
#######################################################
#                                                     #
#                        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   34 (   34),  selected   34 , name T0320TS464_1_2-D1
# Molecule2: number of CA atoms  214 ( 1760),  selected  214 , name T0320_D1.pdb
# PARAMETERS: T0320TS464_1_2-D1.T0320_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      M       1           -
LGA    -       -      Q       2           -
LGA    -       -      L       3           -
LGA    -       -      S       4           -
LGA    -       -      K       5           -
LGA    -       -      A       6           -
LGA    -       -      A       7           -
LGA    -       -      E       8           -
LGA    -       -      M       9           -
LGA    -       -      C      10           -
LGA    -       -      Y      11           -
LGA    -       -      E      12           -
LGA    -       -      I      13           -
LGA    -       -      T      14           -
LGA    -       -      N      15           -
LGA    -       -      S      16           -
LGA    -       -      Y      17           -
LGA    -       -      L      18           -
LGA    -       -      H      19           -
LGA    -       -      I      20           -
LGA    -       -      D      21           -
LGA    -       -      Q      22           -
LGA    -       -      K      23           -
LGA    -       -      S      24           -
LGA    -       -      Q      25           -
LGA    -       -      I      26           -
LGA    -       -      I      27           -
LGA    -       -      A      28           -
LGA    -       -      S      29           -
LGA    -       -      T      30           -
LGA    -       -      Q      31           -
LGA    -       -      E      32           -
LGA    -       -      A      33           -
LGA    -       -      I      34           -
LGA    -       -      R      35           -
LGA    -       -      L      36           -
LGA    -       -      T      37           -
LGA    -       -      R      38           -
LGA    -       -      K      39           -
LGA    -       -      Y      40           -
LGA    -       -      L      41           -
LGA    -       -      L      42           -
LGA    -       -      S      43           -
LGA    -       -      E      44           -
LGA    -       -      I      45           -
LGA    -       -      F      46           -
LGA    -       -      V      47           -
LGA    -       -      R      48           -
LGA    -       -      W      49           -
LGA    -       -      S      50           -
LGA    -       -      P      51           -
LGA    -       -      L      52           -
LGA    -       -      N      53           -
LGA    -       -      G      54           -
LGA    -       -      E      55           -
LGA    -       -      I      56           -
LGA    -       -      S      57           -
LGA    F      58      F      58          4.931
LGA    S      59      S      59          3.779
LGA    Y      60      Y      60           #
LGA    N      61      -       -           -
LGA    G      62      N      61          5.615
LGA    G      63      G      62          2.327
LGA    K      64      G      63          2.088
LGA    D      65      K      64          3.302
LGA    -       -      D      65           -
LGA    C      66      C      66          2.330
LGA    Q      67      Q      67          2.339
LGA    V      68      V      68          2.385
LGA    L      69      L      69          2.344
LGA    L      70      L      70          2.230
LGA    L      71      L      71          2.969
LGA    L      72      L      72          2.411
LGA    Y      73      Y      73          2.506
LGA    -       -      L      74           -
LGA    -       -      S      75           -
LGA    -       -      C      76           -
LGA    -       -      L      77           -
LGA    -       -      W      78           -
LGA    -       -      E      79           -
LGA    -       -      Y      80           -
LGA    -       -      F      81           -
LGA    -       -      F      82           -
LGA    -       -      I      83           -
LGA    -       -      K      84           -
LGA    -       -      A      85           -
LGA    -       -      Q      86           -
LGA    -       -      N      87           -
LGA    -       -      S      88           -
LGA    -       -      F      97           -
LGA    -       -      P      98           -
LGA    -       -      M      99           -
LGA    -       -      Q     100           -
LGA    -       -      R     101           -
LGA    -       -      L     102           -
LGA    -       -      P     103           -
LGA    -       -      T     104           -
LGA    -       -      V     105           -
LGA    -       -      F     106           -
LGA    -       -      I     107           -
LGA    -       -      D     108           -
LGA    -       -      Q     109           -
LGA    -       -      E     110           -
LGA    -       -      E     111           -
LGA    -       -      T     112           -
LGA    -       -      F     113           -
LGA    -       -      P     114           -
LGA    -       -      T     115           -
LGA    -       -      L     116           -
LGA    A     145      E     117          2.443
LGA    D     146      N     118          2.857
LGA    A     147      F     119          3.817
LGA    -       -      V     120           -
LGA    F     148      L     121          2.277
LGA    R     149      E     122          1.472
LGA    D     150      T     123          1.895
LGA    F     151      S     124          2.543
LGA    I     152      E     125          1.581
LGA    K     153      R     126          1.854
LGA    I     154      Y     127          2.407
LGA    Y     155      C     128          2.961
LGA    P     156      -       -           -
LGA    E     157      L     129          4.276
LGA    S     223      S     130           -
LGA    -       -      L     131           -
LGA    -       -      Y     132           -
LGA    -       -      E     133           -
LGA    -       -      S     134           -
LGA    -       -      Q     135           -
LGA    -       -      R     136           -
LGA    -       -      V     142           -
LGA    -       -      N     143           -
LGA    -       -      M     144           -
LGA    -       -      A     145           -
LGA    -       -      D     146           -
LGA    -       -      A     147           -
LGA    -       -      F     148           -
LGA    -       -      R     149           -
LGA    -       -      D     150           -
LGA    -       -      F     151           -
LGA    -       -      I     152           -
LGA    -       -      K     153           -
LGA    -       -      I     154           -
LGA    -       -      Y     155           -
LGA    -       -      P     156           -
LGA    -       -      E     157           -
LGA    -       -      T     158           -
LGA    -       -      E     159           -
LGA    -       -      A     160           -
LGA    -       -      I     161           -
LGA    -       -      V     162           -
LGA    I     224      I     163           #
LGA    G     225      -       -           -
LGA    G     226      G     164          5.108
LGA    I     227      I     165          2.586
LGA    -       -      R     166           -
LGA    -       -      H     167           -
LGA    -       -      T     168           -
LGA    -       -      D     169           -
LGA    -       -      P     170           -
LGA    -       -      F     171           -
LGA    -       -      G     172           -
LGA    -       -      E     173           -
LGA    -       -      A     174           -
LGA    -       -      L     175           -
LGA    -       -      K     176           -
LGA    -       -      P     177           -
LGA    -       -      I     178           -
LGA    -       -      Q     179           -
LGA    -       -      R     180           -
LGA    -       -      T     181           -
LGA    -       -      D     182           -
LGA    -       -      S     183           -
LGA    -       -      N     184           -
LGA    -       -      W     185           -
LGA    -       -      P     186           -
LGA    -       -      D     187           -
LGA    -       -      F     188           -
LGA    -       -      M     189           -
LGA    -       -      R     190           -
LGA    -       -      L     191           -
LGA    -       -      Q     192           -
LGA    -       -      P     193           -
LGA    -       -      L     194           -
LGA    -       -      L     195           -
LGA    -       -      H     196           -
LGA    -       -      W     197           -
LGA    -       -      D     198           -
LGA    -       -      L     199           -
LGA    -       -      T     200           -
LGA    -       -      N     201           -
LGA    -       -      I     202           -
LGA    -       -      W     203           -
LGA    -       -      S     204           -
LGA    -       -      F     205           -
LGA    -       -      L     206           -
LGA    -       -      L     207           -
LGA    -       -      Y     208           -
LGA    -       -      S     209           -
LGA    -       -      N     210           -
LGA    -       -      E     211           -
LGA    -       -      P     212           -
LGA    -       -      I     213           -
LGA    -       -      C     214           -
LGA    -       -      G     215           -
LGA    -       -      L     216           -
LGA    -       -      Y     217           -
LGA    -       -      G     218           -
LGA    -       -      K     219           -
LGA    -       -      G     220           -
LGA    -       -      F     221           -
LGA    -       -      T     222           -
LGA    -       -      S     223           -
LGA    -       -      I     224           -
LGA    -       -      G     225           -
LGA    -       -      G     226           -
LGA    -       -      I     227           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   34  214    5.0     28    3.03    46.43      8.957     0.896

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.277922 * X  +  -0.285305 * Y  +   0.917257 * Z  +  89.383934
  Y_new =  -0.800018 * X  +  -0.459808 * Y  +  -0.385419 * Z  + 117.236229
  Z_new =   0.531724 * X  +  -0.840938 * Y  +  -0.100459 * Z  +  73.990273 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.689693    1.451900  [ DEG:   -96.8123     83.1877 ]
  Theta =  -0.560635   -2.580957  [ DEG:   -32.1220   -147.8780 ]
  Phi   =  -1.905148    1.236444  [ DEG:  -109.1569     70.8431 ]
 
# 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: T0320TS464_1_2-D1                             
REMARK     2: T0320_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0320TS464_1_2-D1.T0320_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   34  214   5.0   28   3.03   46.43   8.957
REMARK  ---------------------------------------------------------- 
MOLECULE T0320TS464_1_2-D1
REMARK PARENT number 2
PFRMAT TS
TARGET T0320
PARENT N/A
ATOM      1  CA  PHE    58      21.245  25.403  27.692  1.00  0.00
ATOM      2  CA  SER    59      22.829  24.931  24.307  1.00  0.00
ATOM      3  CA  TYR    60      20.570  22.901  22.039  1.00  0.00
ATOM      4  CA  ASN    61      22.037  20.980  19.109  1.00  0.00
ATOM      5  CA  GLY    62      19.412  22.772  17.020  1.00  0.00
ATOM      6  CA  GLY    63      18.376  26.407  16.816  1.00  0.00
ATOM      7  CA  LYS    64      14.926  25.121  15.920  1.00  0.00
ATOM      8  CA  ASP    65      14.900  23.438  19.326  1.00  0.00
ATOM      9  CA  CYS    66      16.070  26.685  20.919  1.00  0.00
ATOM     10  CA  GLN    67      13.305  28.613  19.152  1.00  0.00
ATOM     11  CA  VAL    68      10.747  26.251  20.635  1.00  0.00
ATOM     12  CA  LEU    69      12.302  26.437  24.115  1.00  0.00
ATOM     13  CA  LEU    70      11.848  30.197  24.009  1.00  0.00
ATOM     14  CA  LEU    71       8.157  31.072  23.766  1.00  0.00
ATOM     15  CA  LEU    72       8.360  27.818  25.926  1.00  0.00
ATOM     16  CA  TYR    73      10.493  30.026  28.162  1.00  0.00
ATOM     17  CA  ALA   145      22.077  33.777  14.784  1.00  0.00
ATOM     18  CA  ASP   146      18.783  33.530  12.980  1.00  0.00
ATOM     19  CA  ALA   147      17.028  32.684  16.248  1.00  0.00
ATOM     20  CA  PHE   148      18.138  36.086  17.579  1.00  0.00
ATOM     21  CA  ARG   149      16.296  37.651  14.617  1.00  0.00
ATOM     22  CA  ASP   150      13.137  35.625  15.277  1.00  0.00
ATOM     23  CA  PHE   151      13.250  36.322  19.013  1.00  0.00
ATOM     24  CA  ILE   152      12.089  39.901  18.478  1.00  0.00
ATOM     25  CA  LYS   153       8.728  38.273  17.775  1.00  0.00
ATOM     26  CA  ILE   154       8.988  35.795  20.628  1.00  0.00
ATOM     27  CA  TYR   155       9.947  37.894  23.605  1.00  0.00
ATOM     28  CA  PRO   156      10.743  41.517  24.583  1.00  0.00
ATOM     29  CA  GLU   157      13.598  40.341  26.786  1.00  0.00
ATOM     30  CA  SER   223      11.914  17.879  26.013  1.00  0.00
ATOM     31  CA  ILE   224      12.541  20.401  23.228  1.00  0.00
ATOM     32  CA  GLY   225      15.388  18.374  21.745  1.00  0.00
ATOM     33  CA  GLY   226      19.009  17.344  22.213  1.00  0.00
ATOM     34  CA  ILE   227      20.896  19.757  24.421  1.00  0.00
TER
END
