
#######################################################
#                                                     #
#                        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_2
# Molecule2: number of CA atoms  109 ( 1766),  selected  109 , name T0352.pdb
# PARAMETERS: T0352TS102_2.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    H     113      R       8          1.433
LGA    H     114      L       9          0.730
LGA    H     115      Q      10          1.328
LGA    -       -      L      11           -
LGA    -       -      Q      12           -
LGA    H     116      A      13          0.764
LGA    H     117      L      14          0.518
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    1.02     0.00      4.515     0.446

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.967854 * X  +  -0.195150 * Y  +   0.158666 * Z  +  44.594795
  Y_new =  -0.249350 * X  +   0.827051 * Y  +  -0.503796 * Z  +   8.285375
  Z_new =  -0.032909 * X  +  -0.527165 * Y  +  -0.849126 * Z  +  12.084309 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.585996    0.555597  [ DEG:  -148.1666     31.8334 ]
  Theta =   0.032915    3.108678  [ DEG:     1.8859    178.1141 ]
  Phi   =  -2.889444    0.252149  [ DEG:  -165.5529     14.4471 ]
 
# 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_2                                  
REMARK     2: T0352.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0352TS102_2.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   1.02    0.00   4.515
REMARK  ---------------------------------------------------------- 
MOLECULE T0352TS102_2
PFRMAT TS
TARGET T0352
MODEL 2
PARENT 2aml_A
ATOM      1  N   HIS   113      -3.365   1.804  -8.364  1.00  1.00
ATOM      2  CA  HIS   113      -4.543   0.876  -8.340  1.00  1.00
ATOM      3  C   HIS   113      -5.759   1.703  -8.781  1.00  1.00
ATOM      4  O   HIS   113      -6.097   2.712  -8.152  1.00  1.00
ATOM      5  CB  HIS   113      -4.814   0.302  -6.925  1.00  1.00
ATOM      6  N   HIS   114      -6.403   1.303  -9.882  1.00  1.00
ATOM      7  CA  HIS   114      -7.607   1.966 -10.378  1.00  1.00
ATOM      8  C   HIS   114      -8.753   1.622  -9.441  1.00  1.00
ATOM      9  O   HIS   114      -9.126   0.432  -9.279  1.00  1.00
ATOM     10  CB  HIS   114      -7.902   1.482 -11.802  1.00  1.00
ATOM     11  N   HIS   115      -9.264   2.657  -8.777  1.00  1.00
ATOM     12  CA  HIS   115     -10.490   2.529  -7.993  1.00  1.00
ATOM     13  C   HIS   115     -11.469   3.535  -8.567  1.00  1.00
ATOM     14  O   HIS   115     -11.259   4.742  -8.439  1.00  1.00
ATOM     15  CB  HIS   115     -10.252   2.785  -6.497  1.00  1.00
ATOM     16  N   HIS   116     -12.484   3.018  -9.286  1.00  1.00
ATOM     17  CA  HIS   116     -13.454   3.845 -10.054  1.00  1.00
ATOM     18  C   HIS   116     -14.032   5.032  -9.246  1.00  1.00
ATOM     19  O   HIS   116     -14.162   6.126  -9.784  1.00  1.00
ATOM     20  CB  HIS   116     -14.581   2.906 -10.557  1.00  1.00
ATOM     21  N   HIS   117     -14.350   4.807  -7.973  1.00  1.00
ATOM     22  CA  HIS   117     -14.980   5.855  -7.178  1.00  1.00
ATOM     23  C   HIS   117     -13.957   6.796  -6.538  1.00  1.00
ATOM     24  O   HIS   117     -14.353   7.800  -5.959  1.00  1.00
ATOM     25  CB  HIS   117     -15.937   5.261  -6.142  1.00  1.00
TER
END
