
#######################################################
#                                                     #
#                        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 T0312TS102_5
# Molecule2: number of CA atoms  140 ( 1114),  selected  140 , name T0312.pdb
# PARAMETERS: T0312TS102_5.T0312.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    -       -      K       2           -
LGA    -       -      V       3           -
LGA    -       -      F       4           -
LGA    -       -      E       5           -
LGA    -       -      F       6           -
LGA    -       -      E       7           -
LGA    -       -      V       8           -
LGA    -       -      G       9           -
LGA    -       -      K      10           -
LGA    -       -      G      11           -
LGA    -       -      F      12           -
LGA    -       -      L      13           -
LGA    -       -      L      14           -
LGA    -       -      R      15           -
LGA    -       -      L      16           -
LGA    -       -      D      17           -
LGA    -       -      Y      18           -
LGA    -       -      G      19           -
LGA    -       -      K      20           -
LGA    -       -      D      21           -
LGA    -       -      L      22           -
LGA    -       -      V      23           -
LGA    -       -      R      24           -
LGA    -       -      Q      25           -
LGA    -       -      I      26           -
LGA    -       -      E      27           -
LGA    -       -      E      28           -
LGA    -       -      F      29           -
LGA    -       -      L      30           -
LGA    -       -      E      31           -
LGA    -       -      E      32           -
LGA    -       -      K      33           -
LGA    -       -      G      34           -
LGA    -       -      I      35           -
LGA    -       -      H      36           -
LGA    -       -      A      37           -
LGA    -       -      A      38           -
LGA    -       -      H      39           -
LGA    -       -      I      40           -
LGA    -       -      S      41           -
LGA    -       -      A      42           -
LGA    -       -      I      43           -
LGA    -       -      G      44           -
LGA    -       -      A      45           -
LGA    -       -      V      46           -
LGA    -       -      R      47           -
LGA    -       -      S      48           -
LGA    -       -      A      49           -
LGA    -       -      V      50           -
LGA    -       -      I      51           -
LGA    -       -      G      52           -
LGA    -       -      Y      53           -
LGA    -       -      Y      54           -
LGA    -       -      D      55           -
LGA    -       -      Q      56           -
LGA    -       -      E      57           -
LGA    -       -      K      58           -
LGA    -       -      K      59           -
LGA    -       -      E      60           -
LGA    -       -      Y      61           -
LGA    -       -      V      62           -
LGA    -       -      K      63           -
LGA    -       -      K      64           -
LGA    -       -      E      65           -
LGA    -       -      L      66           -
LGA    -       -      M      67           -
LGA    -       -      E      68           -
LGA    -       -      P      69           -
LGA    -       -      L      70           -
LGA    -       -      E      71           -
LGA    -       -      I      72           -
LGA    -       -      L      73           -
LGA    -       -      S      74           -
LGA    -       -      L      75           -
LGA    -       -      S      76           -
LGA    -       -      G      77           -
LGA    -       -      N      78           -
LGA    -       -      V      79           -
LGA    -       -      S      80           -
LGA    -       -      M      81           -
LGA    -       -      K      82           -
LGA    -       -      D      83           -
LGA    -       -      S      84           -
LGA    -       -      K      85           -
LGA    -       -      P      86           -
LGA    -       -      F      87           -
LGA    -       -      C      88           -
LGA    -       -      H      89           -
LGA    -       -      I      90           -
LGA    -       -      H      91           -
LGA    -       -      V      92           -
LGA    -       -      L      93           -
LGA    -       -      L      94           -
LGA    -       -      G      95           -
LGA    -       -      K      96           -
LGA    -       -      D      97           -
LGA    -       -      G      98           -
LGA    -       -      E      99           -
LGA    -       -      V     100           -
LGA    -       -      Y     101           -
LGA    -       -      G     102           -
LGA    -       -      G     103           -
LGA    -       -      H     104           -
LGA    -       -      L     105           -
LGA    -       -      F     106           -
LGA    -       -      S     107           -
LGA    -       -      A     108           -
LGA    -       -      E     109           -
LGA    -       -      V     110           -
LGA    -       -      F     111           -
LGA    -       -      A     112           -
LGA    -       -      C     113           -
LGA    -       -      E     114           -
LGA    -       -      V     115           -
LGA    -       -      F     116           -
LGA    -       -      V     117           -
LGA    -       -      L     118           -
LGA    -       -      P     119           -
LGA    -       -      L     120           -
LGA    H     142      S     121          0.575
LGA    H     143      G     122          1.238
LGA    H     144      E     123          0.540
LGA    -       -      A     124           -
LGA    H     145      P     125          1.246
LGA    H     146      E     126          1.668
LGA    -       -      R     127           -
LGA    -       -      A     128           -
LGA    -       -      F     129           -
LGA    -       -      D     130           -
LGA    -       -      E     131           -
LGA    -       -      Q     132           -
LGA    -       -      T     133           -
LGA    -       -      G     134           -
LGA    -       -      L     135           -
LGA    -       -      F     136           -
LGA    -       -      L     137           -
LGA    -       -      W     138           -
LGA    -       -      L     139           -
LGA    -       -      E     140           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)    5  140    5.0      5    1.14     0.00      3.462     0.404

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.460745 * X  +  -0.887423 * Y  +   0.013951 * Z  +  91.140350
  Y_new =  -0.646338 * X  +   0.324720 * Y  +  -0.690510 * Z  +  20.344202
  Z_new =   0.608244 * X  +  -0.327166 * Y  +  -0.723188 * Z  +   3.280517 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.716750    0.424843  [ DEG:  -155.6583     24.3417 ]
  Theta =  -0.653847   -2.487746  [ DEG:   -37.4627   -142.5374 ]
  Phi   =  -2.190098    0.951495  [ DEG:  -125.4834     54.5166 ]
 
# 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: T0312TS102_5                                  
REMARK     2: T0312.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0312TS102_5.T0312.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:    5  140   5.0    5   1.14    0.00   3.462
REMARK  ---------------------------------------------------------- 
MOLECULE T0312TS102_5
PFRMAT TS
TARGET T0312
MODEL 5
PARENT 1ryq_A
ATOM      1  N   HIS   142      68.954  12.234  30.855  1.00  1.00
ATOM      2  CA  HIS   142      69.609  12.515  29.578  1.00  1.00
ATOM      3  C   HIS   142      70.757  11.539  29.305  1.00  1.00
ATOM      4  O   HIS   142      71.268  11.514  28.216  1.00  1.00
ATOM      5  CB  HIS   142      70.096  13.978  29.510  1.00  1.00
ATOM      6  N   HIS   143      71.160  10.746  30.297  1.00  1.00
ATOM      7  CA  HIS   143      72.228   9.743  30.115  1.00  1.00
ATOM      8  C   HIS   143      71.797   8.366  30.590  1.00  1.00
ATOM      9  O   HIS   143      70.756   8.220  31.221  1.00  1.00
ATOM     10  CB  HIS   143      73.500  10.154  30.852  1.00  1.00
ATOM     11  N   HIS   144      72.623   7.365  30.298  1.00  1.00
ATOM     12  CA  HIS   144      72.344   5.982  30.669  1.00  1.00
ATOM     13  C   HIS   144      72.107   5.748  32.169  1.00  1.00
ATOM     14  O   HIS   144      71.323   4.867  32.530  1.00  1.00
ATOM     15  CB  HIS   144      73.465   5.062  30.152  1.00  1.00
ATOM     16  N   HIS   145      67.098   0.649  28.764  1.00  1.00
ATOM     17  CA  HIS   145      67.434   1.413  27.517  1.00  1.00
ATOM     18  C   HIS   145      68.922   1.337  27.175  1.00  1.00
ATOM     19  O   HIS   145      69.789   1.762  27.953  1.00  1.00
ATOM     20  CB  HIS   145      66.991   2.879  27.629  1.00  1.00
ATOM     21  N   HIS   146      69.195   0.819  25.979  1.00  1.00
ATOM     22  CA  HIS   146      70.562   0.674  25.485  1.00  1.00
ATOM     23  C   HIS   146      70.666   1.394  24.149  1.00  1.00
ATOM     24  O   HIS   146      69.676   1.518  23.411  1.00  1.00
ATOM     25  CB  HIS   146      70.919  -0.793  25.285  1.00  1.00
TER
END
