
#######################################################
#                                                     #
#                        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_1
# Molecule2: number of CA atoms  132 ( 2030),  selected  132 , name T0357.pdb
# PARAMETERS: T0357TS102_1.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    -       -      Y      67           -
LGA    -       -      V      68           -
LGA    -       -      L      69           -
LGA    -       -      L      70           -
LGA    -       -      N      71           -
LGA    -       -      L      72           -
LGA    -       -      R      73           -
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    H     137      E     108          1.156
LGA    H     138      K     109          0.733
LGA    H     139      F     110          1.120
LGA    -       -      F     111           -
LGA    -       -      E     112           -
LGA    H     140      A     113          0.834
LGA    H     141      V     114          0.549
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    0.91     0.00      3.728     0.496

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.670596 * X  +  -0.720182 * Y  +   0.177873 * Z  + -29.113808
  Y_new =  -0.165114 * X  +   0.088857 * Y  +   0.982264 * Z  +   9.027417
  Z_new =  -0.723214 * X  +  -0.688071 * Y  +  -0.059325 * Z  +  47.116249 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.656802    1.484790  [ DEG:   -94.9278     85.0722 ]
  Theta =   0.808445    2.333148  [ DEG:    46.3205    133.6795 ]
  Phi   =  -0.241417    2.900176  [ DEG:   -13.8322    166.1678 ]
 
# 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_1                                  
REMARK     2: T0357.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0357TS102_1.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   0.91    0.00   3.728
REMARK  ---------------------------------------------------------- 
MOLECULE T0357TS102_1
PFRMAT TS
TARGET T0357
MODEL 1
PARENT 2aml_A
ATOM      1  N   HIS   137      -4.779  15.087   0.949  1.00  1.00
ATOM      2  CA  HIS   137      -3.416  15.067   0.321  1.00  1.00
ATOM      3  C   HIS   137      -3.629  14.776  -1.171  1.00  1.00
ATOM      4  O   HIS   137      -4.197  13.741  -1.537  1.00  1.00
ATOM      5  CB  HIS   137      -2.505  13.966   0.921  1.00  1.00
ATOM      6  N   HIS   138      -3.206  15.699  -2.039  1.00  1.00
ATOM      7  CA  HIS   138      -3.295  15.522  -3.488  1.00  1.00
ATOM      8  C   HIS   138      -2.258  14.491  -3.900  1.00  1.00
ATOM      9  O   HIS   138      -1.032  14.691  -3.710  1.00  1.00
ATOM     10  CB  HIS   138      -3.035  16.865  -4.179  1.00  1.00
ATOM     11  N   HIS   139      -2.758  13.364  -4.402  1.00  1.00
ATOM     12  CA  HIS   139      -1.898  12.360  -5.025  1.00  1.00
ATOM     13  C   HIS   139      -2.404  12.188  -6.445  1.00  1.00
ATOM     14  O   HIS   139      -3.507  11.680  -6.648  1.00  1.00
ATOM     15  CB  HIS   139      -1.922  11.024  -4.268  1.00  1.00
ATOM     16  N   HIS   140      -1.624  12.711  -7.411  1.00  1.00
ATOM     17  CA  HIS   140      -2.021  12.780  -8.843  1.00  1.00
ATOM     18  C   HIS   140      -2.590  11.449  -9.392  1.00  1.00
ATOM     19  O   HIS   140      -3.570  11.465 -10.127  1.00  1.00
ATOM     20  CB  HIS   140      -0.784  13.241  -9.655  1.00  1.00
ATOM     21  N   HIS   141      -1.982  10.325  -9.018  1.00  1.00
ATOM     22  CA  HIS   141      -2.408   9.043  -9.566  1.00  1.00
ATOM     23  C   HIS   141      -3.570   8.430  -8.781  1.00  1.00
ATOM     24  O   HIS   141      -4.116   7.424  -9.215  1.00  1.00
ATOM     25  CB  HIS   141      -1.229   8.077  -9.690  1.00  1.00
TER
END
