
#######################################################
#                                                     #
#                        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_1-D1
# Molecule2: number of CA atoms  188 ( 1493),  selected  188 , name T0316_D1.pdb
# PARAMETERS: T0316TS464_1-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    S     189      N       4          0.790
LGA    T     190      S       5          0.339
LGA    A     191      K       6          0.431
LGA    K     192      T       7          0.708
LGA    K     193      R       8          0.887
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    -       -      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    0.67     0.00      2.660     0.653

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.881779 * X  +   0.379355 * Y  +  -0.280277 * Z  +  31.186953
  Y_new =   0.451898 * X  +   0.849705 * Y  +  -0.271642 * Z  +  -3.550226
  Z_new =   0.135104 * X  +  -0.366185 * Y  +  -0.920682 * Z  +  64.967766 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.763042    0.378550  [ DEG:  -158.3107     21.6893 ]
  Theta =  -0.135518   -3.006074  [ DEG:    -7.7646   -172.2354 ]
  Phi   =   2.668007   -0.473585  [ DEG:   152.8656    -27.1344 ]
 
# 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_1-D1                               
REMARK     2: T0316_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0316TS464_1-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   0.67    0.00   2.660
REMARK  ---------------------------------------------------------- 
MOLECULE T0316TS464_1-D1
PFRMAT TS
TARGET T0316
MODEL 1
PARENT N/A
ATOM    753  N   SER   189      18.806  31.768  34.379  1.00  0.00
ATOM    754  CA  SER   189      19.207  31.817  33.008  1.00  0.00
ATOM    755  CB  SER   189      18.208  32.573  32.116  1.00  0.00
ATOM    756  OG  SER   189      18.664  32.585  30.772  1.00  0.00
ATOM    757  C   SER   189      20.481  32.580  33.008  1.00  0.00
ATOM    758  O   SER   189      21.317  32.418  32.121  1.00  0.00
ATOM    759  N   THR   190      20.662  33.433  34.036  1.00  0.00
ATOM    760  CA  THR   190      21.873  34.180  34.094  1.00  0.00
ATOM    761  CB  THR   190      21.978  35.080  35.294  1.00  0.00
ATOM    762  OG1 THR   190      21.849  34.325  36.489  1.00  0.00
ATOM    763  CG2 THR   190      20.896  36.167  35.208  1.00  0.00
ATOM    764  C   THR   190      22.990  33.202  34.152  1.00  0.00
ATOM    765  O   THR   190      23.962  33.332  33.410  1.00  0.00
ATOM    766  N   ALA   191      22.886  32.186  35.032  1.00  0.00
ATOM    767  CA  ALA   191      23.920  31.203  34.963  1.00  0.00
ATOM    768  CB  ALA   191      23.768  30.060  35.978  1.00  0.00
ATOM    769  C   ALA   191      23.714  30.612  33.621  1.00  0.00
ATOM    770  O   ALA   191      22.701  29.979  33.333  1.00  0.00
ATOM    771  N   LYS   192      24.701  30.847  32.761  1.00  0.00
ATOM    772  CA  LYS   192      24.716  30.381  31.421  1.00  0.00
ATOM    773  CB  LYS   192      24.151  31.405  30.416  1.00  0.00
ATOM    774  CG  LYS   192      24.705  32.826  30.567  1.00  0.00
ATOM    775  CD  LYS   192      24.347  33.749  29.401  1.00  0.00
ATOM    776  CE  LYS   192      25.123  33.450  28.117  1.00  0.00
ATOM    777  NZ  LYS   192      24.601  32.217  27.485  1.00  0.00
ATOM    778  C   LYS   192      26.171  30.210  31.214  1.00  0.00
ATOM    779  O   LYS   192      26.809  29.430  31.920  1.00  0.00
ATOM    780  N   LYS   193      26.756  30.920  30.243  1.00  0.00
ATOM    781  CA  LYS   193      28.168  30.783  30.194  1.00  0.00
ATOM    782  CB  LYS   193      28.781  31.237  28.860  1.00  0.00
ATOM    783  CG  LYS   193      28.306  30.386  27.685  1.00  0.00
ATOM    784  CD  LYS   193      28.588  28.895  27.878  1.00  0.00
ATOM    785  CE  LYS   193      27.618  28.209  28.842  1.00  0.00
ATOM    786  NZ  LYS   193      26.316  27.984  28.173  1.00  0.00
ATOM    787  C   LYS   193      28.706  31.663  31.273  1.00  0.00
ATOM    788  O   LYS   193      28.879  32.865  31.084  1.00  0.00
TER
END
