
#######################################################
#                                                     #
#                        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_2_2-D1
# Molecule2: number of CA atoms  206 ( 1668),  selected  206 , name T0386_D1.pdb
# PARAMETERS: T0386TS074_2_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    P     209      R     162          4.634
LGA    M     210      E     163          2.241
LGA    Q     211      G     164          2.420
LGA    H     212      N     165          2.112
LGA    L     213      G     166          1.900
LGA    F     214      R     167          1.789
LGA    E     215      T     168          0.182
LGA    D     216      Q     169          0.565
LGA    I     217      R     170          1.700
LGA    S     218      L     171          2.076
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    2.26     0.00      4.340     0.423

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.101210 * X  +  -0.930264 * Y  +   0.352654 * Z  +  67.919029
  Y_new =   0.058512 * X  +   0.359427 * Y  +   0.931337 * Z  +  44.657944
  Z_new =  -0.993143 * X  +  -0.073626 * Y  +   0.090809 * Z  +  54.109436 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.681279    2.460314  [ DEG:   -39.0344    140.9656 ]
  Theta =   1.453622    1.687971  [ DEG:    83.2864     96.7136 ]
  Phi   =   0.524179   -2.617414  [ DEG:    30.0332   -149.9668 ]
 
# 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_2_2-D1                             
REMARK     2: T0386_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0386TS074_2_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   2.26    0.00   4.340
REMARK  ---------------------------------------------------------- 
MOLECULE T0386TS074_2_2-D1
REMARK PARENT number 2
PFRMAT TS
TARGET T0386
PARENT 2g03_A
ATOM   1386  N   PRO   209      17.370  59.857  48.558  1.00  0.92
ATOM   1387  CA  PRO   209      17.813  60.075  49.926  1.00  0.92
ATOM   1388  C   PRO   209      17.024  61.261  50.402  1.00  0.92
ATOM   1389  O   PRO   209      16.242  61.117  51.334  1.00  0.92
ATOM   1390  CB  PRO   209      19.296  60.468  50.054  1.00  0.92
ATOM   1391  CG  PRO   209      20.058  60.563  48.730  1.00  1.02
ATOM   1392  CD  PRO   209      18.600  60.848  47.764  1.00  1.02
ATOM   1393  N   MET   210      17.202  62.386  49.690  1.00  0.80
ATOM   1394  CA  MET   210      16.618  63.648  50.061  1.00  0.80
ATOM   1395  C   MET   210      15.140  63.623  50.341  1.00  0.80
ATOM   1396  O   MET   210      14.755  63.986  51.441  1.00  0.80
ATOM   1397  CB  MET   210      16.932  64.676  48.973  1.00  0.80
ATOM   1398  CG  MET   210      16.436  66.096  49.259  1.00  0.90
ATOM   1399  SD  MET   210      17.275  66.849  50.710  1.00  0.90
ATOM   1400  CE  MET   210      16.502  68.429  50.766  1.00  1.10
ATOM   1401  N   GLN   211      14.395  63.013  49.696  1.00  0.80
ATOM   1402  CA  GLN   211      12.942  63.193  49.745  1.00  0.80
ATOM   1403  C   GLN   211      12.208  62.067  50.503  1.00  0.80
ATOM   1404  O   GLN   211      11.293  62.340  51.272  1.00  0.80
ATOM   1405  CB  GLN   211      12.363  63.389  48.333  1.00  0.80
ATOM   1406  CG  GLN   211      10.883  63.652  48.286  1.00  0.90
ATOM   1407  CD  GLN   211      10.435  64.899  48.896  1.00  0.90
ATOM   1408  OE1 GLN   211      10.867  65.979  48.454  1.00  1.10
ATOM   1409  NE2 GLN   211       9.545  64.844  49.882  1.00  1.10
ATOM   1410  N   HIS   212      12.622  60.819  50.310  1.00  0.80
ATOM   1411  CA  HIS   212      11.951  59.695  50.940  1.00  0.80
ATOM   1412  C   HIS   212      12.168  59.665  52.459  1.00  0.80
ATOM   1413  O   HIS   212      11.228  59.425  53.235  1.00  0.80
ATOM   1414  CB  HIS   212      12.406  58.387  50.307  1.00  0.80
ATOM   1415  CG  HIS   212      11.705  57.136  50.849  1.00  0.90
ATOM   1416  ND1 HIS   212      12.102  56.558  52.068  1.00  0.90
ATOM   1417  CD2 HIS   212      10.642  56.515  50.371  1.00  1.10
ATOM   1418  CE1 HIS   212      11.253  55.513  52.334  1.00  1.10
ATOM   1419  NE2 HIS   212      10.342  55.473  51.282  1.00  1.40
ATOM   1420  N   LEU   213      13.404  59.923  52.887  1.00  0.80
ATOM   1421  CA  LEU   213      13.732  60.018  54.304  1.00  0.80
ATOM   1422  C   LEU   213      12.983  61.181  54.938  1.00  0.80
ATOM   1423  O   LEU   213      12.412  61.028  56.019  1.00  0.80
ATOM   1424  CB  LEU   213      15.269  60.128  54.528  1.00  0.80
ATOM   1425  CG  LEU   213      15.556  60.149  56.028  1.00  0.90
ATOM   1426  CD1 LEU   213      15.180  58.883  56.655  1.00  0.90
ATOM   1427  CD2 LEU   213      17.206  60.128  56.135  1.00  1.10
ATOM   1428  N   PHE   214      12.970  62.339  54.282  1.00  0.80
ATOM   1429  CA  PHE   214      12.242  63.488  54.829  1.00  0.80
ATOM   1430  C   PHE   214      10.725  63.174  54.950  1.00  0.80
ATOM   1431  O   PHE   214      10.154  63.224  56.035  1.00  0.80
ATOM   1432  CB  PHE   214      12.474  64.777  53.997  1.00  0.80
ATOM   1433  CG  PHE   214      13.948  65.210  54.078  1.00  0.90
ATOM   1434  CD1 PHE   214      14.649  64.895  55.251  1.00  0.90
ATOM   1435  CD2 PHE   214      14.402  66.249  53.300  1.00  1.10
ATOM   1436  CE1 PHE   214      15.883  65.474  55.466  1.00  1.10
ATOM   1437  CE2 PHE   214      15.632  66.827  53.476  1.00  1.40
ATOM   1438  CZ  PHE   214      16.406  66.406  54.591  1.00  1.40
ATOM   1439  N   GLU   215      10.089  62.798  53.855  1.00  0.80
ATOM   1440  CA  GLU   215       8.640  62.640  53.866  1.00  0.80
ATOM   1441  C   GLU   215       8.083  61.410  54.607  1.00  0.80
ATOM   1442  O   GLU   215       7.076  61.538  55.285  1.00  0.80
ATOM   1443  CB  GLU   215       8.060  62.837  52.456  1.00  0.80
ATOM   1444  CG  GLU   215       6.558  62.753  52.444  1.00  0.90
ATOM   1445  CD  GLU   215       5.891  63.911  53.254  1.00  0.90
ATOM   1446  OE1 GLU   215       6.551  64.876  53.668  1.00  1.10
ATOM   1447  OE2 GLU   215       4.660  63.792  53.501  1.00  1.10
ATOM   1448  N   ASP   216       8.729  60.251  54.487  1.00  0.80
ATOM   1449  CA  ASP   216       8.346  59.084  55.282  1.00  0.80
ATOM   1450  C   ASP   216       8.627  59.333  56.759  1.00  0.80
ATOM   1451  O   ASP   216       7.925  58.798  57.622  1.00  0.80
ATOM   1452  CB  ASP   216       9.050  57.810  54.815  1.00  0.80
ATOM   1453  CG  ASP   216       8.579  57.306  53.471  1.00  0.90
ATOM   1454  OD1 ASP   216       7.514  57.724  52.951  1.00  0.90
ATOM   1455  OD2 ASP   216       9.176  56.401  52.881  1.00  1.10
ATOM   1456  N   ILE   217       9.644  60.150  57.042  1.00  0.80
ATOM   1457  CA  ILE   217       9.980  60.558  58.392  1.00  0.80
ATOM   1458  C   ILE   217       8.935  61.453  59.029  1.00  0.80
ATOM   1459  O   ILE   217       8.571  61.256  60.182  1.00  0.80
ATOM   1460  CB  ILE   217       9.018  59.473  58.879  1.00  0.80
ATOM   1461  CG1 ILE   217       8.835  59.404  60.396  1.00  0.90
ATOM   1462  CG2 ILE   217       9.472  58.146  58.260  1.00  0.90
ATOM   1463  CD1 ILE   217       7.657  58.603  60.850  1.00  1.10
ATOM   1464  N   SER   218       8.484  62.471  58.299  1.00  0.80
ATOM   1465  CA  SER   218       7.377  63.328  58.719  1.00  0.80
ATOM   1466  C   SER   218       6.119  62.492  58.988  1.00  0.80
ATOM   1467  O   SER   218       5.452  62.688  59.993  1.00  0.80
ATOM   1468  CB  SER   218       7.061  64.416  57.649  1.00  0.80
ATOM   1469  OG  SER   218       6.626  63.780  56.329  1.00  0.90
TER
END
