
#######################################################
#                                                     #
#                        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 (   25),  selected    5 , name T0357TS102_2
# Molecule2: number of CA atoms  132 ( 2030),  selected  132 , name T0357.pdb
# PARAMETERS: T0357TS102_2.T0357.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    -       -      V       2           -
LGA    -       -      K       3           -
LGA    -       -      F       4           -
LGA    -       -      A       5           -
LGA    -       -      C       6           -
LGA    -       -      R       7           -
LGA    -       -      A       8           -
LGA    -       -      I       9           -
LGA    -       -      T      10           -
LGA    -       -      R      11           -
LGA    -       -      G      12           -
LGA    -       -      R      13           -
LGA    -       -      A      14           -
LGA    -       -      E      15           -
LGA    -       -      G      16           -
LGA    -       -      E      17           -
LGA    -       -      A      18           -
LGA    -       -      L      19           -
LGA    -       -      V      20           -
LGA    -       -      T      21           -
LGA    -       -      K      22           -
LGA    -       -      E      23           -
LGA    -       -      Y      24           -
LGA    -       -      I      25           -
LGA    -       -      S      26           -
LGA    -       -      F      27           -
LGA    -       -      L      28           -
LGA    -       -      G      29           -
LGA    -       -      G      30           -
LGA    -       -      I      31           -
LGA    -       -      D      32           -
LGA    -       -      K      33           -
LGA    -       -      E      34           -
LGA    -       -      T      35           -
LGA    -       -      G      36           -
LGA    -       -      I      37           -
LGA    -       -      V      38           -
LGA    -       -      K      39           -
LGA    -       -      E      40           -
LGA    -       -      D      41           -
LGA    -       -      C      42           -
LGA    -       -      E      43           -
LGA    -       -      I      44           -
LGA    -       -      K      45           -
LGA    -       -      G      46           -
LGA    -       -      E      47           -
LGA    -       -      S      48           -
LGA    -       -      V      49           -
LGA    -       -      A      50           -
LGA    -       -      G      51           -
LGA    -       -      R      52           -
LGA    -       -      I      53           -
LGA    -       -      L      54           -
LGA    -       -      V      55           -
LGA    -       -      F      56           -
LGA    -       -      P      57           -
LGA    -       -      G      58           -
LGA    -       -      G      59           -
LGA    -       -      K      60           -
LGA    -       -      G      61           -
LGA    -       -      S      62           -
LGA    -       -      T      63           -
LGA    -       -      V      64           -
LGA    -       -      G      65           -
LGA    -       -      S      66           -
LGA    H     137      Y      67          1.663
LGA    H     138      V      68          2.324
LGA    H     139      L      69          2.567
LGA    H     140      L      70          1.900
LGA    -       -      N      71           -
LGA    -       -      L      72           -
LGA    H     141      R      73          1.444
LGA    -       -      K      74           -
LGA    -       -      N      75           -
LGA    -       -      G      76           -
LGA    -       -      V      77           -
LGA    -       -      A      78           -
LGA    -       -      P      79           -
LGA    -       -      K      80           -
LGA    -       -      A      81           -
LGA    -       -      I      82           -
LGA    -       -      I      83           -
LGA    -       -      N      84           -
LGA    -       -      K      85           -
LGA    -       -      K      86           -
LGA    -       -      T      87           -
LGA    -       -      E      88           -
LGA    -       -      T      89           -
LGA    -       -      I      90           -
LGA    -       -      I      91           -
LGA    -       -      A      92           -
LGA    -       -      V      93           -
LGA    -       -      G      94           -
LGA    -       -      A      95           -
LGA    -       -      A      96           -
LGA    -       -      M      97           -
LGA    -       -      A      98           -
LGA    -       -      E      99           -
LGA    -       -      I     100           -
LGA    -       -      P     101           -
LGA    -       -      L     102           -
LGA    -       -      V     103           -
LGA    -       -      E     104           -
LGA    -       -      V     105           -
LGA    -       -      R     106           -
LGA    -       -      D     107           -
LGA    -       -      E     108           -
LGA    -       -      K     109           -
LGA    -       -      F     110           -
LGA    -       -      F     111           -
LGA    -       -      E     112           -
LGA    -       -      A     113           -
LGA    -       -      V     114           -
LGA    -       -      K     115           -
LGA    -       -      T     116           -
LGA    -       -      G     117           -
LGA    -       -      D     118           -
LGA    -       -      R     119           -
LGA    -       -      V     120           -
LGA    -       -      V     121           -
LGA    -       -      V     122           -
LGA    -       -      N     123           -
LGA    -       -      A     124           -
LGA    -       -      D     125           -
LGA    -       -      E     126           -
LGA    -       -      G     127           -
LGA    -       -      Y     128           -
LGA    -       -      V     129           -
LGA    -       -      E     130           -
LGA    -       -      L     131           -
LGA    -       -      I     132           -
LGA    -       -      E     133           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)    5  132    5.0      5    2.02     0.00      3.225     0.236

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.033676 * X  +   0.509177 * Y  +  -0.860002 * Z  +  37.708393
  Y_new =  -0.839456 * X  +  -0.481392 * Y  +  -0.252143 * Z  +   5.462878
  Z_new =  -0.542384 * X  +   0.713443 * Y  +   0.443643 * Z  + -29.181465 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.014476   -2.127116  [ DEG:    58.1252   -121.8748 ]
  Theta =   0.573272    2.568321  [ DEG:    32.8461    147.1539 ]
  Phi   =  -1.610892    1.530701  [ DEG:   -92.2973     87.7027 ]
 
# 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: T0357TS102_2                                  
REMARK     2: T0357.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0357TS102_2.T0357.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:    5  132   5.0    5   2.02    0.00   3.225
REMARK  ---------------------------------------------------------- 
MOLECULE T0357TS102_2
PFRMAT TS
TARGET T0357
MODEL 2
PARENT 1zko_A
ATOM      1  N   HIS   137      -1.493 -12.505   9.123  1.00  1.00
ATOM      2  CA  HIS   137      -0.441 -12.795   8.109  1.00  1.00
ATOM      3  C   HIS   137      -0.817 -12.205   6.766  1.00  1.00
ATOM      4  O   HIS   137      -1.983 -12.229   6.369  1.00  1.00
ATOM      5  CB  HIS   137      -0.214 -14.300   7.986  1.00  1.00
ATOM      6  N   HIS   138       0.187 -11.683   6.077  1.00  1.00
ATOM      7  CA  HIS   138      -0.016 -10.953   4.837  1.00  1.00
ATOM      8  C   HIS   138       0.575 -11.713   3.664  1.00  1.00
ATOM      9  O   HIS   138       1.530 -12.473   3.834  1.00  1.00
ATOM     10  CB  HIS   138       0.574  -9.553   4.966  1.00  1.00
ATOM     11  N   HIS   139      -0.022 -11.529   2.487  1.00  1.00
ATOM     12  CA  HIS   139       0.398 -12.230   1.277  1.00  1.00
ATOM     13  C   HIS   139       1.881 -12.005   0.991  1.00  1.00
ATOM     14  O   HIS   139       2.340 -10.867   0.883  1.00  1.00
ATOM     15  CB  HIS   139      -0.465 -11.773   0.096  1.00  1.00
ATOM     16  N   HIS   140       2.627 -13.099   0.882  1.00  1.00
ATOM     17  CA  HIS   140       4.055 -13.022   0.616  1.00  1.00
ATOM     18  C   HIS   140       4.308 -12.540  -0.803  1.00  1.00
ATOM     19  O   HIS   140       3.687 -13.026  -1.742  1.00  1.00
ATOM     20  CB  HIS   140       4.680 -14.401   0.809  1.00  1.00
ATOM     21  N   HIS   141       5.211 -11.574  -0.940  1.00  1.00
ATOM     22  CA  HIS   141       5.698 -11.158  -2.246  1.00  1.00
ATOM     23  C   HIS   141       6.631 -12.226  -2.795  1.00  1.00
ATOM     24  O   HIS   141       7.226 -12.991  -2.036  1.00  1.00
ATOM     25  CB  HIS   141       6.488  -9.863  -2.157  1.00  1.00
TER
END
