
#######################################################
#                                                     #
#                        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    5 (   36),  selected    5 , name T0316TS464_3-D1
# Molecule2: number of CA atoms  188 ( 1493),  selected  188 , name T0316_D1.pdb
# PARAMETERS: T0316TS464_3-D1.T0316_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    -       -      S       2           -
LGA    -       -      D       3           -
LGA    -       -      N       4           -
LGA    -       -      S       5           -
LGA    -       -      K       6           -
LGA    -       -      T       7           -
LGA    -       -      R       8           -
LGA    -       -      V       9           -
LGA    -       -      V      10           -
LGA    -       -      V      11           -
LGA    -       -      G      12           -
LGA    -       -      M      13           -
LGA    -       -      S      14           -
LGA    -       -      G      15           -
LGA    -       -      G      16           -
LGA    -       -      V      17           -
LGA    -       -      D      18           -
LGA    -       -      S      19           -
LGA    -       -      S      20           -
LGA    -       -      V      21           -
LGA    -       -      T      22           -
LGA    -       -      A      23           -
LGA    -       -      L      24           -
LGA    -       -      L      25           -
LGA    -       -      L      26           -
LGA    -       -      K      27           -
LGA    -       -      E      28           -
LGA    -       -      Q      29           -
LGA    -       -      G      30           -
LGA    -       -      Y      31           -
LGA    -       -      D      32           -
LGA    -       -      V      33           -
LGA    -       -      I      34           -
LGA    -       -      G      35           -
LGA    -       -      I      36           -
LGA    -       -      F      37           -
LGA    -       -      M      38           -
LGA    -       -      K      39           -
LGA    -       -      N      40           -
LGA    -       -      W      41           -
LGA    -       -      D      42           -
LGA    -       -      D      43           -
LGA    -       -      T      44           -
LGA    -       -      D      45           -
LGA    -       -      C      50           -
LGA    -       -      T      51           -
LGA    -       -      A      52           -
LGA    -       -      T      53           -
LGA    -       -      E      54           -
LGA    -       -      D      55           -
LGA    -       -      Y      56           -
LGA    -       -      K      57           -
LGA    -       -      D      58           -
LGA    -       -      V      59           -
LGA    -       -      V      60           -
LGA    -       -      A      61           -
LGA    -       -      V      62           -
LGA    -       -      A      63           -
LGA    -       -      D      64           -
LGA    -       -      Q      65           -
LGA    -       -      I      66           -
LGA    -       -      G      67           -
LGA    -       -      I      68           -
LGA    -       -      P      69           -
LGA    -       -      Y      70           -
LGA    -       -      Y      71           -
LGA    -       -      S      72           -
LGA    -       -      V      73           -
LGA    -       -      N      74           -
LGA    -       -      F      75           -
LGA    -       -      E      76           -
LGA    -       -      K      77           -
LGA    -       -      E      78           -
LGA    -       -      Y      79           -
LGA    -       -      W      80           -
LGA    -       -      D      81           -
LGA    -       -      R      82           -
LGA    -       -      V      83           -
LGA    -       -      F      84           -
LGA    -       -      E      85           -
LGA    -       -      Y      86           -
LGA    -       -      F      87           -
LGA    -       -      L      88           -
LGA    -       -      A      89           -
LGA    -       -      E      90           -
LGA    -       -      Y      91           -
LGA    -       -      R      92           -
LGA    -       -      A      93           -
LGA    -       -      G      94           -
LGA    -       -      R      95           -
LGA    -       -      T      96           -
LGA    -       -      P      97           -
LGA    -       -      N      98           -
LGA    -       -      P      99           -
LGA    -       -      D     100           -
LGA    -       -      V     101           -
LGA    -       -      M     102           -
LGA    -       -      C     103           -
LGA    -       -      N     104           -
LGA    -       -      K     105           -
LGA    -       -      E     106           -
LGA    -       -      I     107           -
LGA    -       -      K     108           -
LGA    -       -      F     109           -
LGA    -       -      K     110           -
LGA    -       -      A     111           -
LGA    -       -      F     112           -
LGA    -       -      L     113           -
LGA    -       -      D     114           -
LGA    -       -      Y     115           -
LGA    -       -      A     116           -
LGA    -       -      I     117           -
LGA    -       -      T     118           -
LGA    -       -      L     119           -
LGA    -       -      G     120           -
LGA    -       -      A     121           -
LGA    -       -      D     122           -
LGA    -       -      Y     123           -
LGA    -       -      V     124           -
LGA    -       -      A     125           -
LGA    -       -      T     126           -
LGA    -       -      G     127           -
LGA    -       -      H     128           -
LGA    -       -      Y     129           -
LGA    -       -      A     130           -
LGA    -       -      R     131           -
LGA    -       -      V     132           -
LGA    -       -      A     133           -
LGA    -       -      R     134           -
LGA    -       -      D     135           -
LGA    -       -      E     136           -
LGA    -       -      D     137           -
LGA    -       -      G     138           -
LGA    -       -      T     139           -
LGA    -       -      V     140           -
LGA    -       -      H     141           -
LGA    -       -      M     142           -
LGA    -       -      L     143           -
LGA    -       -      R     144           -
LGA    -       -      G     145           -
LGA    -       -      V     146           -
LGA    -       -      D     147           -
LGA    -       -      N     148           -
LGA    -       -      G     149           -
LGA    -       -      K     150           -
LGA    -       -      D     151           -
LGA    -       -      Q     152           -
LGA    -       -      T     153           -
LGA    -       -      Y     154           -
LGA    -       -      F     155           -
LGA    -       -      L     156           -
LGA    -       -      S     157           -
LGA    -       -      Q     158           -
LGA    -       -      L     159           -
LGA    -       -      S     160           -
LGA    -       -      Q     161           -
LGA    -       -      E     162           -
LGA    -       -      Q     163           -
LGA    -       -      L     164           -
LGA    -       -      Q     165           -
LGA    -       -      K     166           -
LGA    -       -      T     167           -
LGA    -       -      M     168           -
LGA    -       -      F     169           -
LGA    -       -      P     170           -
LGA    -       -      L     171           -
LGA    -       -      G     172           -
LGA    -       -      H     173           -
LGA    -       -      L     174           -
LGA    S     189      E     175          0.695
LGA    T     190      K     176          1.517
LGA    A     191      P     177          1.723
LGA    -       -      E     178           -
LGA    -       -      V     179           -
LGA    K     192      R     180          0.517
LGA    K     193      R     181          1.414
LGA    -       -      L     182           -
LGA    -       -      A     183           -
LGA    -       -      E     184           -
LGA    -       -      E     185           -
LGA    -       -      A     186           -
LGA    -       -      G     187           -
LGA    -       -      L     188           -
LGA    -       -      S     189           -
LGA    -       -      T     190           -
LGA    -       -      A     191           -
LGA    -       -      K     192           -
LGA    -       -      K     193           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)    5  188    5.0      5    1.27     0.00      2.536     0.366

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.697070 * X  +  -0.709044 * Y  +  -0.106537 * Z  +  28.812723
  Y_new =   0.012974 * X  +   0.161035 * Y  +  -0.986863 * Z  +  45.998749
  Z_new =   0.716885 * X  +   0.686531 * Y  +   0.121452 * Z  + -37.638447 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.395701   -1.745892  [ DEG:    79.9678   -100.0322 ]
  Theta =  -0.799325   -2.342268  [ DEG:   -45.7979   -134.2021 ]
  Phi   =   0.018610   -3.122982  [ DEG:     1.0663   -178.9337 ]
 
# 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: T0316TS464_3-D1                               
REMARK     2: T0316_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0316TS464_3-D1.T0316_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:    5  188   5.0    5   1.27    0.00   2.536
REMARK  ---------------------------------------------------------- 
MOLECULE T0316TS464_3-D1
PFRMAT TS
TARGET T0316
MODEL 3
PARENT N/A
ATOM    753  N   SER   189      14.315  33.339  10.577  1.00  0.00
ATOM    754  CA  SER   189      13.951  32.929   9.258  1.00  0.00
ATOM    755  CB  SER   189      12.431  32.919   9.029  1.00  0.00
ATOM    756  OG  SER   189      11.820  31.958   9.878  1.00  0.00
ATOM    757  C   SER   189      14.557  33.885   8.283  1.00  0.00
ATOM    758  O   SER   189      15.403  33.498   7.478  1.00  0.00
ATOM    759  N   THR   190      14.159  35.173   8.327  1.00  0.00
ATOM    760  CA  THR   190      14.733  36.057   7.356  1.00  0.00
ATOM    761  CB  THR   190      14.119  35.894   5.999  1.00  0.00
ATOM    762  OG1 THR   190      14.802  36.697   5.048  1.00  0.00
ATOM    763  CG2 THR   190      12.638  36.303   6.081  1.00  0.00
ATOM    764  C   THR   190      14.518  37.484   7.748  1.00  0.00
ATOM    765  O   THR   190      13.710  37.795   8.623  1.00  0.00
ATOM    766  N   ALA   191      15.284  38.384   7.095  1.00  0.00
ATOM    767  CA  ALA   191      15.128  39.804   7.224  1.00  0.00
ATOM    768  CB  ALA   191      13.666  40.254   7.402  1.00  0.00
ATOM    769  C   ALA   191      15.910  40.322   8.382  1.00  0.00
ATOM    770  O   ALA   191      16.326  39.569   9.261  1.00  0.00
ATOM    771  N   LYS   192      16.150  41.652   8.382  1.00  0.00
ATOM    772  CA  LYS   192      16.771  42.263   9.516  1.00  0.00
ATOM    773  CB  LYS   192      17.060  43.763   9.416  1.00  0.00
ATOM    774  CG  LYS   192      17.916  44.210  10.604  1.00  0.00
ATOM    775  CD  LYS   192      18.580  45.576  10.451  1.00  0.00
ATOM    776  CE  LYS   192      19.616  45.849  11.544  1.00  0.00
ATOM    777  NZ  LYS   192      18.966  45.837  12.873  1.00  0.00
ATOM    778  C   LYS   192      15.764  42.090  10.575  1.00  0.00
ATOM    779  O   LYS   192      16.091  42.015  11.759  1.00  0.00
ATOM    780  N   LYS   193      14.499  42.062  10.107  1.00  0.00
ATOM    781  CA  LYS   193      13.340  41.808  10.895  1.00  0.00
ATOM    782  CB  LYS   193      12.177  41.388   9.979  1.00  0.00
ATOM    783  CG  LYS   193      10.837  41.068  10.635  1.00  0.00
ATOM    784  CD  LYS   193       9.747  40.836   9.586  1.00  0.00
ATOM    785  CE  LYS   193      10.161  39.798   8.536  1.00  0.00
ATOM    786  NZ  LYS   193       9.161  39.728   7.448  1.00  0.00
ATOM    787  C   LYS   193      13.755  40.623  11.688  1.00  0.00
ATOM    788  O   LYS   193      13.809  39.505  11.179  1.00  0.00
TER
END
