
#######################################################
#                                                     #
#                        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   18 (   90),  selected   18 , name T0289TS239_5_1-D1
# Molecule2: number of CA atoms  233 ( 1850),  selected  233 , name T0289_D1.pdb
# PARAMETERS: T0289TS239_5_1-D1.T0289_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    -       -      C       4           -
LGA    -       -      V       5           -
LGA    -       -      A       6           -
LGA    -       -      E       7           -
LGA    -       -      E       8           -
LGA    -       -      P       9           -
LGA    -       -      I      10           -
LGA    -       -      K      11           -
LGA    -       -      K      12           -
LGA    -       -      I      13           -
LGA    -       -      A      14           -
LGA    -       -      I      15           -
LGA    -       -      F      16           -
LGA    -       -      G      17           -
LGA    -       -      G      18           -
LGA    -       -      T      19           -
LGA    -       -      H      20           -
LGA    -       -      G      21           -
LGA    -       -      N      22           -
LGA    -       -      E      23           -
LGA    -       -      L      24           -
LGA    -       -      T      25           -
LGA    -       -      G      26           -
LGA    -       -      V      27           -
LGA    -       -      F      28           -
LGA    -       -      L      29           -
LGA    -       -      V      30           -
LGA    -       -      T      31           -
LGA    -       -      H      32           -
LGA    -       -      W      33           -
LGA    -       -      L      34           -
LGA    -       -      K      35           -
LGA    -       -      N      36           -
LGA    -       -      G      37           -
LGA    -       -      A      38           -
LGA    -       -      E      39           -
LGA    -       -      V      40           -
LGA    -       -      H      41           -
LGA    -       -      R      42           -
LGA    -       -      A      43           -
LGA    -       -      G      44           -
LGA    -       -      L      45           -
LGA    -       -      E      46           -
LGA    -       -      V      47           -
LGA    -       -      K      48           -
LGA    -       -      P      49           -
LGA    -       -      F      50           -
LGA    -       -      I      51           -
LGA    -       -      T      52           -
LGA    -       -      N      53           -
LGA    -       -      P      54           -
LGA    -       -      R      55           -
LGA    -       -      A      56           -
LGA    -       -      V      57           -
LGA    -       -      E      58           -
LGA    -       -      K      59           -
LGA    -       -      C      60           -
LGA    -       -      T      61           -
LGA    -       -      R      62           -
LGA    -       -      Y      63           -
LGA    K     212      I      64          2.309
LGA    E     213      D      65          1.331
LGA    F     214      C      66          2.242
LGA    -       -      D      67           -
LGA    -       -      L      68           -
LGA    -       -      N      69           -
LGA    -       -      R      70           -
LGA    -       -      V      71           -
LGA    -       -      F      72           -
LGA    -       -      D      73           -
LGA    -       -      L      74           -
LGA    -       -      E      75           -
LGA    -       -      N      76           -
LGA    -       -      L      77           -
LGA    -       -      S      78           -
LGA    -       -      K      79           -
LGA    -       -      E      80           -
LGA    -       -      M      81           -
LGA    -       -      S      82           -
LGA    -       -      E      83           -
LGA    -       -      D      84           -
LGA    -       -      L      85           -
LGA    P     215      P      86          0.826
LGA    P     216      Y      87          2.563
LGA    -       -      E      88           -
LGA    C     217      V      89          1.515
LGA    -       -      R      90           -
LGA    -       -      R      91           -
LGA    A     218      A      92          1.527
LGA    I     219      Q      93          2.252
LGA    -       -      E      94           -
LGA    -       -      I      95           -
LGA    D     220      N      96          1.554
LGA    -       -      H      97           -
LGA    -       -      L      98           -
LGA    V     221      F      99          3.232
LGA    Y     222      G     100          2.534
LGA    -       -      P     101           -
LGA    -       -      K     102           -
LGA    -       -      N     103           -
LGA    -       -      S     104           -
LGA    -       -      D     105           -
LGA    -       -      D     106           -
LGA    -       -      A     107           -
LGA    K     223      Y     108          1.767
LGA    T     298      D     109           -
LGA    K     299      V     110           -
LGA    -       -      V     111           -
LGA    -       -      F     112           -
LGA    L     300      D     113          2.939
LGA    -       -      L     114           -
LGA    -       -      H     115           -
LGA    -       -      N     116           -
LGA    -       -      T     117           -
LGA    -       -      T     118           -
LGA    -       -      S     119           -
LGA    -       -      N     120           -
LGA    -       -      M     121           -
LGA    -       -      G     122           -
LGA    -       -      C     123           -
LGA    -       -      T     124           -
LGA    -       -      L     125           -
LGA    -       -      I     126           -
LGA    -       -      L     127           -
LGA    -       -      E     128           -
LGA    -       -      D     129           -
LGA    -       -      S     130           -
LGA    -       -      R     131           -
LGA    -       -      N     132           -
LGA    -       -      D     133           -
LGA    -       -      F     134           -
LGA    -       -      L     135           -
LGA    -       -      I     136           -
LGA    -       -      Q     137           -
LGA    -       -      M     138           -
LGA    -       -      F     139           -
LGA    -       -      H     140           -
LGA    -       -      Y     141           -
LGA    -       -      I     142           -
LGA    -       -      K     143           -
LGA    -       -      T     144           -
LGA    -       -      C     145           -
LGA    -       -      M     146           -
LGA    -       -      A     147           -
LGA    -       -      P     148           -
LGA    -       -      L     149           -
LGA    -       -      P     150           -
LGA    -       -      C     151           -
LGA    -       -      S     152           -
LGA    -       -      V     153           -
LGA    -       -      Y     154           -
LGA    -       -      L     155           -
LGA    -       -      I     156           -
LGA    -       -      E     157           -
LGA    -       -      H     158           -
LGA    -       -      P     159           -
LGA    -       -      S     160           -
LGA    -       -      L     161           -
LGA    -       -      K     162           -
LGA    -       -      Y     163           -
LGA    -       -      A     164           -
LGA    -       -      T     165           -
LGA    -       -      T     166           -
LGA    T     301      R     167          3.457
LGA    -       -      S     168           -
LGA    -       -      I     169           -
LGA    L     302      A     170          1.972
LGA    N     303      K     171          2.431
LGA    -       -      Y     172           -
LGA    -       -      P     173           -
LGA    -       -      V     174           -
LGA    -       -      G     175           -
LGA    -       -      I     176           -
LGA    -       -      E     177           -
LGA    -       -      V     178           -
LGA    -       -      G     179           -
LGA    -       -      P     180           -
LGA    -       -      Q     181           -
LGA    -       -      P     182           -
LGA    -       -      H     183           -
LGA    -       -      G     184           -
LGA    -       -      V     185           -
LGA    -       -      L     186           -
LGA    -       -      R     187           -
LGA    -       -      A     188           -
LGA    -       -      D     189           -
LGA    -       -      I     190           -
LGA    -       -      L     191           -
LGA    -       -      D     192           -
LGA    -       -      Q     193           -
LGA    -       -      M     194           -
LGA    -       -      R     195           -
LGA    -       -      R     196           -
LGA    -       -      M     197           -
LGA    -       -      L     198           -
LGA    -       -      K     199           -
LGA    -       -      H     200           -
LGA    -       -      A     201           -
LGA    -       -      L     202           -
LGA    -       -      D     203           -
LGA    -       -      F     204           -
LGA    -       -      I     205           -
LGA    -       -      Q     206           -
LGA    -       -      R     207           -
LGA    -       -      F     208           -
LGA    -       -      N     209           -
LGA    -       -      E     210           -
LGA    -       -      G     211           -
LGA    -       -      K     212           -
LGA    -       -      E     213           -
LGA    -       -      F     214           -
LGA    -       -      P     215           -
LGA    -       -      P     216           -
LGA    -       -      C     217           -
LGA    -       -      A     218           -
LGA    -       -      I     219           -
LGA    -       -      D     220           -
LGA    -       -      V     221           -
LGA    -       -      Y     222           -
LGA    -       -      K     223           -
LGA    -       -      T     298           -
LGA    -       -      K     299           -
LGA    -       -      L     300           -
LGA    -       -      T     301           -
LGA    -       -      L     302           -
LGA    -       -      N     303           -
LGA    -       -      A     304           -
LGA    -       -      K     305           -
LGA    -       -      S     306           -
LGA    -       -      I     307           -
LGA    -       -      R     308           -
LGA    -       -      S     309           -
LGA    -       -      T     310           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   18  233    5.0     16    2.26    12.50      5.107     0.677

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.461467 * X  +   0.417603 * Y  +   0.782723 * Z  +  -8.903801
  Y_new =   0.852129 * X  +  -0.454117 * Y  +  -0.260104 * Z  +  59.217827
  Z_new =   0.246828 * X  +   0.787011 * Y  +  -0.565411 * Z  + -33.811783 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.193784   -0.947809  [ DEG:   125.6946    -54.3054 ]
  Theta =  -0.249405   -2.892188  [ DEG:   -14.2899   -165.7101 ]
  Phi   =   1.074467   -2.067126  [ DEG:    61.5624   -118.4376 ]
 
# 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: T0289TS239_5_1-D1                             
REMARK     2: T0289_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0289TS239_5_1-D1.T0289_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   18  233   5.0   16   2.26   12.50   5.107
REMARK  ---------------------------------------------------------- 
MOLECULE T0289TS239_5_1-D1
REMARK PARENT number 1
PFRMAT TS
TARGET T0289
PARENT 2bco_A
ATOM    979  N   LYS   212       7.834  49.842  10.169  1.00  9.99
ATOM    980  CA  LYS   212       8.690  48.656  10.090  1.00  9.99
ATOM    981  C   LYS   212       8.017  47.436  10.729  1.00  9.99
ATOM    982  O   LYS   212       8.238  47.144  11.906  1.00  9.99
ATOM    983  CB  LYS   212       9.939  49.092  10.844  1.00  9.99
ATOM    984  N   GLU   213       7.196  46.730   9.956  1.00  9.99
ATOM    985  CA  GLU   213       6.496  45.557  10.471  1.00  9.99
ATOM    986  C   GLU   213       6.964  44.268   9.804  1.00  9.99
ATOM    987  O   GLU   213       7.661  44.297   8.790  1.00  9.99
ATOM    988  CB  GLU   213       4.982  45.725  10.286  1.00  9.99
ATOM    989  N   PHE   214       6.576  43.136  10.387  1.00  9.99
ATOM    990  CA  PHE   214       6.953  41.817   9.881  1.00  9.99
ATOM    991  C   PHE   214       5.745  40.882   9.812  1.00  9.99
ATOM    992  O   PHE   214       5.881  39.670   9.975  1.00  9.99
ATOM    993  CB  PHE   214       8.017  41.202  10.798  1.00  9.99
ATOM    994  N   PRO   215       4.572  41.451   9.560  1.00  9.99
ATOM    995  CA  PRO   215       3.342  40.676   9.493  1.00  9.99
ATOM    996  C   PRO   215       3.146  39.977   8.145  1.00  9.99
ATOM    997  O   PRO   215       2.412  38.991   8.052  1.00  9.99
ATOM    998  CB  PRO   215       2.148  41.590   9.786  1.00  9.99
ATOM    999  N   PRO   216       3.804  40.485   7.106  1.00  9.99
ATOM   1000  CA  PRO   216       3.708  39.914   5.759  1.00  9.99
ATOM   1001  C   PRO   216       4.418  38.570   5.632  1.00  9.99
ATOM   1002  O   PRO   216       5.249  38.206   6.465  1.00  9.99
ATOM   1003  CB  PRO   216       4.301  40.884   4.736  1.00  9.99
ATOM   1004  N   CYS   217       4.094  37.839   4.572  1.00  9.99
ATOM   1005  CA  CYS   217       4.703  36.537   4.331  1.00  9.99
ATOM   1006  C   CYS   217       6.024  36.648   3.573  1.00  9.99
ATOM   1007  O   CYS   217       6.296  37.660   2.914  1.00  9.99
ATOM   1008  CB  CYS   217       3.757  35.641   3.531  1.00  9.99
ATOM   1009  N   ALA   218       6.865  35.604   3.661  1.00  9.99
ATOM   1010  CA  ALA   218       8.146  35.636   2.950  1.00  9.99
ATOM   1011  C   ALA   218       7.935  35.422   1.456  1.00  9.99
ATOM   1012  O   ALA   218       7.148  34.560   1.053  1.00  9.99
ATOM   1013  CB  ALA   218       8.924  34.487   3.582  1.00  9.99
ATOM   1014  N   ILE   219       8.617  36.220   0.638  1.00  9.99
ATOM   1015  CA  ILE   219       8.515  36.057  -0.806  1.00  9.99
ATOM   1016  C   ILE   219       9.200  34.731  -1.129  1.00  9.99
ATOM   1017  O   ILE   219      10.036  34.256  -0.358  1.00  9.99
ATOM   1018  CB  ILE   219       9.225  37.208  -1.528  1.00  9.99
ATOM   1019  N   ASP   220       8.841  34.120  -2.247  1.00  9.99
ATOM   1020  CA  ASP   220       9.468  32.866  -2.628  1.00  9.99
ATOM   1021  C   ASP   220      10.913  33.162  -3.053  1.00  9.99
ATOM   1022  O   ASP   220      11.169  34.145  -3.756  1.00  9.99
ATOM   1023  CB  ASP   220       8.690  32.203  -3.781  1.00  9.99
ATOM   1024  N   VAL   221      11.850  32.330  -2.606  1.00  9.99
ATOM   1025  CA  VAL   221      13.257  32.518  -2.939  1.00  9.99
ATOM   1026  C   VAL   221      13.651  31.477  -3.988  1.00  9.99
ATOM   1027  O   VAL   221      13.406  30.279  -3.814  1.00  9.99
ATOM   1028  CB  VAL   221      14.135  32.338  -1.691  1.00  9.99
ATOM   1029  N   TYR   222      14.253  31.938  -5.080  1.00  9.99
ATOM   1030  CA  TYR   222      14.678  31.051  -6.159  1.00  9.99
ATOM   1031  C   TYR   222      16.188  31.133  -6.319  1.00  9.99
ATOM   1032  O   TYR   222      16.803  32.108  -5.914  1.00  9.99
ATOM   1033  CB  TYR   222      14.030  31.459  -7.488  1.00  9.99
ATOM   1034  N   LYS   223      16.777  30.094  -6.895  1.00  9.99
ATOM   1035  CA  LYS   223      18.210  30.062  -7.163  1.00  9.99
ATOM   1036  C   LYS   223      18.315  29.563  -8.594  1.00  9.99
ATOM   1037  O   LYS   223      17.368  28.973  -9.116  1.00  9.99
ATOM   1038  CB  LYS   223      18.952  29.103  -6.215  1.00  9.99
ATOM   1370  N   THR   298      23.925  38.257   8.326  1.00  9.99
ATOM   1371  CA  THR   298      23.178  39.325   7.684  1.00  9.99
ATOM   1372  C   THR   298      23.055  39.206   6.174  1.00  9.99
ATOM   1373  O   THR   298      22.575  40.129   5.515  1.00  9.99
ATOM   1374  CB  THR   298      23.839  40.662   8.062  1.00  9.99
ATOM   1375  N   LYS   299      23.486  38.073   5.628  1.00  9.99
ATOM   1376  CA  LYS   299      23.435  37.825   4.193  1.00  9.99
ATOM   1377  C   LYS   299      22.506  36.642   3.898  1.00  9.99
ATOM   1378  O   LYS   299      22.589  35.597   4.554  1.00  9.99
ATOM   1379  CB  LYS   299      24.849  37.519   3.676  1.00  9.99
ATOM   1380  N   LEU   300      21.624  36.799   2.917  1.00  9.99
ATOM   1381  CA  LEU   300      20.715  35.711   2.581  1.00  9.99
ATOM   1382  C   LEU   300      21.442  34.730   1.670  1.00  9.99
ATOM   1383  O   LEU   300      21.787  35.068   0.534  1.00  9.99
ATOM   1384  CB  LEU   300      19.446  36.231   1.883  1.00  9.99
ATOM   1385  N   THR   301      21.679  33.521   2.174  1.00  9.99
ATOM   1386  CA  THR   301      22.366  32.489   1.403  1.00  9.99
ATOM   1387  C   THR   301      21.488  31.251   1.312  1.00  9.99
ATOM   1388  O   THR   301      20.494  31.137   2.027  1.00  9.99
ATOM   1389  CB  THR   301      23.725  32.083   2.058  1.00  9.99
ATOM   1390  N   LEU   302      21.836  30.329   0.427  1.00  9.99
ATOM   1391  CA  LEU   302      21.052  29.105   0.302  1.00  9.99
ATOM   1392  C   LEU   302      21.863  27.820   0.478  1.00  9.99
ATOM   1393  O   LEU   302      23.087  27.805   0.314  1.00  9.99
ATOM   1394  CB  LEU   302      20.302  29.065  -1.030  1.00  9.99
ATOM   1395  N   ASN   303      21.147  26.744   0.804  1.00  9.99
ATOM   1396  CA  ASN   303      21.720  25.420   1.051  1.00  9.99
ATOM   1397  C   ASN   303      22.394  25.361   2.420  1.00  9.99
ATOM   1398  O   ASN   303      21.758  24.829   3.352  1.00  9.99
ATOM   1399  CB  ASN   303      22.731  25.045  -0.039  1.00  9.99
TER
END
