
#######################################################
#                                                     #
#                        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_3
# Molecule2: number of CA atoms  109 ( 1766),  selected  109 , name T0352.pdb
# PARAMETERS: T0352TS102_3.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    H     113      V       7          1.163
LGA    H     114      R       8          0.886
LGA    -       -      L       9           -
LGA    -       -      Q      10           -
LGA    H     115      L      11          1.555
LGA    H     116      Q      12          2.954
LGA    H     117      A      13          2.170
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    -       -      L     103           -
LGA    -       -      F     104           -
LGA    -       -      A     105           -
LGA    -       -      D     106           -
LGA    -       -      D     107           -
LGA    -       -      A     108           -
LGA    -       -      S     109           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)    5  109    5.0      5    1.90     0.00      4.249     0.250

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.665050 * X  +  -0.348302 * Y  +   0.660602 * Z  + -37.596375
  Y_new =   0.392459 * X  +  -0.915585 * Y  +  -0.087640 * Z  +  19.911463
  Z_new =   0.635362 * X  +   0.200974 * Y  +   0.745604 * Z  + -46.356712 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.263289   -2.878304  [ DEG:    15.0853   -164.9147 ]
  Theta =  -0.688477   -2.453116  [ DEG:   -39.4468   -140.5532 ]
  Phi   =   2.608469   -0.533123  [ DEG:   149.4543    -30.5457 ]
 
# 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_3                                  
REMARK     2: T0352.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0352TS102_3.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   1.90    0.00   4.249
REMARK  ---------------------------------------------------------- 
MOLECULE T0352TS102_3
PFRMAT TS
TARGET T0352
MODEL 3
PARENT 1zko_A
ATOM      1  N   HIS   113      -3.778  -1.310  -4.731  1.00  1.00
ATOM      2  CA  HIS   113      -5.111  -0.857  -5.214  1.00  1.00
ATOM      3  C   HIS   113      -5.053   0.589  -5.660  1.00  1.00
ATOM      4  O   HIS   113      -4.385   1.416  -5.039  1.00  1.00
ATOM      5  CB  HIS   113      -6.167  -1.038  -4.127  1.00  1.00
ATOM      6  N   HIS   114      -5.767   0.877  -6.739  1.00  1.00
ATOM      7  CA  HIS   114      -5.715   2.179  -7.383  1.00  1.00
ATOM      8  C   HIS   114      -7.042   2.900  -7.245  1.00  1.00
ATOM      9  O   HIS   114      -8.089   2.258  -7.135  1.00  1.00
ATOM     10  CB  HIS   114      -5.305   2.010  -8.843  1.00  1.00
ATOM     11  N   HIS   115      -6.985   4.231  -7.213  1.00  1.00
ATOM     12  CA  HIS   115      -8.171   5.063  -7.031  1.00  1.00
ATOM     13  C   HIS   115      -9.233   4.753  -8.084  1.00  1.00
ATOM     14  O   HIS   115      -8.973   4.816  -9.286  1.00  1.00
ATOM     15  CB  HIS   115      -7.770   6.541  -7.075  1.00  1.00
ATOM     16  N   HIS   116     -10.428   4.404  -7.621  1.00  1.00
ATOM     17  CA  HIS   116     -11.526   4.077  -8.518  1.00  1.00
ATOM     18  C   HIS   116     -12.014   5.324  -9.238  1.00  1.00
ATOM     19  O   HIS   116     -12.218   6.360  -8.614  1.00  1.00
ATOM     20  CB  HIS   116     -12.672   3.466  -7.715  1.00  1.00
ATOM     21  N   HIS   117     -12.182   5.212 -10.552  1.00  1.00
ATOM     22  CA  HIS   117     -12.831   6.252 -11.334  1.00  1.00
ATOM     23  C   HIS   117     -14.326   6.229 -11.055  1.00  1.00
ATOM     24  O   HIS   117     -14.877   5.201 -10.663  1.00  1.00
ATOM     25  CB  HIS   117     -12.642   6.026 -12.825  1.00  1.00
TER
END
