
#######################################################
#                                                     #
#                        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   10 (   84),  selected   10 , name T0386TS074_1_2-D1
# Molecule2: number of CA atoms  206 ( 1668),  selected  206 , name T0386_D1.pdb
# PARAMETERS: T0386TS074_1_2-D1.T0386_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    -       -      I      13           -
LGA    -       -      I      14           -
LGA    -       -      S      15           -
LGA    -       -      P      16           -
LGA    -       -      H      17           -
LGA    -       -      H      18           -
LGA    -       -      Y      19           -
LGA    -       -      V      20           -
LGA    -       -      Y      21           -
LGA    -       -      P      22           -
LGA    -       -      N      23           -
LGA    -       -      T      24           -
LGA    -       -      T      25           -
LGA    -       -      T      26           -
LGA    -       -      L      27           -
LGA    -       -      K      28           -
LGA    -       -      N      29           -
LGA    -       -      K      30           -
LGA    -       -      Y      31           -
LGA    -       -      G      32           -
LGA    -       -      I      33           -
LGA    -       -      K      34           -
LGA    -       -      N      35           -
LGA    -       -      L      36           -
LGA    -       -      N      37           -
LGA    -       -      A      38           -
LGA    -       -      F      39           -
LGA    -       -      L      40           -
LGA    -       -      E      41           -
LGA    -       -      K      42           -
LGA    -       -      C      43           -
LGA    -       -      S      44           -
LGA    -       -      H      45           -
LGA    -       -      D      46           -
LGA    -       -      T      47           -
LGA    -       -      A      48           -
LGA    -       -      K      49           -
LGA    -       -      A      50           -
LGA    -       -      M      51           -
LGA    -       -      I      52           -
LGA    -       -      N      53           -
LGA    -       -      L      54           -
LGA    -       -      R      55           -
LGA    -       -      E      56           -
LGA    -       -      E      57           -
LGA    -       -      S      58           -
LGA    -       -      L      59           -
LGA    -       -      P      60           -
LGA    -       -      E      61           -
LGA    -       -      Y      62           -
LGA    -       -      F      63           -
LGA    -       -      D      64           -
LGA    -       -      T      65           -
LGA    -       -      A      66           -
LGA    -       -      Y      67           -
LGA    -       -      L      68           -
LGA    -       -      C      69           -
LGA    -       -      H      70           -
LGA    -       -      I      71           -
LGA    -       -      H      72           -
LGA    -       -      Q      73           -
LGA    -       -      Q      74           -
LGA    -       -      L      75           -
LGA    -       -      F      76           -
LGA    -       -      K      77           -
LGA    -       -      N      78           -
LGA    -       -      T      79           -
LGA    -       -      F      80           -
LGA    -       -      E      81           -
LGA    -       -      W      82           -
LGA    -       -      A      83           -
LGA    -       -      G      84           -
LGA    P     209      Y      85          4.474
LGA    M     210      L      86          2.225
LGA    -       -      R      87           -
LGA    -       -      H      88           -
LGA    -       -      I      89           -
LGA    -       -      P      90           -
LGA    -       -      F      91           -
LGA    -       -      T      92           -
LGA    -       -      F      93           -
LGA    -       -      A      94           -
LGA    -       -      D      95           -
LGA    -       -      G      96           -
LGA    -       -      T      97           -
LGA    -       -      T      98           -
LGA    -       -      A      99           -
LGA    -       -      A     100           -
LGA    -       -      M     101           -
LGA    -       -      P     102           -
LGA    -       -      E     103           -
LGA    -       -      M     104           -
LGA    -       -      K     105           -
LGA    -       -      R     106           -
LGA    -       -      T     107           -
LGA    -       -      G     108           -
LGA    -       -      W     109           -
LGA    -       -      K     110           -
LGA    -       -      N     111           -
LGA    -       -      A     112           -
LGA    -       -      F     113           -
LGA    -       -      A     114           -
LGA    -       -      I     115           -
LGA    -       -      G     116           -
LGA    -       -      D     117           -
LGA    -       -      E     118           -
LGA    -       -      I     119           -
LGA    -       -      Q     120           -
LGA    -       -      E     121           -
LGA    -       -      G     122           -
LGA    -       -      L     123           -
LGA    -       -      Q     124           -
LGA    -       -      R     125           -
LGA    -       -      L     126           -
LGA    -       -      D     127           -
LGA    -       -      Q     128           -
LGA    -       -      T     129           -
LGA    -       -      L     130           -
LGA    -       -      A     131           -
LGA    -       -      E     132           -
LGA    -       -      K     133           -
LGA    -       -      N     134           -
LGA    -       -      N     135           -
LGA    -       -      L     136           -
LGA    -       -      Q     137           -
LGA    -       -      G     138           -
LGA    -       -      L     139           -
LGA    -       -      T     140           -
LGA    -       -      R     141           -
LGA    -       -      E     142           -
LGA    -       -      E     143           -
LGA    -       -      F     144           -
LGA    -       -      N     145           -
LGA    -       -      S     146           -
LGA    -       -      E     147           -
LGA    -       -      A     148           -
LGA    -       -      I     149           -
LGA    -       -      E     150           -
LGA    -       -      L     151           -
LGA    -       -      F     152           -
LGA    -       -      N     153           -
LGA    -       -      S     154           -
LGA    -       -      L     155           -
LGA    -       -      N     156           -
LGA    -       -      Q     157           -
LGA    -       -      L     158           -
LGA    -       -      H     159           -
LGA    -       -      P     160           -
LGA    Q     211      F     161          1.144
LGA    H     212      R     162          2.762
LGA    L     213      E     163          3.937
LGA    F     214      G     164          5.050
LGA    E     215      N     165          1.467
LGA    D     216      G     166          3.290
LGA    I     217      R     167          2.659
LGA    -       -      T     168           -
LGA    S     218      Q     169          3.012
LGA    -       -      R     170           -
LGA    -       -      L     171           -
LGA    -       -      F     172           -
LGA    -       -      F     173           -
LGA    -       -      E     174           -
LGA    -       -      N     175           -
LGA    -       -      L     176           -
LGA    -       -      A     177           -
LGA    -       -      K     178           -
LGA    -       -      A     179           -
LGA    -       -      A     180           -
LGA    -       -      G     181           -
LGA    -       -      H     182           -
LGA    -       -      Q     183           -
LGA    -       -      L     184           -
LGA    -       -      N     185           -
LGA    -       -      F     186           -
LGA    -       -      S     187           -
LGA    -       -      L     188           -
LGA    -       -      I     189           -
LGA    -       -      T     190           -
LGA    -       -      K     191           -
LGA    -       -      E     192           -
LGA    -       -      R     193           -
LGA    -       -      M     194           -
LGA    -       -      M     195           -
LGA    -       -      V     196           -
LGA    -       -      A     197           -
LGA    -       -      S     198           -
LGA    -       -      V     199           -
LGA    -       -      A     200           -
LGA    -       -      V     201           -
LGA    -       -      A     202           -
LGA    -       -      E     203           -
LGA    -       -      N     204           -
LGA    -       -      G     205           -
LGA    -       -      D     206           -
LGA    -       -      L     207           -
LGA    -       -      E     208           -
LGA    -       -      P     209           -
LGA    -       -      M     210           -
LGA    -       -      Q     211           -
LGA    -       -      H     212           -
LGA    -       -      L     213           -
LGA    -       -      F     214           -
LGA    -       -      E     215           -
LGA    -       -      D     216           -
LGA    -       -      I     217           -
LGA    -       -      S     218           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   10  206    5.0     10    3.23     0.00      3.442     0.301

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.396474 * X  +  -0.071750 * Y  +  -0.915238 * Z  +  15.493393
  Y_new =  -0.665867 * X  +  -0.708792 * Y  +  -0.232883 * Z  +  97.931946
  Z_new =  -0.632004 * X  +   0.701759 * Y  +  -0.328794 * Z  +   5.378340 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.008951   -1.132641  [ DEG:   115.1044    -64.8956 ]
  Theta =   0.684136    2.457456  [ DEG:    39.1981    140.8019 ]
  Phi   =  -1.033747    2.107845  [ DEG:   -59.2294    120.7706 ]
 
# 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: T0386TS074_1_2-D1                             
REMARK     2: T0386_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0386TS074_1_2-D1.T0386_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   10  206   5.0   10   3.23    0.00   3.442
REMARK  ---------------------------------------------------------- 
MOLECULE T0386TS074_1_2-D1
REMARK PARENT number 2
PFRMAT TS
TARGET T0386
PARENT 2g03_A
ATOM   1386  N   PRO   209      14.951  61.449  42.063  1.00  1.05
ATOM   1387  CA  PRO   209      13.991  62.420  42.566  1.00  1.05
ATOM   1388  C   PRO   209      13.080  61.635  43.462  1.00  1.05
ATOM   1389  O   PRO   209      13.043  61.905  44.656  1.00  1.05
ATOM   1390  CB  PRO   209      13.095  63.041  41.478  1.00  1.05
ATOM   1391  CG  PRO   209      13.357  62.538  40.058  1.00  1.15
ATOM   1392  CD  PRO   209      14.075  61.008  40.593  1.00  1.15
ATOM   1393  N   MET   210      12.423  60.626  42.865  1.00  0.90
ATOM   1394  CA  MET   210      11.425  59.835  43.533  1.00  0.90
ATOM   1395  C   MET   210      11.833  59.266  44.863  1.00  0.90
ATOM   1396  O   MET   210      11.168  59.556  45.845  1.00  0.90
ATOM   1397  CB  MET   210      10.973  58.715  42.596  1.00  0.90
ATOM   1398  CG  MET   210       9.853  57.824  43.142  1.00  1.00
ATOM   1399  SD  MET   210       8.281  58.745  43.377  1.00  1.00
ATOM   1400  CE  MET   210       7.232  57.473  43.996  1.00  1.20
ATOM   1401  N   GLN   211      12.888  58.822  45.056  1.00  0.90
ATOM   1402  CA  GLN   211      13.225  58.001  46.219  1.00  0.90
ATOM   1403  C   GLN   211      14.055  58.751  47.283  1.00  0.90
ATOM   1404  O   GLN   211      13.799  58.611  48.474  1.00  0.90
ATOM   1405  CB  GLN   211      13.912  56.693  45.792  1.00  0.90
ATOM   1406  CG  GLN   211      14.235  55.749  46.916  1.00  1.00
ATOM   1407  CD  GLN   211      13.092  55.187  47.628  1.00  1.00
ATOM   1408  OE1 GLN   211      12.260  54.508  47.000  1.00  1.20
ATOM   1409  NE2 GLN   211      12.997  55.387  48.941  1.00  1.20
ATOM   1410  N   HIS   212      15.019  59.560  46.856  1.00  0.90
ATOM   1411  CA  HIS   212      15.885  60.261  47.789  1.00  0.90
ATOM   1412  C   HIS   212      15.138  61.354  48.565  1.00  0.90
ATOM   1413  O   HIS   212      15.308  61.500  49.788  1.00  0.90
ATOM   1414  CB  HIS   212      17.085  60.846  47.058  1.00  0.90
ATOM   1415  CG  HIS   212      18.106  61.548  47.963  1.00  1.00
ATOM   1416  ND1 HIS   212      17.881  62.860  48.418  1.00  1.00
ATOM   1417  CD2 HIS   212      19.203  61.054  48.507  1.00  1.20
ATOM   1418  CE1 HIS   212      18.910  63.192  49.264  1.00  1.20
ATOM   1419  NE2 HIS   212      19.742  62.078  49.322  1.00  1.50
ATOM   1420  N   LEU   213      14.300  62.115  47.861  1.00  0.90
ATOM   1421  CA  LEU   213      13.460  63.129  48.486  1.00  0.90
ATOM   1422  C   LEU   213      12.479  62.477  49.450  1.00  0.90
ATOM   1423  O   LEU   213      12.308  62.957  50.571  1.00  0.90
ATOM   1424  CB  LEU   213      12.730  64.000  47.420  1.00  0.90
ATOM   1425  CG  LEU   213      11.926  65.089  48.129  1.00  1.00
ATOM   1426  CD1 LEU   213      12.808  66.022  48.833  1.00  1.00
ATOM   1427  CD2 LEU   213      11.320  66.020  46.904  1.00  1.20
ATOM   1428  N   PHE   214      11.837  61.387  49.034  1.00  0.90
ATOM   1429  CA  PHE   214      10.901  60.699  49.928  1.00  0.90
ATOM   1430  C   PHE   214      11.632  60.174  51.195  1.00  0.90
ATOM   1431  O   PHE   214      11.294  60.539  52.316  1.00  0.90
ATOM   1432  CB  PHE   214      10.146  59.549  49.211  1.00  0.90
ATOM   1433  CG  PHE   214       9.240  60.111  48.101  1.00  1.00
ATOM   1434  CD1 PHE   214       8.718  61.398  48.287  1.00  1.00
ATOM   1435  CD2 PHE   214       8.589  59.253  47.246  1.00  1.20
ATOM   1436  CE1 PHE   214       7.716  61.838  47.447  1.00  1.20
ATOM   1437  CE2 PHE   214       7.607  59.668  46.385  1.00  1.50
ATOM   1438  CZ  PHE   214       7.171  61.016  46.479  1.00  1.50
ATOM   1439  N   GLU   215      12.663  59.367  51.017  1.00  0.90
ATOM   1440  CA  GLU   215      13.292  58.717  52.159  1.00  0.90
ATOM   1441  C   GLU   215      14.153  59.608  53.074  1.00  0.90
ATOM   1442  O   GLU   215      14.090  59.446  54.283  1.00  0.90
ATOM   1443  CB  GLU   215      13.979  57.410  51.733  1.00  0.90
ATOM   1444  CG  GLU   215      12.991  56.383  51.248  1.00  1.00
ATOM   1445  CD  GLU   215      12.021  55.908  52.379  1.00  1.00
ATOM   1446  OE1 GLU   215      12.425  55.712  53.535  1.00  1.20
ATOM   1447  OE2 GLU   215      10.825  55.694  52.044  1.00  1.20
ATOM   1448  N   ASP   216      14.931  60.532  52.510  1.00  0.90
ATOM   1449  CA  ASP   216      15.655  61.511  53.322  1.00  0.90
ATOM   1450  C   ASP   216      14.679  62.450  54.018  1.00  0.90
ATOM   1451  O   ASP   216      14.965  62.944  55.112  1.00  0.90
ATOM   1452  CB  ASP   216      16.665  62.309  52.498  1.00  0.90
ATOM   1453  CG  ASP   216      17.857  61.503  52.038  1.00  1.00
ATOM   1454  OD1 ASP   216      18.123  60.384  52.542  1.00  1.00
ATOM   1455  OD2 ASP   216      18.658  61.956  51.217  1.00  1.20
ATOM   1456  N   ILE   217      13.525  62.684  53.387  1.00  0.90
ATOM   1457  CA  ILE   217      12.457  63.479  53.958  1.00  0.90
ATOM   1458  C   ILE   217      11.797  62.831  55.158  1.00  0.90
ATOM   1459  O   ILE   217      11.559  63.489  56.165  1.00  0.90
ATOM   1460  CB  ILE   217      13.457  63.918  55.029  1.00  0.90
ATOM   1461  CG1 ILE   217      12.883  64.827  56.118  1.00  1.00
ATOM   1462  CG2 ILE   217      14.668  64.522  54.307  1.00  1.00
ATOM   1463  CD1 ILE   217      13.741  64.968  57.334  1.00  1.20
ATOM   1464  N   SER   218      11.374  61.129  56.485  1.00  0.90
ATOM   1465  CA  SER   218      10.771  60.306  57.534  1.00  0.90
ATOM   1466  C   SER   218      11.691  60.232  58.758  1.00  0.90
ATOM   1467  O   SER   218      11.233  60.383  59.882  1.00  0.90
ATOM   1468  CB  SER   218      10.467  58.866  57.021  1.00  0.90
ATOM   1469  OG  SER   218       9.770  58.035  58.098  1.00  1.00
TER
END
