
#######################################################
#                                                     #
#                        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   32 (   32),  selected   32 , name T0301TS464_5_2-D1
# Molecule2: number of CA atoms  200 ( 1505),  selected  200 , name T0301_D1.pdb
# PARAMETERS: T0301TS464_5_2-D1.T0301_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      M       1           -
LGA    -       -      A       2           -
LGA    -       -      H       3           -
LGA    -       -      P       4           -
LGA    -       -      P       5           -
LGA    -       -      Q       6           -
LGA    -       -      I       7           -
LGA    -       -      R       8           -
LGA    -       -      I       9           -
LGA    -       -      P      10           -
LGA    -       -      A      11           -
LGA    -       -      T      12           -
LGA    -       -      Y      13           -
LGA    -       -      L      14           -
LGA    -       -      R      15           -
LGA    -       -      G      16           -
LGA    -       -      G      17           -
LGA    -       -      T      18           -
LGA    -       -      S      19           -
LGA    -       -      K      20           -
LGA    -       -      G      21           -
LGA    -       -      V      22           -
LGA    -       -      F      23           -
LGA    -       -      F      24           -
LGA    -       -      R      25           -
LGA    -       -      L      26           -
LGA    -       -      E      27           -
LGA    -       -      D      28           -
LGA    -       -      L      29           -
LGA    -       -      P      30           -
LGA    -       -      E      31           -
LGA    -       -      S      32           -
LGA    -       -      C      33           -
LGA    -       -      R      34           -
LGA    -       -      V      35           -
LGA    -       -      P      36           -
LGA    -       -      G      37           -
LGA    -       -      E      38           -
LGA    -       -      A      39           -
LGA    -       -      R      40           -
LGA    -       -      D      41           -
LGA    -       -      R      42           -
LGA    -       -      L      43           -
LGA    -       -      F      44           -
LGA    -       -      M      45           -
LGA    -       -      R      46           -
LGA    -       -      V      47           -
LGA    -       -      I      48           -
LGA    -       -      G      49           -
LGA    -       -      S      50           -
LGA    -       -      P      51           -
LGA    -       -      D      52           -
LGA    -       -      P      53           -
LGA    -       -      Y      54           -
LGA    -       -      A      55           -
LGA    -       -      A      56           -
LGA    -       -      H      57           -
LGA    -       -      I      58           -
LGA    -       -      D      59           -
LGA    -       -      G      60           -
LGA    -       -      M      61           -
LGA    -       -      G      62           -
LGA    -       -      G      63           -
LGA    -       -      A      64           -
LGA    -       -      T      65           -
LGA    -       -      S      66           -
LGA    -       -      S      67           -
LGA    -       -      T      68           -
LGA    -       -      S      69           -
LGA    -       -      K      70           -
LGA    -       -      C      71           -
LGA    -       -      V      72           -
LGA    -       -      I      73           -
LGA    -       -      L      74           -
LGA    -       -      S      75           -
LGA    -       -      K      76           -
LGA    -       -      S      77           -
LGA    -       -      S      78           -
LGA    -       -      Q      79           -
LGA    -       -      P      80           -
LGA    -       -      G      81           -
LGA    -       -      H      82           -
LGA    -       -      D      83           -
LGA    -       -      V      84           -
LGA    -       -      D      85           -
LGA    -       -      Y      86           -
LGA    -       -      L      87           -
LGA    -       -      Y      88           -
LGA    -       -      G      89           -
LGA    -       -      Q      90           -
LGA    -       -      V      91           -
LGA    -       -      S      92           -
LGA    -       -      I      93           -
LGA    -       -      D      94           -
LGA    -       -      K      95           -
LGA    -       -      P      96           -
LGA    -       -      F      97           -
LGA    -       -      V      98           -
LGA    -       -      D      99           -
LGA    -       -      W     100           -
LGA    -       -      S     101           -
LGA    -       -      G     102           -
LGA    -       -      N     103           -
LGA    -       -      C     104           -
LGA    -       -      G     105           -
LGA    -       -      N     106           -
LGA    K      20      L     107          1.714
LGA    G      21      S     108          1.214
LGA    V      22      T     109          1.609
LGA    F      23      G     110          0.711
LGA    F      24      A     111          0.902
LGA    R      25      G     112          1.434
LGA    L      26      A     113          1.758
LGA    E      27      F     114          1.763
LGA    D      28      A     115          1.473
LGA    L      29      L     116          1.347
LGA    P      30      H     117          1.511
LGA    E      31      A     118          1.546
LGA    S      32      G     119          1.247
LGA    C      33      L     120           #
LGA    -       -      V     121           -
LGA    -       -      D     122           -
LGA    -       -      P     123           -
LGA    -       -      A     124           -
LGA    -       -      R     125           -
LGA    -       -      I     126           -
LGA    -       -      P     127           -
LGA    C      71      E     128           #
LGA    -       -      D     129           -
LGA    -       -      G     130           -
LGA    -       -      I     131           -
LGA    -       -      C     132           -
LGA    -       -      E     133           -
LGA    -       -      V     134           -
LGA    -       -      R     135           -
LGA    -       -      I     136           -
LGA    -       -      W     137           -
LGA    -       -      Q     138           -
LGA    -       -      A     139           -
LGA    -       -      N     140           -
LGA    -       -      I     141           -
LGA    -       -      G     142           -
LGA    -       -      K     143           -
LGA    -       -      T     144           -
LGA    -       -      I     145           -
LGA    -       -      I     146           -
LGA    -       -      A     147           -
LGA    -       -      H     148           -
LGA    -       -      V     149           -
LGA    -       -      P     150           -
LGA    -       -      V     151           -
LGA    V      72      S     152          3.459
LGA    -       -      G     153           -
LGA    -       -      G     154           -
LGA    -       -      Q     155           -
LGA    -       -      V     156           -
LGA    I      73      Q     157          1.703
LGA    -       -      E     158           -
LGA    -       -      T     159           -
LGA    -       -      G     160           -
LGA    -       -      D     161           -
LGA    -       -      F     162           -
LGA    -       -      E     163           -
LGA    -       -      L     164           -
LGA    -       -      D     165           -
LGA    -       -      G     166           -
LGA    -       -      V     167           -
LGA    -       -      T     168           -
LGA    -       -      F     169           -
LGA    -       -      P     170           -
LGA    -       -      A     171           -
LGA    L      74      A     172          3.010
LGA    S      75      E     173          0.644
LGA    K      76      I     174          5.636
LGA    -       -      V     175           -
LGA    -       -      L     176           -
LGA    -       -      E     177           -
LGA    -       -      F     178           -
LGA    -       -      L     179           -
LGA    -       -      D     180           -
LGA    -       -      P     181           -
LGA    -       -      S     182           -
LGA    S      77      R     378          4.240
LGA    G     110      S     379           -
LGA    -       -      A     380           -
LGA    -       -      R     381           -
LGA    A     111      I     382           #
LGA    G     112      L     383           -
LGA    A     113      M     384          4.733
LGA    F     114      E     385          2.759
LGA    A     115      G     386           #
LGA    I     141      -       -           -
LGA    G     142      W     387           #
LGA    K     143      V     388           -
LGA    T     144      R     389           -
LGA    I     145      V     390           -
LGA    -       -      P     391           -
LGA    -       -      G     392           -
LGA    -       -      D     393           -
LGA    -       -      A     394           -
LGA    -       -      F     395           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   32  200    5.0     21    2.50     4.76      8.285     0.809

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.885295 * X  +  -0.212592 * Y  +   0.413590 * Z  +  64.134094
  Y_new =   0.075373 * X  +  -0.943223 * Y  +  -0.323495 * Z  +  57.283810
  Z_new =   0.458881 * X  +  -0.255215 * Y  +   0.851055 * Z  +  20.106060 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.291347    2.850245  [ DEG:   -16.6930    163.3070 ]
  Theta =  -0.476735   -2.664858  [ DEG:   -27.3149   -152.6851 ]
  Phi   =   3.056659   -0.084934  [ DEG:   175.1336     -4.8664 ]
 
# 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: T0301TS464_5_2-D1                             
REMARK     2: T0301_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0301TS464_5_2-D1.T0301_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   32  200   5.0   21   2.50    4.76   8.285
REMARK  ---------------------------------------------------------- 
MOLECULE T0301TS464_5_2-D1
REMARK PARENT number 2
PFRMAT TS
TARGET T0301
PARENT N/A
ATOM      1  CA  LYS    20      78.512  21.354  11.199  1.00  0.00
ATOM      2  CA  GLY    21      76.080  18.595  10.347  1.00  0.00
ATOM      3  CA  VAL    22      74.090  18.946  13.548  1.00  0.00
ATOM      4  CA  PHE    23      73.915  22.694  13.035  1.00  0.00
ATOM      5  CA  PHE    24      72.026  22.193   9.758  1.00  0.00
ATOM      6  CA  ARG    25      69.816  19.686  11.527  1.00  0.00
ATOM      7  CA  LEU    26      68.983  22.154  14.316  1.00  0.00
ATOM      8  CA  GLU    27      68.243  24.900  11.817  1.00  0.00
ATOM      9  CA  ASP    28      65.721  22.564  10.186  1.00  0.00
ATOM     10  CA  LEU    29      63.990  21.929  13.481  1.00  0.00
ATOM     11  CA  PRO    30      64.032  25.580  14.576  1.00  0.00
ATOM     12  CA  GLU    31      62.609  26.736  11.227  1.00  0.00
ATOM     13  CA  SER    32      59.884  24.096  11.228  1.00  0.00
ATOM     14  CA  CYS    33      59.363  24.685  14.952  1.00  0.00
ATOM     15  CA  CYS    71      61.780  17.700  25.633  1.00  0.00
ATOM     16  CA  VAL    72      65.477  16.908  25.209  1.00  0.00
ATOM     17  CA  ILE    73      68.496  17.533  22.992  1.00  0.00
ATOM     18  CA  LEU    74      71.289  15.103  23.759  1.00  0.00
ATOM     19  CA  SER    75      74.781  14.910  22.306  1.00  0.00
ATOM     20  CA  LYS    76      78.277  13.463  22.637  1.00  0.00
ATOM     21  CA  SER    77      81.726  14.420  21.314  1.00  0.00
ATOM     22  CA  GLY   110      71.039  32.127  10.973  1.00  0.00
ATOM     23  CA  ALA   111      70.346  28.703  12.485  1.00  0.00
ATOM     24  CA  GLY   112      66.893  29.669  13.751  1.00  0.00
ATOM     25  CA  ALA   113      67.722  30.250  17.404  1.00  0.00
ATOM     26  CA  PHE   114      64.922  32.347  18.910  1.00  0.00
ATOM     27  CA  ALA   115      65.889  32.070  22.551  1.00  0.00
ATOM     28  CA  ILE   141      66.881  41.459  17.491  1.00  0.00
ATOM     29  CA  GLY   142      63.419  40.574  18.773  1.00  0.00
ATOM     30  CA  LYS   143      64.635  37.405  20.500  1.00  0.00
ATOM     31  CA  THR   144      64.227  36.048  24.020  1.00  0.00
ATOM     32  CA  ILE   145      66.895  35.930  26.701  1.00  0.00
TER
END
