
#######################################################
#                                                     #
#                        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_2-D1
# Molecule2: number of CA atoms  188 ( 1493),  selected  188 , name T0316_D1.pdb
# PARAMETERS: T0316TS464_2-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     189      S     160          1.182
LGA    T     190      Q     161          0.593
LGA    A     191      E     162          1.723
LGA    -       -      Q     163           -
LGA    -       -      L     164           -
LGA    K     192      Q     165          1.033
LGA    K     193      K     166          0.719
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    -       -      E     175           -
LGA    -       -      K     176           -
LGA    -       -      P     177           -
LGA    -       -      E     178           -
LGA    -       -      V     179           -
LGA    -       -      R     180           -
LGA    -       -      R     181           -
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    1.12    40.00      2.578     0.409

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.788053 * X  +  -0.472591 * Y  +   0.394500 * Z  +  39.893822
  Y_new =  -0.276403 * X  +   0.844234 * Y  +   0.459207 * Z  + -21.364374
  Z_new =  -0.550067 * X  +   0.252839 * Y  +  -0.795926 * Z  +  52.782665 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.834008   -0.307584  [ DEG:   162.3767    -17.6233 ]
  Theta =   0.582445    2.559148  [ DEG:    33.3716    146.6284 ]
  Phi   =  -2.804257    0.337335  [ DEG:  -160.6721     19.3279 ]
 
# 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_2-D1                               
REMARK     2: T0316_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0316TS464_2-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   1.12   40.00   2.578
REMARK  ---------------------------------------------------------- 
MOLECULE T0316TS464_2-D1
PFRMAT TS
TARGET T0316
MODEL 2
PARENT N/A
ATOM    753  N   SER   189      29.829  14.996  15.183  1.00  0.00
ATOM    754  CA  SER   189      29.693  14.097  16.287  1.00  0.00
ATOM    755  CB  SER   189      30.992  13.902  17.087  1.00  0.00
ATOM    756  OG  SER   189      30.770  13.020  18.177  1.00  0.00
ATOM    757  C   SER   189      28.667  14.654  17.207  1.00  0.00
ATOM    758  O   SER   189      28.343  15.840  17.155  1.00  0.00
ATOM    759  N   THR   190      28.097  13.787  18.062  1.00  0.00
ATOM    760  CA  THR   190      27.136  14.274  18.998  1.00  0.00
ATOM    761  CB  THR   190      26.321  13.191  19.643  1.00  0.00
ATOM    762  OG1 THR   190      25.617  12.451  18.656  1.00  0.00
ATOM    763  CG2 THR   190      25.333  13.837  20.628  1.00  0.00
ATOM    764  C   THR   190      27.912  14.950  20.072  1.00  0.00
ATOM    765  O   THR   190      28.833  14.373  20.647  1.00  0.00
ATOM    766  N   ALA   191      27.567  16.218  20.356  1.00  0.00
ATOM    767  CA  ALA   191      28.263  16.926  21.383  1.00  0.00
ATOM    768  CB  ALA   191      29.430  17.774  20.849  1.00  0.00
ATOM    769  C   ALA   191      27.270  17.842  22.009  1.00  0.00
ATOM    770  O   ALA   191      26.292  18.237  21.376  1.00  0.00
ATOM    771  N   LYS   192      27.484  18.193  23.291  1.00  0.00
ATOM    772  CA  LYS   192      26.548  19.057  23.942  1.00  0.00
ATOM    773  CB  LYS   192      25.942  18.427  25.201  1.00  0.00
ATOM    774  CG  LYS   192      25.113  17.182  24.870  1.00  0.00
ATOM    775  CD  LYS   192      24.784  16.300  26.074  1.00  0.00
ATOM    776  CE  LYS   192      23.956  15.061  25.725  1.00  0.00
ATOM    777  NZ  LYS   192      23.691  14.271  26.949  1.00  0.00
ATOM    778  C   LYS   192      27.263  20.314  24.280  1.00  0.00
ATOM    779  O   LYS   192      28.463  20.316  24.547  1.00  0.00
ATOM    780  N   LYS   193      26.554  21.450  24.216  1.00  0.00
ATOM    781  CA  LYS   193      27.263  22.663  24.463  1.00  0.00
ATOM    782  CB  LYS   193      28.354  22.912  23.416  1.00  0.00
ATOM    783  CG  LYS   193      27.723  23.218  22.050  1.00  0.00
ATOM    784  CD  LYS   193      28.694  23.675  20.961  1.00  0.00
ATOM    785  CE  LYS   193      28.002  23.974  19.630  1.00  0.00
ATOM    786  NZ  LYS   193      28.995  24.415  18.626  1.00  0.00
ATOM    787  C   LYS   193      26.297  23.763  24.229  1.00  0.00
ATOM    788  O   LYS   193      25.196  23.552  23.723  1.00  0.00
TER
END
