
#######################################################
#                                                     #
#                        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   17 (   85),  selected   17 , name T0289TS239_4_1-D1
# Molecule2: number of CA atoms  233 ( 1850),  selected  233 , name T0289_D1.pdb
# PARAMETERS: T0289TS239_4_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     213      E       8           #
LGA    F     214      P       9          5.060
LGA    P     215      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    P     216      A      43           #
LGA    C     217      G      44          1.347
LGA    A     218      L      45          0.943
LGA    I     219      E      46          1.516
LGA    D     220      V      47          1.991
LGA    V     221      K      48          1.911
LGA    Y     222      P      49          1.228
LGA    K     223      F      50          0.723
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    -       -      I      64           -
LGA    -       -      D      65           -
LGA    -       -      C      66           -
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      86           -
LGA    -       -      Y      87           -
LGA    -       -      E      88           -
LGA    -       -      V      89           -
LGA    -       -      R      90           -
LGA    -       -      R      91           -
LGA    -       -      A      92           -
LGA    -       -      Q      93           -
LGA    -       -      E      94           -
LGA    -       -      I      95           -
LGA    -       -      N      96           -
LGA    -       -      H      97           -
LGA    -       -      L      98           -
LGA    -       -      F      99           -
LGA    -       -      G     100           -
LGA    -       -      P     101           -
LGA    -       -      K     102           -
LGA    -       -      N     103           -
LGA    T     298      S     104          4.073
LGA    -       -      D     105           -
LGA    -       -      D     106           -
LGA    K     299      A     107          2.651
LGA    L     300      Y     108          2.393
LGA    -       -      D     109           -
LGA    -       -      V     110           -
LGA    T     301      V     111          3.953
LGA    L     302      F     112          3.936
LGA    N     303      D     113          0.941
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    -       -      R     167           -
LGA    -       -      S     168           -
LGA    -       -      I     169           -
LGA    -       -      A     170           -
LGA    -       -      K     171           -
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)   17  233    5.0     14    2.69     0.00      4.522     0.501

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.681047 * X  +   0.264342 * Y  +  -0.682860 * Z  +  12.871771
  Y_new =  -0.703838 * X  +  -0.493533 * Y  +   0.510918 * Z  +  53.368629
  Z_new =  -0.201957 * X  +   0.828582 * Y  +   0.522174 * Z  + -50.916965 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.008466   -2.133127  [ DEG:    57.7808   -122.2192 ]
  Theta =   0.203355    2.938237  [ DEG:    11.6514    168.3486 ]
  Phi   =  -2.339739    0.801853  [ DEG:  -134.0572     45.9428 ]
 
# 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_4_1-D1                             
REMARK     2: T0289_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0289TS239_4_1-D1.T0289_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   17  233   5.0   14   2.69    0.00   4.522
REMARK  ---------------------------------------------------------- 
MOLECULE T0289TS239_4_1-D1
REMARK PARENT number 1
PFRMAT TS
TARGET T0289
PARENT 2bco_A
ATOM    984  N   GLU   213      26.159  20.363 -18.285  1.00  9.99
ATOM    985  CA  GLU   213      27.508  20.613 -17.788  1.00  9.99
ATOM    986  C   GLU   213      27.552  21.774 -16.800  1.00  9.99
ATOM    987  O   GLU   213      26.591  22.532 -16.671  1.00  9.99
ATOM    988  CB  GLU   213      28.459  20.883 -18.961  1.00  9.99
ATOM    989  N   PHE   214      28.679  21.905 -16.104  1.00  9.99
ATOM    990  CA  PHE   214      28.875  22.957 -15.107  1.00  9.99
ATOM    991  C   PHE   214      30.226  23.650 -15.288  1.00  9.99
ATOM    992  O   PHE   214      30.829  24.109 -14.319  1.00  9.99
ATOM    993  CB  PHE   214      28.802  22.350 -13.701  1.00  9.99
ATOM    994  N   PRO   215      30.688  23.728 -16.531  1.00  9.99
ATOM    995  CA  PRO   215      31.972  24.340 -16.835  1.00  9.99
ATOM    996  C   PRO   215      31.908  25.869 -16.900  1.00  9.99
ATOM    997  O   PRO   215      32.926  26.546 -16.740  1.00  9.99
ATOM    998  CB  PRO   215      32.501  23.783 -18.160  1.00  9.99
ATOM    999  N   PRO   216      30.714  26.409 -17.132  1.00  9.99
ATOM   1000  CA  PRO   216      30.509  27.858 -17.218  1.00  9.99
ATOM   1001  C   PRO   216      30.634  28.556 -15.867  1.00  9.99
ATOM   1002  O   PRO   216      30.566  27.924 -14.813  1.00  9.99
ATOM   1003  CB  PRO   216      29.128  28.157 -17.803  1.00  9.99
ATOM   1004  N   CYS   217      30.803  29.872 -15.907  1.00  9.99
ATOM   1005  CA  CYS   217      30.932  30.659 -14.687  1.00  9.99
ATOM   1006  C   CYS   217      29.575  31.076 -14.123  1.00  9.99
ATOM   1007  O   CYS   217      28.565  31.086 -14.837  1.00  9.99
ATOM   1008  CB  CYS   217      31.758  31.921 -14.945  1.00  9.99
ATOM   1009  N   ALA   218      29.538  31.421 -12.825  1.00  9.99
ATOM   1010  CA  ALA   218      28.273  31.842 -12.217  1.00  9.99
ATOM   1011  C   ALA   218      27.903  33.251 -12.669  1.00  9.99
ATOM   1012  O   ALA   218      28.764  34.135 -12.723  1.00  9.99
ATOM   1013  CB  ALA   218      28.568  31.787 -10.722  1.00  9.99
ATOM   1014  N   ILE   219      26.635  33.451 -13.015  1.00  9.99
ATOM   1015  CA  ILE   219      26.180  34.776 -13.414  1.00  9.99
ATOM   1016  C   ILE   219      26.229  35.635 -12.153  1.00  9.99
ATOM   1017  O   ILE   219      26.189  35.112 -11.039  1.00  9.99
ATOM   1018  CB  ILE   219      24.746  34.713 -13.954  1.00  9.99
ATOM   1019  N   ASP   220      26.338  36.945 -12.316  1.00  9.99
ATOM   1020  CA  ASP   220      26.368  37.824 -11.160  1.00  9.99
ATOM   1021  C   ASP   220      24.965  37.847 -10.537  1.00  9.99
ATOM   1022  O   ASP   220      23.963  37.911 -11.256  1.00  9.99
ATOM   1023  CB  ASP   220      26.797  39.244 -11.575  1.00  9.99
ATOM   1024  N   VAL   221      24.898  37.767  -9.211  1.00  9.99
ATOM   1025  CA  VAL   221      23.619  37.770  -8.510  1.00  9.99
ATOM   1026  C   VAL   221      23.426  39.141  -7.860  1.00  9.99
ATOM   1027  O   VAL   221      24.307  39.633  -7.149  1.00  9.99
ATOM   1028  CB  VAL   221      23.597  36.684  -7.424  1.00  9.99
ATOM   1029  N   TYR   222      22.275  39.757  -8.112  1.00  9.99
ATOM   1030  CA  TYR   222      21.965  41.070  -7.556  1.00  9.99
ATOM   1031  C   TYR   222      20.739  40.967  -6.662  1.00  9.99
ATOM   1032  O   TYR   222      19.948  40.046  -6.798  1.00  9.99
ATOM   1033  CB  TYR   222      21.664  42.078  -8.672  1.00  9.99
ATOM   1034  N   LYS   223      20.602  41.908  -5.738  1.00  9.99
ATOM   1035  CA  LYS   223      19.446  41.965  -4.850  1.00  9.99
ATOM   1036  C   LYS   223      19.020  43.423  -4.879  1.00  9.99
ATOM   1037  O   LYS   223      19.805  44.291  -5.262  1.00  9.99
ATOM   1038  CB  LYS   223      19.804  41.549  -3.413  1.00  9.99
ATOM   1370  N   THR   298      17.542  23.867  -1.922  1.00  9.99
ATOM   1371  CA  THR   298      17.261  23.968  -3.343  1.00  9.99
ATOM   1372  C   THR   298      16.771  25.330  -3.807  1.00  9.99
ATOM   1373  O   THR   298      16.362  25.485  -4.958  1.00  9.99
ATOM   1374  CB  THR   298      16.236  22.881  -3.705  1.00  9.99
ATOM   1375  N   LYS   299      16.812  26.314  -2.915  1.00  9.99
ATOM   1376  CA  LYS   299      16.369  27.669  -3.219  1.00  9.99
ATOM   1377  C   LYS   299      17.547  28.643  -3.115  1.00  9.99
ATOM   1378  O   LYS   299      18.311  28.605  -2.144  1.00  9.99
ATOM   1379  CB  LYS   299      15.264  28.079  -2.233  1.00  9.99
ATOM   1380  N   LEU   300      17.699  29.514  -4.107  1.00  9.99
ATOM   1381  CA  LEU   300      18.795  30.472  -4.067  1.00  9.99
ATOM   1382  C   LEU   300      18.383  31.651  -3.195  1.00  9.99
ATOM   1383  O   LEU   300      17.468  32.400  -3.546  1.00  9.99
ATOM   1384  CB  LEU   300      19.163  30.968  -5.476  1.00  9.99
ATOM   1385  N   THR   301      19.055  31.806  -2.056  1.00  9.99
ATOM   1386  CA  THR   301      18.758  32.896  -1.132  1.00  9.99
ATOM   1387  C   THR   301      20.015  33.718  -0.894  1.00  9.99
ATOM   1388  O   THR   301      21.113  33.298  -1.254  1.00  9.99
ATOM   1389  CB  THR   301      18.247  32.368   0.246  1.00  9.99
ATOM   1390  N   LEU   302      19.863  34.895  -0.304  1.00  9.99
ATOM   1391  CA  LEU   302      21.029  35.726  -0.024  1.00  9.99
ATOM   1392  C   LEU   302      21.176  36.124   1.446  1.00  9.99
ATOM   1393  O   LEU   302      20.211  36.111   2.216  1.00  9.99
ATOM   1394  CB  LEU   302      21.036  36.979  -0.902  1.00  9.99
ATOM   1395  N   ASN   303      22.406  36.487   1.808  1.00  9.99
ATOM   1396  CA  ASN   303      22.781  36.875   3.169  1.00  9.99
ATOM   1397  C   ASN   303      22.897  35.652   4.076  1.00  9.99
ATOM   1398  O   ASN   303      24.042  35.212   4.304  1.00  9.99
ATOM   1399  CB  ASN   303      21.766  37.861   3.760  1.00  9.99
TER
END
