
#######################################################
#                                                     #
#                        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_3_2-D1
# Molecule2: number of CA atoms  206 ( 1668),  selected  206 , name T0386_D1.pdb
# PARAMETERS: T0386TS074_3_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    -       -      Y      85           -
LGA    -       -      L      86           -
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    -       -      F     161           -
LGA    -       -      R     162           -
LGA    -       -      E     163           -
LGA    -       -      G     164           -
LGA    -       -      N     165           -
LGA    -       -      G     166           -
LGA    -       -      R     167           -
LGA    -       -      T     168           -
LGA    -       -      Q     169           -
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    P     209      M     195          0.884
LGA    M     210      V     196          0.965
LGA    Q     211      A     197          0.629
LGA    H     212      S     198          0.734
LGA    L     213      V     199          0.457
LGA    F     214      A     200          0.781
LGA    E     215      V     201          0.934
LGA    D     216      A     202          0.798
LGA    I     217      E     203          0.804
LGA    S     218      N     204          0.673
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    0.78     0.00      4.854     1.137

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.822953 * X  +  -0.521978 * Y  +   0.224248 * Z  +  48.629559
  Y_new =   0.558700 * X  +  -0.815147 * Y  +   0.152933 * Z  + 100.104301
  Z_new =   0.102968 * X  +   0.251145 * Y  +   0.962457 * Z  +  50.993118 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.255249   -2.886343  [ DEG:    14.6247   -165.3753 ]
  Theta =  -0.103150   -3.038442  [ DEG:    -5.9101   -174.0899 ]
  Phi   =   2.545171   -0.596422  [ DEG:   145.8275    -34.1725 ]
 
# 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_3_2-D1                             
REMARK     2: T0386_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0386TS074_3_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   0.78    0.00   4.854
REMARK  ---------------------------------------------------------- 
MOLECULE T0386TS074_3_2-D1
REMARK PARENT number 2
PFRMAT TS
TARGET T0386
PARENT 2g03_A
ATOM   1386  N   PRO   209      19.446  56.456  62.385  1.00  0.57
ATOM   1387  CA  PRO   209      20.779  55.879  62.466  1.00  0.57
ATOM   1388  C   PRO   209      20.616  54.649  63.312  1.00  0.57
ATOM   1389  O   PRO   209      20.799  53.550  62.801  1.00  0.57
ATOM   1390  CB  PRO   209      21.808  56.766  63.191  1.00  0.57
ATOM   1391  CG  PRO   209      21.265  58.100  63.705  1.00  0.67
ATOM   1392  CD  PRO   209      19.587  57.537  63.778  1.00  0.67
ATOM   1393  N   MET   210      20.200  54.874  64.569  1.00  0.50
ATOM   1394  CA  MET   210      20.095  53.833  65.558  1.00  0.50
ATOM   1395  C   MET   210      19.247  52.653  65.169  1.00  0.50
ATOM   1396  O   MET   210      19.757  51.543  65.194  1.00  0.50
ATOM   1397  CB  MET   210      19.584  54.443  66.862  1.00  0.50
ATOM   1398  CG  MET   210      20.529  55.452  67.522  1.00  0.60
ATOM   1399  SD  MET   210      22.097  54.677  68.082  1.00  0.60
ATOM   1400  CE  MET   210      21.528  53.697  69.430  1.00  0.80
ATOM   1401  N   GLN   211      18.084  52.923  64.622  1.00  0.50
ATOM   1402  CA  GLN   211      17.219  51.757  64.436  1.00  0.50
ATOM   1403  C   GLN   211      17.400  51.069  63.066  1.00  0.50
ATOM   1404  O   GLN   211      17.431  49.844  62.991  1.00  0.50
ATOM   1405  CB  GLN   211      15.745  52.115  64.691  1.00  0.50
ATOM   1406  CG  GLN   211      14.785  50.963  64.592  1.00  0.60
ATOM   1407  CD  GLN   211      14.944  49.910  65.589  1.00  0.60
ATOM   1408  OE1 GLN   211      14.826  50.194  66.795  1.00  0.80
ATOM   1409  NE2 GLN   211      15.170  48.666  65.174  1.00  0.80
ATOM   1410  N   HIS   212      17.549  51.846  61.998  1.00  0.50
ATOM   1411  CA  HIS   212      17.669  51.283  60.664  1.00  0.50
ATOM   1412  C   HIS   212      18.998  50.541  60.464  1.00  0.50
ATOM   1413  O   HIS   212      19.035  49.439  59.891  1.00  0.50
ATOM   1414  CB  HIS   212      17.499  52.373  59.615  1.00  0.50
ATOM   1415  CG  HIS   212      17.536  51.874  58.164  1.00  0.60
ATOM   1416  ND1 HIS   212      18.759  51.602  57.527  1.00  0.60
ATOM   1417  CD2 HIS   212      16.526  51.541  57.381  1.00  0.80
ATOM   1418  CE1 HIS   212      18.480  51.102  56.280  1.00  0.80
ATOM   1419  NE2 HIS   212      17.094  51.064  56.176  1.00  1.10
ATOM   1420  N   LEU   213      20.088  51.137  60.948  1.00  0.50
ATOM   1421  CA  LEU   213      21.401  50.504  60.909  1.00  0.50
ATOM   1422  C   LEU   213      21.395  49.235  61.749  1.00  0.50
ATOM   1423  O   LEU   213      21.898  48.201  61.305  1.00  0.50
ATOM   1424  CB  LEU   213      22.522  51.489  61.355  1.00  0.50
ATOM   1425  CG  LEU   213      23.884  50.841  61.106  1.00  0.60
ATOM   1426  CD1 LEU   213      24.875  51.837  60.703  1.00  0.60
ATOM   1427  CD2 LEU   213      24.411  50.397  62.609  1.00  0.80
ATOM   1428  N   PHE   214      20.831  49.293  62.954  1.00  0.50
ATOM   1429  CA  PHE   214      20.771  48.095  63.798  1.00  0.50
ATOM   1430  C   PHE   214      19.940  46.977  63.110  1.00  0.50
ATOM   1431  O   PHE   214      20.439  45.883  62.859  1.00  0.50
ATOM   1432  CB  PHE   214      20.216  48.405  65.213  1.00  0.50
ATOM   1433  CG  PHE   214      21.174  49.337  65.973  1.00  0.60
ATOM   1434  CD1 PHE   214      22.539  49.246  65.668  1.00  0.60
ATOM   1435  CD2 PHE   214      20.807  49.852  67.195  1.00  0.80
ATOM   1436  CE1 PHE   214      23.450  49.877  66.491  1.00  0.80
ATOM   1437  CE2 PHE   214      21.684  50.504  68.020  1.00  1.10
ATOM   1438  CZ  PHE   214      23.053  50.531  67.641  1.00  1.10
ATOM   1439  N   GLU   215      18.701  47.264  62.757  1.00  0.50
ATOM   1440  CA  GLU   215      17.820  46.218  62.253  1.00  0.50
ATOM   1441  C   GLU   215      18.102  45.702  60.830  1.00  0.50
ATOM   1442  O   GLU   215      18.008  44.505  60.607  1.00  0.50
ATOM   1443  CB  GLU   215      16.347  46.575  62.509  1.00  0.50
ATOM   1444  CG  GLU   215      15.413  45.482  62.065  1.00  0.60
ATOM   1445  CD  GLU   215      15.597  44.169  62.895  1.00  0.60
ATOM   1446  OE1 GLU   215      16.296  44.144  63.919  1.00  0.80
ATOM   1447  OE2 GLU   215      15.035  43.134  62.445  1.00  0.80
ATOM   1448  N   ASP   216      18.447  46.586  59.892  1.00  0.50
ATOM   1449  CA  ASP   216      18.877  46.150  58.563  1.00  0.50
ATOM   1450  C   ASP   216      20.201  45.403  58.650  1.00  0.50
ATOM   1451  O   ASP   216      20.466  44.510  57.841  1.00  0.50
ATOM   1452  CB  ASP   216      18.989  47.317  57.581  1.00  0.50
ATOM   1453  CG  ASP   216      17.659  47.913  57.182  1.00  0.60
ATOM   1454  OD1 ASP   216      16.579  47.310  57.402  1.00  0.60
ATOM   1455  OD2 ASP   216      17.596  48.969  56.547  1.00  0.80
ATOM   1456  N   ILE   217      21.024  45.762  59.640  1.00  0.50
ATOM   1457  CA  ILE   217      22.277  45.088  59.913  1.00  0.50
ATOM   1458  C   ILE   217      22.101  43.672  60.424  1.00  0.50
ATOM   1459  O   ILE   217      22.789  42.764  59.975  1.00  0.50
ATOM   1460  CB  ILE   217      22.105  44.383  58.567  1.00  0.50
ATOM   1461  CG1 ILE   217      22.079  45.308  57.350  1.00  0.60
ATOM   1462  CG2 ILE   217      20.864  43.486  58.676  1.00  0.60
ATOM   1463  CD1 ILE   217      23.369  45.389  56.598  1.00  0.80
ATOM   1464  N   SER   218      21.213  43.487  61.397  1.00  0.50
ATOM   1465  CA  SER   218      20.829  42.164  61.888  1.00  0.50
ATOM   1466  C   SER   218      20.293  41.297  60.742  1.00  0.50
ATOM   1467  O   SER   218      20.665  40.138  60.620  1.00  0.50
ATOM   1468  CB  SER   218      19.756  42.264  63.014  1.00  0.50
ATOM   1469  OG  SER   218      18.472  42.910  62.492  1.00  0.60
TER
END
