
#######################################################
#                                                     #
#                        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   30 (   30),  selected   30 , name T0331TS464_4_2
# Molecule2: number of CA atoms  139 ( 1101),  selected  139 , name T0331.pdb
# PARAMETERS: T0331TS464_4_2.T0331.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    -       -      E       2           -
LGA    -       -      L       3           -
LGA    -       -      K       4           -
LGA    -       -      D       5           -
LGA    -       -      I       6           -
LGA    -       -      M       7           -
LGA    -       -      H       8           -
LGA    -       -      I       9           -
LGA    -       -      L      10           -
LGA    -       -      E      11           -
LGA    -       -      D      12           -
LGA    -       -      M      13           -
LGA    -       -      K      14           -
LGA    -       -      V      15           -
LGA    -       -      G      16           -
LGA    -       -      V      17           -
LGA    -       -      F      18           -
LGA    -       -      A      19           -
LGA    -       -      T      20           -
LGA    -       -      L      21           -
LGA    -       -      D      22           -
LGA    -       -      E      23           -
LGA    -       -      Y      24           -
LGA    -       -      G      25           -
LGA    -       -      N      26           -
LGA    -       -      P      27           -
LGA    -       -      H      28           -
LGA    -       -      A      29           -
LGA    -       -      R      30           -
LGA    -       -      H      31           -
LGA    -       -      A      32           -
LGA    T      82      H      33          3.196
LGA    A      83      I      34          0.209
LGA    -       -      T      35           -
LGA    R      84      A      36          3.308
LGA    P      85      A      37          1.587
LGA    V      86      N      38          1.261
LGA    E      87      E      39          3.451
LGA    N      88      E      40          3.217
LGA    D      89      -       -           -
LGA    Y      90      G      41          0.512
LGA    L      91      I      42          0.460
LGA    K      92      F      43          0.614
LGA    T      93      F      44          1.049
LGA    V      94      M      45          3.136
LGA    -       -      T      46           -
LGA    -       -      S      47           -
LGA    -       -      P      48           -
LGA    -       -      E      49           -
LGA    -       -      T      50           -
LGA    -       -      H      51           -
LGA    -       -      F      52           -
LGA    -       -      Y      53           -
LGA    -       -      D      54           -
LGA    -       -      Q      55           -
LGA    -       -      L      56           -
LGA    -       -      M      57           -
LGA    -       -      G      58           -
LGA    -       -      D      59           -
LGA    -       -      Q      60           -
LGA    -       -      R      61           -
LGA    -       -      V      62           -
LGA    -       -      A      63           -
LGA    -       -      M      64           -
LGA    -       -      T      65           -
LGA    -       -      A      66           -
LGA    -       -      I      67           -
LGA    -       -      S      68           -
LGA    -       -      E      69           -
LGA    -       -      E      70           -
LGA    -       -      G      71           -
LGA    -       -      Y      72           -
LGA    -       -      L      73           -
LGA    -       -      I      74           -
LGA    -       -      Q      75           -
LGA    -       -      V      76           -
LGA    -       -      V      77           -
LGA    -       -      R      78           -
LGA    -       -      V      79           -
LGA    G     123      E      80          5.606
LGA    F     124      G      81          2.961
LGA    Y     125      T      82          2.229
LGA    H     126      A      83          2.012
LGA    S     127      R      84          0.584
LGA    L     128      P      85          0.598
LGA    T     129      V      86          1.360
LGA    Q     130      E      87          3.188
LGA    G     131      N      88          3.841
LGA    -       -      D      89           -
LGA    -       -      Y      90           -
LGA    -       -      L      91           -
LGA    -       -      K      92           -
LGA    -       -      T      93           -
LGA    -       -      V      94           -
LGA    -       -      F      95           -
LGA    -       -      A      96           -
LGA    -       -      D      97           -
LGA    -       -      N      98           -
LGA    -       -      P      99           -
LGA    -       -      Y     100           -
LGA    -       -      Y     101           -
LGA    -       -      Q     102           -
LGA    -       -      H     103           -
LGA    -       -      I     104           -
LGA    -       -      Y     105           -
LGA    H     132      K     106           #
LGA    -       -      T     112           -
LGA    -       -      M     113           -
LGA    -       -      Q     114           -
LGA    K     133      V     115          1.911
LGA    Y     134      F     116          0.839
LGA    I     135      Q     117          0.571
LGA    F     136      I     118          0.164
LGA    S     137      Y     119          1.993
LGA    I     138      A     120          2.746
LGA    -       -      G     121           -
LGA    G     139      H     122          3.098
LGA    -       -      G     123           -
LGA    -       -      F     124           -
LGA    -       -      Y     125           -
LGA    -       -      H     126           -
LGA    -       -      S     127           -
LGA    -       -      L     128           -
LGA    -       -      T     129           -
LGA    -       -      Q     130           -
LGA    -       -      G     131           -
LGA    -       -      H     132           -
LGA    -       -      K     133           -
LGA    -       -      Y     134           -
LGA    -       -      I     135           -
LGA    -       -      F     136           -
LGA    -       -      S     137           -
LGA    -       -      I     138           -
LGA    -       -      G     139           -
LGA    -       -      E     145           -
LGA    -       -      V     146           -
LGA    -       -      R     147           -
LGA    -       -      A     148           -
LGA    -       -      L     149           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   30  139    5.0     28    2.40     3.57     14.342     1.118

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.733805 * X  +  -0.305393 * Y  +  -0.606849 * Z  +  66.866417
  Y_new =   0.675952 * X  +  -0.417583 * Y  +  -0.607218 * Z  +  46.291187
  Z_new =  -0.067969 * X  +  -0.855780 * Y  +   0.512855 * Z  +  71.768051 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.030903    2.110689  [ DEG:   -59.0664    120.9336 ]
  Theta =   0.068022    3.073571  [ DEG:     3.8974    176.1026 ]
  Phi   =   2.397209   -0.744384  [ DEG:   137.3500    -42.6500 ]
 
# 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: T0331TS464_4_2                                
REMARK     2: T0331.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0331TS464_4_2.T0331.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   30  139   5.0   28   2.40    3.57  14.342
REMARK  ---------------------------------------------------------- 
MOLECULE T0331TS464_4_2
REMARK PARENT number 2
PFRMAT TS
TARGET T0331
PARENT N/A
ATOM      1  CA  THR    82      13.059  32.405  32.808  1.00  0.00
ATOM      2  CA  ALA    83      15.240  33.350  29.842  1.00  0.00
ATOM      3  CA  ARG    84      13.692  33.884  26.453  1.00  0.00
ATOM      4  CA  PRO    85      14.405  35.460  23.101  1.00  0.00
ATOM      5  CA  VAL    86      11.953  38.069  21.752  1.00  0.00
ATOM      6  CA  GLU    87      10.844  38.423  18.116  1.00  0.00
ATOM      7  CA  ASN    88      12.539  41.875  18.222  1.00  0.00
ATOM      8  CA  ASP    89      15.914  40.114  18.841  1.00  0.00
ATOM      9  CA  TYR    90      16.511  40.658  22.566  1.00  0.00
ATOM     10  CA  LEU    91      17.549  37.982  25.039  1.00  0.00
ATOM     11  CA  LYS    92      15.487  38.804  28.186  1.00  0.00
ATOM     12  CA  THR    93      17.318  36.944  30.921  1.00  0.00
ATOM     13  CA  VAL    94      14.669  37.648  33.544  1.00  0.00
ATOM     14  CA  GLY   123      28.733  41.911  21.546  1.00  0.00
ATOM     15  CA  PHE   124      28.186  40.240  24.925  1.00  0.00
ATOM     16  CA  TYR   125      26.616  42.978  27.020  1.00  0.00
ATOM     17  CA  HIS   126      23.861  41.858  29.402  1.00  0.00
ATOM     18  CA  SER   127      22.567  45.445  29.574  1.00  0.00
ATOM     19  CA  LEU   128      20.880  46.589  32.784  1.00  0.00
ATOM     20  CA  THR   129      17.809  48.591  31.821  1.00  0.00
ATOM     21  CA  GLN   130      16.401  51.510  33.890  1.00  0.00
ATOM     22  CA  GLY   131      13.607  49.247  35.121  1.00  0.00
ATOM     23  CA  HIS   132      15.912  46.537  36.440  1.00  0.00
ATOM     24  CA  LYS   133      15.425  44.192  33.506  1.00  0.00
ATOM     25  CA  TYR   134      18.310  42.942  31.337  1.00  0.00
ATOM     26  CA  ILE   135      18.627  42.886  27.535  1.00  0.00
ATOM     27  CA  PHE   136      21.280  41.277  25.333  1.00  0.00
ATOM     28  CA  SER   137      21.550  42.836  21.845  1.00  0.00
ATOM     29  CA  ILE   138      23.607  41.074  19.110  1.00  0.00
ATOM     30  CA  GLY   139      23.529  40.099  15.387  1.00  0.00
TER
END
