
#######################################################
#                                                     #
#                        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   38 (   38),  selected   38 , name T0304TS464_4_2
# Molecule2: number of CA atoms  107 (  848),  selected  107 , name T0304.pdb
# PARAMETERS: T0304TS464_4_2.T0304.pdb  -4  -ie  -o1  -sia  -d:55A/  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    A      45      D      16           -
LGA    D      46      R      17           -
LGA    R      47      P      18           -
LGA    -       -      W      19           -
LGA    -       -      W      20           -
LGA    -       -      G      21           -
LGA    -       -      L      22           -
LGA    -       -      P      23           -
LGA    -       -      C      24           -
LGA    -       -      T      25           -
LGA    -       -      V      26           -
LGA    -       -      T      27           -
LGA    -       -      P      28           -
LGA    -       -      C      29           -
LGA    -       -      F      30           -
LGA    -       -      G      31           -
LGA    -       -      A      32           -
LGA    -       -      R      33           -
LGA    -       -      L      34           -
LGA    -       -      V      35           -
LGA    A      48      Q      36           #
LGA    G      49      E      37          3.247
LGA    I      50      G      38          3.809
LGA    R      51      N      39          3.788
LGA    G      52      R      40          4.609
LGA    L      53      -       -           -
LGA    F      54      L      41          1.537
LGA    S      55      H      42          1.145
LGA    D      56      -       -           -
LGA    A      57      Y      43          2.994
LGA    D      58      L      44          5.131
LGA    A      59      A      45          4.251
LGA    Y      60      D      46           #
LGA    -       -      R      47           -
LGA    -       -      A      48           -
LGA    -       -      G      49           -
LGA    -       -      I      50           -
LGA    -       -      R      51           -
LGA    -       -      G      52           -
LGA    -       -      L      53           -
LGA    -       -      F      54           -
LGA    -       -      S      55           -
LGA    -       -      D      56           -
LGA    -       -      A      57           -
LGA    -       -      D      58           -
LGA    -       -      A      59           -
LGA    -       -      Y      60           -
LGA    -       -      H      61           -
LGA    -       -      L      62           -
LGA    -       -      D      63           -
LGA    -       -      Q      64           -
LGA    -       -      A      65           -
LGA    -       -      F      66           -
LGA    -       -      P      67           -
LGA    -       -      L      68           -
LGA    -       -      L      69           -
LGA    F      66      M      70          1.532
LGA    P      67      K      71          1.221
LGA    L      68      Q      72          1.428
LGA    L      69      L      73          1.642
LGA    M      70      E      74          1.947
LGA    K      71      L      75          2.140
LGA    Q      72      M      76          2.074
LGA    L      73      L      77          2.998
LGA    E      74      T      78          3.016
LGA    -       -      S      79           -
LGA    L      75      G      80          2.168
LGA    -       -      E      81           -
LGA    -       -      L      82           -
LGA    M      76      N      83          2.464
LGA    L      77      P      84           -
LGA    -       -      R      85           -
LGA    -       -      H      86           -
LGA    T      78      Q      87           #
LGA    S      79      H      88           #
LGA    G      80      T      89          3.338
LGA    E      81      V      90          1.485
LGA    L      82      T      91          3.261
LGA    N      83      -       -           -
LGA    P      84      L      92          3.776
LGA    R      85      Y      93          3.004
LGA    H      86      A      94          4.601
LGA    -       -      K      95           -
LGA    -       -      G      96           -
LGA    Q      87      L      97          1.674
LGA    -       -      T      98           -
LGA    -       -      C      99           -
LGA    -       -      K     100           -
LGA    -       -      A     101           -
LGA    -       -      D     102           -
LGA    -       -      T     103           -
LGA    -       -      L     104           -
LGA    -       -      S     105           -
LGA    -       -      S     106           -
LGA    -       -      C     107           -
LGA    -       -      D     108           -
LGA    -       -      Y     109           -
LGA    -       -      V     110           -
LGA    -       -      Y     111           -
LGA    -       -      L     112           -
LGA    -       -      A     113           -
LGA    -       -      V     114           -
LGA    -       -      Y     115           -
LGA    -       -      P     116           -
LGA    -       -      T     117           -
LGA    -       -      P     118           -
LGA    -       -      E     119           -
LGA    -       -      M     120           -
LGA    -       -      K     121           -
LGA    -       -      N     122           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   38  107    5.0     27    2.98    11.11     15.789     0.878

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.632675 * X  +   0.044747 * Y  +  -0.773124 * Z  +  96.536369
  Y_new =   0.739506 * X  +   0.261460 * Y  +   0.620297 * Z  + -49.477249
  Z_new =   0.229897 * X  +  -0.964176 * Y  +   0.132329 * Z  +  70.209663 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.434403    1.707190  [ DEG:   -82.1852     97.8148 ]
  Theta =  -0.231972   -2.909621  [ DEG:   -13.2910   -166.7090 ]
  Phi   =   0.863097   -2.278496  [ DEG:    49.4518   -130.5482 ]
 
# 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: T0304TS464_4_2                                
REMARK     2: T0304.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0304TS464_4_2.T0304.pdb -4 -ie -o1 -sia -d:55A/ 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   38  107   5.0   27   2.98   11.11  15.789
REMARK  ---------------------------------------------------------- 
MOLECULE T0304TS464_4_2
REMARK PARENT number 2
PFRMAT TS
TARGET T0304
PARENT N/A
ATOM      1  CA  ALA    45      58.811  30.824  60.029  1.00  0.00
ATOM      2  CA  ASP    46      58.143  31.931  56.385  1.00  0.00
ATOM      3  CA  ARG    47      59.394  28.669  55.100  1.00  0.00
ATOM      4  CA  ALA    48      56.884  26.795  57.309  1.00  0.00
ATOM      5  CA  GLY    49      54.003  28.744  55.797  1.00  0.00
ATOM      6  CA  ILE    50      54.949  28.670  52.143  1.00  0.00
ATOM      7  CA  ARG    51      55.992  25.094  52.596  1.00  0.00
ATOM      8  CA  GLY    52      52.626  24.396  54.151  1.00  0.00
ATOM      9  CA  LEU    53      50.901  25.981  51.151  1.00  0.00
ATOM     10  CA  PHE    54      52.941  24.366  48.422  1.00  0.00
ATOM     11  CA  SER    55      52.823  20.969  50.045  1.00  0.00
ATOM     12  CA  ASP    56      49.055  21.136  50.267  1.00  0.00
ATOM     13  CA  ALA    57      48.516  21.444  46.540  1.00  0.00
ATOM     14  CA  ASP    58      50.789  18.462  46.011  1.00  0.00
ATOM     15  CA  ALA    59      48.381  16.162  47.880  1.00  0.00
ATOM     16  CA  TYR    60      46.518  15.543  44.665  1.00  0.00
ATOM     17  CA  PHE    66      53.998  23.566  44.160  1.00  0.00
ATOM     18  CA  PRO    67      57.105  24.530  42.204  1.00  0.00
ATOM     19  CA  LEU    68      55.777  28.009  41.614  1.00  0.00
ATOM     20  CA  LEU    69      54.950  28.485  45.308  1.00  0.00
ATOM     21  CA  MET    70      58.356  27.140  46.360  1.00  0.00
ATOM     22  CA  LYS    71      60.193  29.281  43.799  1.00  0.00
ATOM     23  CA  GLN    72      58.384  32.155  45.484  1.00  0.00
ATOM     24  CA  LEU    73      58.496  30.805  49.017  1.00  0.00
ATOM     25  CA  GLU    74      57.416  33.064  51.854  1.00  0.00
ATOM     26  CA  LEU    75      55.604  35.376  49.422  1.00  0.00
ATOM     27  CA  MET    76      51.860  35.175  48.980  1.00  0.00
ATOM     28  CA  LEU    77      50.927  34.317  45.421  1.00  0.00
ATOM     29  CA  THR    78      47.409  35.177  44.127  1.00  0.00
ATOM     30  CA  SER    79      45.128  32.995  41.998  1.00  0.00
ATOM     31  CA  GLY    80      45.633  35.661  39.361  1.00  0.00
ATOM     32  CA  GLU    81      49.427  35.291  39.414  1.00  0.00
ATOM     33  CA  LEU    82      49.103  31.489  39.298  1.00  0.00
ATOM     34  CA  ASN    83      46.605  31.610  36.452  1.00  0.00
ATOM     35  CA  PRO    84      48.942  33.850  34.475  1.00  0.00
ATOM     36  CA  ARG    85      51.836  31.449  34.962  1.00  0.00
ATOM     37  CA  HIS    86      50.136  28.061  34.634  1.00  0.00
ATOM     38  CA  GLN    87      48.861  26.594  31.377  1.00  0.00
TER
END
