
#######################################################
#                                                     #
#                        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_4_2-D1
# Molecule2: number of CA atoms  206 ( 1668),  selected  206 , name T0386_D1.pdb
# PARAMETERS: T0386TS074_4_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    P     209      G     138          2.399
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     210      M     194          2.468
LGA    Q     211      M     195          1.629
LGA    H     212      V     196          0.824
LGA    L     213      A     197          0.606
LGA    F     214      S     198          0.948
LGA    E     215      V     199          0.211
LGA    D     216      A     200          0.141
LGA    I     217      V     201          0.783
LGA    S     218      A     202          2.136
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    1.47    10.00      4.671     0.636

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.691810 * X  +   0.691681 * Y  +  -0.207309 * Z  + -20.897984
  Y_new =   0.620635 * X  +  -0.422842 * Y  +   0.660316 * Z  +  81.295715
  Z_new =   0.369069 * X  +  -0.585476 * Y  +  -0.721807 * Z  +  96.342308 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.460104    0.681488  [ DEG:  -140.9536     39.0464 ]
  Theta =  -0.378007   -2.763585  [ DEG:   -21.6582   -158.3418 ]
  Phi   =   0.731220   -2.410372  [ DEG:    41.8958   -138.1042 ]
 
# 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_4_2-D1                             
REMARK     2: T0386_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0386TS074_4_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   1.47   10.00   4.671
REMARK  ---------------------------------------------------------- 
MOLECULE T0386TS074_4_2-D1
REMARK PARENT number 2
PFRMAT TS
TARGET T0386
PARENT 2g03_A
ATOM   1386  N   PRO   209     -12.195  47.220  63.051  1.00  0.22
ATOM   1387  CA  PRO   209     -11.473  48.404  63.523  1.00  0.22
ATOM   1388  C   PRO   209     -11.852  48.803  64.949  1.00  0.22
ATOM   1389  O   PRO   209     -10.998  48.892  65.829  1.00  0.22
ATOM   1390  CB  PRO   209     -11.863  49.466  62.497  1.00  0.22
ATOM   1391  CG  PRO   209     -12.764  48.711  61.578  1.00  0.32
ATOM   1392  CD  PRO   209     -13.460  47.655  62.346  1.00  0.32
ATOM   1393  N   MET   210      18.352  58.506  65.054  1.00  0.20
ATOM   1394  CA  MET   210      18.581  58.434  63.635  1.00  0.20
ATOM   1395  C   MET   210      19.399  57.260  63.169  1.00  0.20
ATOM   1396  O   MET   210      18.900  56.495  62.358  1.00  0.20
ATOM   1397  CB  MET   210      19.223  59.741  63.171  1.00  0.20
ATOM   1398  CG  MET   210      19.463  59.847  61.662  1.00  0.30
ATOM   1399  SD  MET   210      17.895  59.861  60.705  1.00  0.30
ATOM   1400  CE  MET   210      17.322  61.497  61.017  1.00  0.50
ATOM   1401  N   GLN   211      20.333  56.884  63.743  1.00  0.20
ATOM   1402  CA  GLN   211      21.314  55.956  63.179  1.00  0.20
ATOM   1403  C   GLN   211      21.194  54.520  63.735  1.00  0.20
ATOM   1404  O   GLN   211      21.293  53.559  62.979  1.00  0.20
ATOM   1405  CB  GLN   211      22.745  56.499  63.338  1.00  0.20
ATOM   1406  CG  GLN   211      23.820  55.646  62.725  1.00  0.30
ATOM   1407  CD  GLN   211      23.782  55.514  61.273  1.00  0.30
ATOM   1408  OE1 GLN   211      23.880  56.535  60.567  1.00  0.50
ATOM   1409  NE2 GLN   211      23.683  54.297  60.744  1.00  0.50
ATOM   1410  N   HIS   212      20.955  54.379  65.034  1.00  0.20
ATOM   1411  CA  HIS   212      20.884  53.064  65.650  1.00  0.20
ATOM   1412  C   HIS   212      19.638  52.283  65.207  1.00  0.20
ATOM   1413  O   HIS   212      19.713  51.079  64.905  1.00  0.20
ATOM   1414  CB  HIS   212      20.928  53.188  67.166  1.00  0.20
ATOM   1415  CG  HIS   212      20.932  51.852  67.918  1.00  0.30
ATOM   1416  ND1 HIS   212      19.738  51.137  68.121  1.00  0.30
ATOM   1417  CD2 HIS   212      21.964  51.157  68.361  1.00  0.50
ATOM   1418  CE1 HIS   212      20.057  49.955  68.744  1.00  0.50
ATOM   1419  NE2 HIS   212      21.438  49.960  68.902  1.00  0.80
ATOM   1420  N   LEU   213      18.496  52.967  65.155  1.00  0.20
ATOM   1421  CA  LEU   213      17.257  52.375  64.665  1.00  0.20
ATOM   1422  C   LEU   213      17.403  51.991  63.201  1.00  0.20
ATOM   1423  O   LEU   213      17.007  50.890  62.811  1.00  0.20
ATOM   1424  CB  LEU   213      16.043  53.322  64.897  1.00  0.20
ATOM   1425  CG  LEU   213      15.820  53.493  66.400  1.00  0.30
ATOM   1426  CD1 LEU   213      14.763  54.468  66.669  1.00  0.30
ATOM   1427  CD2 LEU   213      15.130  52.070  66.880  1.00  0.50
ATOM   1428  N   PHE   214      17.969  52.875  62.382  1.00  0.20
ATOM   1429  CA  PHE   214      18.162  52.550  60.966  1.00  0.20
ATOM   1430  C   PHE   214      19.099  51.322  60.805  1.00  0.20
ATOM   1431  O   PHE   214      18.718  50.306  60.232  1.00  0.20
ATOM   1432  CB  PHE   214      18.695  53.762  60.156  1.00  0.20
ATOM   1433  CG  PHE   214      17.650  54.891  60.129  1.00  0.30
ATOM   1434  CD1 PHE   214      16.299  54.520  60.193  1.00  0.30
ATOM   1435  CD2 PHE   214      17.972  56.112  59.585  1.00  0.50
ATOM   1436  CE1 PHE   214      15.335  55.469  59.926  1.00  0.50
ATOM   1437  CE2 PHE   214      17.038  57.081  59.331  1.00  0.80
ATOM   1438  CZ  PHE   214      15.671  56.750  59.529  1.00  0.80
ATOM   1439  N   GLU   215      20.299  51.391  61.354  1.00  0.20
ATOM   1440  CA  GLU   215      21.281  50.343  61.107  1.00  0.20
ATOM   1441  C   GLU   215      21.042  48.993  61.809  1.00  0.20
ATOM   1442  O   GLU   215      21.260  47.961  61.191  1.00  0.20
ATOM   1443  CB  GLU   215      22.710  50.886  61.264  1.00  0.20
ATOM   1444  CG  GLU   215      23.038  51.924  60.226  1.00  0.30
ATOM   1445  CD  GLU   215      23.055  51.334  58.778  1.00  0.30
ATOM   1446  OE1 GLU   215      23.535  50.215  58.540  1.00  0.50
ATOM   1447  OE2 GLU   215      22.597  52.070  57.863  1.00  0.50
ATOM   1448  N   ASP   216      20.597  49.001  63.065  1.00  0.20
ATOM   1449  CA  ASP   216      20.204  47.762  63.737  1.00  0.20
ATOM   1450  C   ASP   216      18.967  47.168  63.077  1.00  0.20
ATOM   1451  O   ASP   216      18.791  45.947  63.073  1.00  0.20
ATOM   1452  CB  ASP   216      19.961  47.970  65.233  1.00  0.20
ATOM   1453  CG  ASP   216      21.216  48.245  66.027  1.00  0.30
ATOM   1454  OD1 ASP   216      22.356  48.021  65.546  1.00  0.30
ATOM   1455  OD2 ASP   216      21.164  48.615  67.203  1.00  0.50
ATOM   1456  N   ILE   217      18.200  47.573  62.154  1.00  0.20
ATOM   1457  CA  ILE   217      17.037  47.144  61.401  1.00  0.20
ATOM   1458  C   ILE   217      17.383  46.363  60.149  1.00  0.20
ATOM   1459  O   ILE   217      16.777  45.335  59.874  1.00  0.20
ATOM   1460  CB  ILE   217      17.227  45.766  62.039  1.00  0.20
ATOM   1461  CG1 ILE   217      17.103  45.736  63.563  1.00  0.30
ATOM   1462  CG2 ILE   217      18.558  45.203  61.525  1.00  0.30
ATOM   1463  CD1 ILE   217      15.781  45.258  64.075  1.00  0.50
ATOM   1464  N   SER   218      17.456  45.576  59.272  1.00  0.20
ATOM   1465  CA  SER   218      18.067  44.984  58.083  1.00  0.20
ATOM   1466  C   SER   218      18.827  43.702  58.447  1.00  0.20
ATOM   1467  O   SER   218      18.699  42.696  57.763  1.00  0.20
ATOM   1468  CB  SER   218      19.038  45.985  57.385  1.00  0.20
ATOM   1469  OG  SER   218      19.616  45.386  56.103  1.00  0.30
TER
END
