LGA    E     173      A     113          0.683
LGA    I     174      F     114          1.390
LGA    V     175      A     115          1.531
LGA    L     176      L     116          2.719
LGA    E     177      H     117          3.070
LGA    -       -      A     118           -
LGA    F     178      G     119          2.024
LGA    -       -      L     120           -
LGA    L     179      V     121          0.930
LGA    -       -      D     122           -
LGA    D     180      P     123          4.180
LGA    P     181      A     124          5.201
LGA    -       -      R     125           -
LGA    S     182      I     126          3.813
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    R     378      I     136          3.734
LGA    S     379      W     137          2.599
LGA    -       -      Q     138           -
LGA    -       -      A     139           -
LGA    -       -      N     140           -
LGA    -       -      I     141           -
LGA    -       -      G     142           -
LGA    -       -      K     143           -
LGA    A     380      T     144          1.817
LGA    R     381      I     145          1.957
LGA    I     382      I     146          1.297
LGA    L     383      A     147           -
LGA    M     384      -       -           -
LGA    E     385      -       -           -
LGA    G     386      -       -           -
LGA    W     387      H     148          4.708
LGA    V     388      V     149           -
LGA    R     389      P     150           -
LGA    V     390      V     151           -
LGA    -       -      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)   35  200    5.0     23    2.63    13.04      8.297     0.843

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.083159 * X  +   0.615460 * Y  +  -0.783769 * Z  +  86.578606
  Y_new =  -0.904977 * X  +  -0.375949 * Y  +  -0.199198 * Z  +  38.337502
  Z_new =  -0.417255 * X  +   0.692727 * Y  +   0.588241 * Z  + -12.227921 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.866786   -2.274806  [ DEG:    49.6632   -130.3368 ]
  Theta =   0.430423    2.711169  [ DEG:    24.6614    155.3386 ]
  Phi   =  -1.662430    1.479163  [ DEG:   -95.2502     84.7498 ]
 
# 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: T0301TS464_3_1-D1                             
REMARK     2: T0301_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0301TS464_3_1-D1.T0301_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   35  200   5.0   23   2.63   13.04   8.297
REMARK  ---------------------------------------------------------- 
MOLECULE T0301TS464_3_1-D1
REMARK PARENT number 1
PFRMAT TS
TARGET T0301
PARENT N/A
ATOM      1  CA  GLY    60      59.371  14.943  18.350  1.00  0.00
ATOM      2  CA  MET    61      61.354  11.666  18.619  1.00  0.00
ATOM      3  CA  GLY    62      64.749  13.051  17.296  1.00  0.00
ATOM      4  CA  GLY    63      64.547  10.828  14.210  1.00  0.00
ATOM      5  CA  ALA    64      63.639  12.310  10.803  1.00  0.00
ATOM      6  CA  GLY   166      79.680  23.350  15.262  1.00  0.00
ATOM      7  CA  VAL   167      77.933  24.479  12.063  1.00  0.00
ATOM      8  CA  THR   168      77.241  20.919  10.909  1.00  0.00
ATOM      9  CA  PHE   169      75.534  20.280  14.232  1.00  0.00
ATOM     10  CA  PRO   170      73.457  23.450  13.898  1.00  0.00
ATOM     11  CA  ALA   171      72.453  21.693  10.659  1.00  0.00
ATOM     12  CA  ALA   172      70.809  18.714  12.443  1.00  0.00
ATOM     13  CA  GLU   173      69.057  21.161  14.770  1.00  0.00
ATOM     14  CA  ILE   174      67.479  23.052  11.866  1.00  0.00
ATOM     15  CA  VAL   175      66.486  19.849  10.067  1.00  0.00
ATOM     16  CA  LEU   176      65.127  18.146  13.224  1.00  0.00
ATOM     17  CA  GLU   177      63.135  21.282  14.155  1.00  0.00
ATOM     18  CA  PHE   178      61.420  21.392  10.750  1.00  0.00
ATOM     19  CA  LEU   179      60.797  17.796   9.803  1.00  0.00
ATOM     20  CA  ASP   180      60.489  15.925  13.065  1.00  0.00
ATOM     21  CA  PRO   181      56.736  16.206  13.433  1.00  0.00
ATOM     22  CA  SER   182      56.296  13.783  16.407  1.00  0.00
ATOM     64  CA  ARG   378      74.131  16.256   3.818  1.00  0.00
ATOM     65  CA  SER   379      70.894  14.276   3.473  1.00  0.00
ATOM     66  CA  ALA   380      72.976  11.258   2.479  1.00  0.00
ATOM     67  CA  ARG   381      75.226  11.362   5.539  1.00  0.00
ATOM     68  CA  ILE   382      72.381  11.790   8.009  1.00  0.00
ATOM     69  CA  LEU   383      70.594   8.986   6.210  1.00  0.00
ATOM     70  CA  MET   384      73.657   6.753   6.444  1.00  0.00
ATOM     71  CA  GLU   385      73.968   7.611  10.155  1.00  0.00
ATOM     72  CA  GLY   386      70.380   6.399  10.598  1.00  0.00
ATOM     73  CA  TRP   387      68.916   9.838  11.343  1.00  0.00
ATOM     74  CA  VAL   388      66.580  10.228   8.376  1.00  0.00
ATOM     75  CA  ARG   389      64.284   8.149   6.187  1.00  0.00
ATOM     76  CA  VAL   390      64.817   9.150   2.542  1.00  0.00
TER
END
