
#######################################################
#                                                     #
#                        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 T0352TS102_1
# Molecule2: number of CA atoms  109 ( 1766),  selected  109 , name T0352.pdb
# PARAMETERS: T0352TS102_1.T0352.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    -       -      M       1           -
LGA    -       -      T       2           -
LGA    -       -      T       3           -
LGA    -       -      H       4           -
LGA    -       -      D       5           -
LGA    -       -      R       6           -
LGA    -       -      V       7           -
LGA    -       -      R       8           -
LGA    -       -      L       9           -
LGA    -       -      Q      10           -
LGA    -       -      L      11           -
LGA    -       -      Q      12           -
LGA    -       -      A      13           -
LGA    -       -      L      14           -
LGA    -       -      E      15           -
LGA    -       -      A      16           -
LGA    -       -      L      17           -
LGA    -       -      L      18           -
LGA    -       -      R      19           -
LGA    -       -      E      20           -
LGA    -       -      H      21           -
LGA    -       -      Q      22           -
LGA    -       -      H      23           -
LGA    -       -      W      24           -
LGA    -       -      R      25           -
LGA    -       -      N      26           -
LGA    -       -      D      27           -
LGA    -       -      E      28           -
LGA    -       -      P      29           -
LGA    -       -      Q      30           -
LGA    -       -      P      31           -
LGA    -       -      H      32           -
LGA    -       -      Q      33           -
LGA    -       -      F      34           -
LGA    -       -      N      35           -
LGA    -       -      S      36           -
LGA    -       -      T      37           -
LGA    -       -      Q      38           -
LGA    -       -      P      39           -
LGA    -       -      F      40           -
LGA    -       -      F      41           -
LGA    -       -      M      42           -
LGA    -       -      D      43           -
LGA    -       -      T      44           -
LGA    -       -      M      45           -
LGA    -       -      E      46           -
LGA    -       -      P      47           -
LGA    -       -      L      48           -
LGA    -       -      E      49           -
LGA    -       -      W      50           -
LGA    -       -      L      51           -
LGA    -       -      Q      52           -
LGA    -       -      W      53           -
LGA    -       -      V      54           -
LGA    -       -      L      55           -
LGA    -       -      I      56           -
LGA    -       -      P      57           -
LGA    -       -      R      58           -
LGA    -       -      M      59           -
LGA    -       -      H      60           -
LGA    -       -      D      61           -
LGA    -       -      L      62           -
LGA    -       -      L      63           -
LGA    -       -      D      64           -
LGA    -       -      N      65           -
LGA    -       -      K      66           -
LGA    -       -      Q      67           -
LGA    -       -      P      68           -
LGA    -       -      L      69           -
LGA    -       -      P      70           -
LGA    -       -      G      71           -
LGA    -       -      A      72           -
LGA    -       -      F      73           -
LGA    -       -      A      74           -
LGA    -       -      V      75           -
LGA    -       -      A      76           -
LGA    -       -      P      77           -
LGA    -       -      Y      78           -
LGA    -       -      Y      79           -
LGA    -       -      E      80           -
LGA    -       -      M      81           -
LGA    -       -      A      82           -
LGA    -       -      L      83           -
LGA    -       -      A      84           -
LGA    -       -      T      85           -
LGA    -       -      D      86           -
LGA    -       -      H      87           -
LGA    -       -      P      88           -
LGA    -       -      Q      89           -
LGA    -       -      R      90           -
LGA    -       -      A      91           -
LGA    -       -      L      92           -
LGA    -       -      I      93           -
LGA    -       -      L      94           -
LGA    -       -      A      95           -
LGA    -       -      E      96           -
LGA    -       -      L      97           -
LGA    -       -      E      98           -
LGA    -       -      K      99           -
LGA    -       -      L     100           -
LGA    -       -      D     101           -
LGA    -       -      A     102           -
LGA    H     113      L     103          0.831
LGA    H     114      F     104          0.660
LGA    H     115      A     105          2.244
LGA    -       -      D     106           -
LGA    H     116      D     107          1.300
LGA    H     117      A     108          1.191
LGA    -       -      S     109           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)    5  109    5.0      5    1.36     0.00      4.382     0.342

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.127850 * X  +   0.974805 * Y  +  -0.182782 * Z  + -147.642365
  Y_new =   0.974940 * X  +   0.157356 * Y  +   0.157262 * Z  + -240.905167
  Z_new =   0.182062 * X  +  -0.158096 * Y  +  -0.970494 * Z  +  43.472164 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.980109    0.161484  [ DEG:  -170.7477      9.2523 ]
  Theta =  -0.183083   -2.958510  [ DEG:   -10.4899   -169.5101 ]
  Phi   =   1.701189   -1.440404  [ DEG:    97.4709    -82.5291 ]
 
# 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: T0352TS102_1                                  
REMARK     2: T0352.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0352TS102_1.T0352.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:    5  109   5.0    5   1.36    0.00   4.382
REMARK  ---------------------------------------------------------- 
MOLECULE T0352TS102_1
PFRMAT TS
TARGET T0352
MODEL 1
PARENT 1vlv_A
ATOM      1  N   HIS   113     -12.448  -6.437  -2.868  1.00  1.00
ATOM      2  CA  HIS   113     -13.360  -5.791  -1.880  1.00  1.00
ATOM      3  C   HIS   113     -12.595  -5.419  -0.618  1.00  1.00
ATOM      4  O   HIS   113     -13.217  -5.391   0.459  1.00  1.00
ATOM      5  CB  HIS   113     -14.506  -6.741  -1.415  1.00  1.00
ATOM      6  N   HIS   114     -11.290  -5.107  -0.731  1.00  1.00
ATOM      7  CA  HIS   114     -10.287  -5.175   0.399  1.00  1.00
ATOM      8  C   HIS   114      -9.908  -6.628   0.759  1.00  1.00
ATOM      9  O   HIS   114      -8.717  -6.943   0.792  1.00  1.00
ATOM     10  CB  HIS   114     -10.703  -4.443   1.675  1.00  1.00
ATOM     11  N   HIS   115     -10.898  -7.462   1.103  1.00  1.00
ATOM     12  CA  HIS   115     -10.762  -8.934   0.993  1.00  1.00
ATOM     13  C   HIS   115     -11.784  -9.360  -0.020  1.00  1.00
ATOM     14  O   HIS   115     -12.985  -9.301   0.229  1.00  1.00
ATOM     15  CB  HIS   115     -10.954  -9.694   2.315  1.00  1.00
ATOM     16  N   HIS   116     -11.291  -9.751  -1.186  1.00  1.00
ATOM     17  CA  HIS   116     -12.129 -10.258  -2.256  1.00  1.00
ATOM     18  C   HIS   116     -12.812 -11.615  -1.892  1.00  1.00
ATOM     19  O   HIS   116     -12.138 -12.571  -1.487  1.00  1.00
ATOM     20  CB  HIS   116     -11.256 -10.382  -3.514  1.00  1.00
ATOM     21  N   HIS   117     -14.140 -11.687  -2.052  1.00  1.00
ATOM     22  CA  HIS   117     -14.896 -12.907  -1.800  1.00  1.00
ATOM     23  C   HIS   117     -14.720 -13.890  -2.967  1.00  1.00
ATOM     24  O   HIS   117     -14.965 -13.506  -4.125  1.00  1.00
ATOM     25  CB  HIS   117     -16.398 -12.611  -1.619  1.00  1.00
TER
END
