
#######################################################
#                                                     #
#                        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_4-D1
# Molecule2: number of CA atoms  188 ( 1493),  selected  188 , name T0316_D1.pdb
# PARAMETERS: T0316TS464_4-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    S     189      N      74          1.243
LGA    T     190      F      75          1.095
LGA    A     191      E      76          0.888
LGA    -       -      K      77           -
LGA    -       -      E      78           -
LGA    K     192      Y      79          1.370
LGA    K     193      W      80          1.476
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    1.23     0.00      2.576     0.375

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.520299 * X  +  -0.515715 * Y  +  -0.680681 * Z  + 112.649963
  Y_new =   0.562073 * X  +   0.393279 * Y  +  -0.727603 * Z  +  51.381550
  Z_new =   0.642933 * X  +  -0.761164 * Y  +   0.085246 * Z  +  54.213142 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.459266    1.682327  [ DEG:   -83.6098     96.3902 ]
  Theta =  -0.698322   -2.443271  [ DEG:   -40.0109   -139.9891 ]
  Phi   =   2.317620   -0.823973  [ DEG:   132.7898    -47.2102 ]
 
# 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_4-D1                               
REMARK     2: T0316_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0316TS464_4-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   1.23    0.00   2.576
REMARK  ---------------------------------------------------------- 
MOLECULE T0316TS464_4-D1
PFRMAT TS
TARGET T0316
MODEL 4
PARENT N/A
ATOM    753  N   SER   189      41.868  34.812  17.648  1.00  0.00
ATOM    754  CA  SER   189      42.004  34.541  16.252  1.00  0.00
ATOM    755  CB  SER   189      42.392  35.773  15.417  1.00  0.00
ATOM    756  OG  SER   189      43.682  36.231  15.794  1.00  0.00
ATOM    757  C   SER   189      43.100  33.544  16.098  1.00  0.00
ATOM    758  O   SER   189      44.143  33.642  16.742  1.00  0.00
ATOM    759  N   THR   190      42.871  32.532  15.241  1.00  0.00
ATOM    760  CA  THR   190      43.882  31.552  14.996  1.00  0.00
ATOM    761  CB  THR   190      43.547  30.191  15.531  1.00  0.00
ATOM    762  OG1 THR   190      43.343  30.252  16.935  1.00  0.00
ATOM    763  CG2 THR   190      44.707  29.235  15.206  1.00  0.00
ATOM    764  C   THR   190      43.985  31.426  13.515  1.00  0.00
ATOM    765  O   THR   190      43.000  31.598  12.800  1.00  0.00
ATOM    766  N   ALA   191      45.198  31.145  13.007  1.00  0.00
ATOM    767  CA  ALA   191      45.325  30.999  11.591  1.00  0.00
ATOM    768  CB  ALA   191      46.781  30.915  11.105  1.00  0.00
ATOM    769  C   ALA   191      44.652  29.719  11.233  1.00  0.00
ATOM    770  O   ALA   191      44.702  28.751  11.989  1.00  0.00
ATOM    771  N   LYS   192      43.975  29.690  10.071  1.00  0.00
ATOM    772  CA  LYS   192      43.340  28.471   9.676  1.00  0.00
ATOM    773  CB  LYS   192      41.803  28.528   9.675  1.00  0.00
ATOM    774  CG  LYS   192      41.199  28.693  11.069  1.00  0.00
ATOM    775  CD  LYS   192      39.685  28.917  11.055  1.00  0.00
ATOM    776  CE  LYS   192      38.887  27.615  10.974  1.00  0.00
ATOM    777  NZ  LYS   192      39.230  26.888   9.730  1.00  0.00
ATOM    778  C   LYS   192      43.778  28.175   8.284  1.00  0.00
ATOM    779  O   LYS   192      43.993  29.079   7.479  1.00  0.00
ATOM    780  N   LYS   193      43.943  26.876   7.976  1.00  0.00
ATOM    781  CA  LYS   193      44.354  26.484   6.663  1.00  0.00
ATOM    782  CB  LYS   193      45.530  25.494   6.679  1.00  0.00
ATOM    783  CG  LYS   193      45.199  24.194   7.417  1.00  0.00
ATOM    784  CD  LYS   193      46.250  23.097   7.244  1.00  0.00
ATOM    785  CE  LYS   193      47.459  23.261   8.168  1.00  0.00
ATOM    786  NZ  LYS   193      47.068  22.987   9.569  1.00  0.00
ATOM    787  C   LYS   193      43.194  25.779   6.047  1.00  0.00
ATOM    788  O   LYS   193      42.587  24.909   6.670  1.00  0.00
TER
END
