
#######################################################
#                                                     #
#                        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   57 (   57),  selected   57 , name T0349TS168_5-D1
# Molecule2: number of CA atoms   57 (  873),  selected   57 , name T0349_D1.pdb
# PARAMETERS: T0349TS168_5-D1.T0349_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      M       1           -
LGA    R       2      R       2           -
LGA    E       3      E       3           -
LGA    L       4      L       4           -
LGA    -       -      L       5           -
LGA    -       -      R       6           -
LGA    L       5      T       7           #
LGA    R       6      N       8          3.730
LGA    T       7      D       9          2.992
LGA    N       8      -       -           -
LGA    D       9      -       -           -
LGA    A      10      A      10          1.367
LGA    V      11      V      11          2.647
LGA    L      12      L      12          2.847
LGA    L      13      L      13          1.445
LGA    S      14      S      14          0.928
LGA    A      15      A      15          1.934
LGA    V      16      V      16          2.358
LGA    G      17      G      17          1.990
LGA    A      18      A      18          1.478
LGA    L      19      L      19          1.294
LGA    L      20      L      20          2.695
LGA    -       -      D      21           -
LGA    D      21      G      22          1.513
LGA    G      22      A      23          4.645
LGA    A      23      D      24           -
LGA    D      24      -       -           -
LGA    I      25      I      25           #
LGA    G      26      G      26           -
LGA    H      27      H      27           -
LGA    L      28      L      28           -
LGA    V      29      V      29           -
LGA    P      45      -       -           -
LGA    R      46      -       -           -
LGA    R      47      -       -           -
LGA    V      48      -       -           -
LGA    L      49      -       -           -
LGA    V      50      -       -           -
LGA    H      51      -       -           -
LGA    E      52      P      45          3.458
LGA    D      53      R      46          1.804
LGA    D      54      -       -           -
LGA    L      55      -       -           -
LGA    A      56      R      47          2.073
LGA    G      57      V      48          2.972
LGA    A      58      -       -           -
LGA    R      59      L      49          1.593
LGA    R      60      -       -           -
LGA    L      61      -       -           -
LGA    L      62      -       -           -
LGA    T      63      V      50          1.833
LGA    D      64      -       -           -
LGA    A      65      -       -           -
LGA    G      66      -       -           -
LGA    L      67      H      51          4.083
LGA    A      68      E      52          1.749
LGA    H      69      D      53          4.802
LGA    E      70      D      54           -
LGA    L      71      L      55           -
LGA    R      72      A      56           -
LGA    -       -      G      57           -
LGA    -       -      A      58           -
LGA    -       -      R      59           -
LGA    -       -      R      60           -
LGA    -       -      L      61           -
LGA    -       -      L      62           -
LGA    -       -      T      63           -
LGA    -       -      D      64           -
LGA    -       -      A      65           -
LGA    -       -      G      66           -
LGA    -       -      L      67           -
LGA    -       -      A      68           -
LGA    -       -      H      69           -
LGA    -       -      E      70           -
LGA    -       -      L      71           -
LGA    -       -      R      72           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   57   57    5.0     24    2.65    45.83     30.619     0.874

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.441124 * X  +  -0.548401 * Y  +   0.710398 * Z  +   1.871490
  Y_new =   0.855674 * X  +  -0.495700 * Y  +   0.148672 * Z  +   2.179425
  Z_new =   0.270613 * X  +   0.673452 * Y  +   0.687918 * Z  +   2.738481 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.774773   -2.366820  [ DEG:    44.3912   -135.6088 ]
  Theta =  -0.274030   -2.867563  [ DEG:   -15.7008   -164.2992 ]
  Phi   =   2.046789   -1.094803  [ DEG:   117.2724    -62.7276 ]
 
# 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: T0349TS168_5-D1                               
REMARK     2: T0349_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0349TS168_5-D1.T0349_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   57   57   5.0   24   2.65   45.83  30.619
REMARK  ---------------------------------------------------------- 
MOLECULE T0349TS168_5-D1
PFRMAT TS
TARGET T0349
MODEL 5
PARENT N/A
ATOM      1  CA  MET     1      -7.870 -18.897   8.081  1.00 25.00           C
ATOM      2  CA  ARG     2      -6.345 -18.168   4.661  1.00 25.00           C
ATOM      3  CA  GLU     3      -3.506 -15.787   3.827  1.00 25.00           C
ATOM      4  CA  LEU     4      -0.526 -14.241   5.672  1.00 25.00           C
ATOM      5  CA  LEU     5       0.088 -11.860   2.736  1.00 25.00           C
ATOM      6  CA  ARG     6      -3.606 -10.850   2.751  1.00 25.00           C
ATOM      7  CA  THR     7      -3.439 -10.199   6.521  1.00 25.00           C
ATOM      8  CA  ASN     8      -0.305  -8.053   6.037  1.00 25.00           C
ATOM      9  CA  ASP     9      -2.062  -6.067   3.275  1.00 25.00           C
ATOM     10  CA  ALA    10      -5.088  -5.521   5.558  1.00 25.00           C
ATOM     11  CA  VAL    11      -2.781  -4.315   8.368  1.00 25.00           C
ATOM     12  CA  LEU    12      -1.058  -1.897   5.948  1.00 25.00           C
ATOM     13  CA  LEU    13      -4.464  -0.561   4.819  1.00 25.00           C
ATOM     14  CA  SER    14      -5.506  -0.060   8.470  1.00 25.00           C
ATOM     15  CA  ALA    15      -2.240   1.812   9.171  1.00 25.00           C
ATOM     16  CA  VAL    16      -2.834   4.044   6.116  1.00 25.00           C
ATOM     17  CA  GLY    17      -6.396   4.779   7.316  1.00 25.00           C
ATOM     18  CA  ALA    18      -5.065   5.674  10.794  1.00 25.00           C
ATOM     19  CA  LEU    19      -2.467   8.011   9.226  1.00 25.00           C
ATOM     20  CA  LEU    20      -5.201   9.686   7.132  1.00 25.00           C
ATOM     21  CA  ASP    21      -7.352  10.150  10.267  1.00 25.00           C
ATOM     22  CA  GLY    22      -4.932  11.022  13.120  1.00 25.00           C
ATOM     23  CA  ALA    23      -1.335  11.486  14.312  1.00 25.00           C
ATOM     24  CA  ASP    24      -1.144  14.677  12.254  1.00 25.00           C
ATOM     25  CA  ILE    25       0.634  12.905   9.461  1.00 25.00           C
ATOM     26  CA  GLY    26       2.686  10.442  11.440  1.00 25.00           C
ATOM     27  CA  HIS    27       3.030   6.895  12.775  1.00 25.00           C
ATOM     28  CA  LEU    28       6.375   5.163  12.238  1.00 25.00           C
ATOM     29  CA  VAL    29       5.563   1.512  11.899  1.00 25.00           C
ATOM     45  CA  PRO    45       6.482  -4.275   3.376  1.00 25.00           C
ATOM     46  CA  ARG    46       4.931  -0.740   3.459  1.00 25.00           C
ATOM     47  CA  ARG    47       6.546   0.268   0.157  1.00 25.00           C
ATOM     48  CA  VAL    48       6.115  -1.651  -3.101  1.00 25.00           C
ATOM     49  CA  LEU    49       5.244  -2.449  -6.694  1.00 25.00           C
ATOM     50  CA  VAL    50       4.495  -5.930  -5.317  1.00 25.00           C
ATOM     51  CA  HIS    51       1.157  -5.886  -7.112  1.00 25.00           C
ATOM     52  CA  GLU    52      -2.432  -5.237  -5.972  1.00 25.00           C
ATOM     53  CA  ASP    53      -2.671  -5.025  -2.156  1.00 25.00           C
ATOM     54  CA  ASP    54       1.079  -4.278  -1.938  1.00 25.00           C
ATOM     55  CA  LEU    55       0.711  -1.532  -4.582  1.00 25.00           C
ATOM     56  CA  ALA    56      -2.215  -0.014  -2.633  1.00 25.00           C
ATOM     57  CA  GLY    57      -0.136  -0.070   0.582  1.00 25.00           C
ATOM     58  CA  ALA    58       2.765   1.649  -1.235  1.00 25.00           C
ATOM     59  CA  ARG    59       0.372   4.326  -2.570  1.00 25.00           C
ATOM     60  CA  ARG    60      -1.002   4.895   0.958  1.00 25.00           C
ATOM     61  CA  LEU    61       2.562   5.239   2.317  1.00 25.00           C
ATOM     62  CA  LEU    62       3.394   7.768  -0.436  1.00 25.00           C
ATOM     63  CA  THR    63       0.236   9.764   0.410  1.00 25.00           C
ATOM     64  CA  ASP    64       1.197   9.758   4.118  1.00 25.00           C
ATOM     65  CA  ALA    65       4.716  10.983   3.233  1.00 25.00           C
ATOM     66  CA  GLY    66       7.277  10.894   0.357  1.00 25.00           C
ATOM     67  CA  LEU    67       4.401  12.598  -1.531  1.00 25.00           C
ATOM     68  CA  ALA    68       3.254  15.887  -3.085  1.00 25.00           C
ATOM     69  CA  HIS    69       4.955  18.081  -5.743  1.00 25.00           C
ATOM     70  CA  GLU    70       1.461  18.395  -7.213  1.00 25.00           C
ATOM     71  CA  LEU    71      -1.863  16.658  -6.538  1.00 25.00           C
ATOM     72  CA  ARG    72      -3.309  19.760  -8.131  1.00 25.00           C
TER
END
