
#######################################################
#                                                     #
#                        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   64 (   64),  selected   64 , name T0311TS393_3-D1
# Molecule2: number of CA atoms   64 (  486),  selected   64 , name T0311_D1.pdb
# PARAMETERS: T0311TS393_3-D1.T0311_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    R       8      R       8           -
LGA    -       -      P       9           -
LGA    P       9      G      10           #
LGA    G      10      -       -           -
LGA    D      11      -       -           -
LGA    I      12      D      11          3.785
LGA    I      13      I      12          2.649
LGA    Q      14      I      13          2.837
LGA    E      15      Q      14          3.278
LGA    S      16      E      15          2.604
LGA    L      17      S      16          2.714
LGA    D      18      L      17          3.182
LGA    E      19      D      18           #
LGA    L      20      E      19          3.067
LGA    N      21      L      20          0.962
LGA    V      22      N      21          2.470
LGA    S      23      V      22          5.301
LGA    L      24      S      23          4.253
LGA    R      25      L      24          0.823
LGA    E      26      R      25          3.794
LGA    F      27      E      26          2.830
LGA    A      28      F      27          2.340
LGA    R      29      A      28          3.976
LGA    A      30      R      29          2.415
LGA    M      31      A      30          2.771
LGA    -       -      M      31           -
LGA    E      32      E      32          1.042
LGA    I      33      I      33          1.547
LGA    A      34      A      34          1.459
LGA    P      35      P      35          1.342
LGA    S      36      S      36          1.389
LGA    T      37      T      37          1.548
LGA    A      38      A      38          1.649
LGA    S      39      S      39          1.723
LGA    R      40      R      40          1.925
LGA    L      41      L      41          2.126
LGA    L      42      L      42          2.064
LGA    T      43      T      43          2.615
LGA    G      44      G      44          2.292
LGA    K      45      K      45          1.668
LGA    A      46      A      46          1.472
LGA    A      47      A      47          1.006
LGA    L      48      L      48          1.335
LGA    T      49      T      49          4.614
LGA    P      50      P      50          2.031
LGA    E      51      E      51          1.866
LGA    M      52      M      52          2.177
LGA    A      53      A      53          1.822
LGA    I      54      I      54          2.328
LGA    K      55      K      55          3.312
LGA    L      56      L      56          3.130
LGA    S      57      S      57          3.952
LGA    V      58      -       -           -
LGA    V      59      -       -           -
LGA    I      60      -       -           -
LGA    G      61      -       -           -
LGA    S      62      -       -           -
LGA    S      63      V      58          3.915
LGA    P      64      -       -           -
LGA    Q      65      -       -           -
LGA    M      66      -       -           -
LGA    W      67      -       -           -
LGA    L      68      V      59           #
LGA    N      69      I      60           #
LGA    L      70      G      61          1.752
LGA    Q      71      S      62          1.462
LGA    -       -      S      63           -
LGA    -       -      P      64           -
LGA    -       -      Q      65           -
LGA    -       -      M      66           -
LGA    -       -      W      67           -
LGA    -       -      L      68           -
LGA    -       -      N      69           -
LGA    -       -      L      70           -
LGA    -       -      Q      71           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   64   64    5.0     48    2.64    56.25     49.911     1.753

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.504018 * X  +  -0.846540 * Y  +  -0.171280 * Z  +  32.527065
  Y_new =  -0.712875 * X  +   0.295781 * Y  +   0.635864 * Z  +   3.645944
  Z_new =  -0.487623 * X  +   0.442588 * Y  +  -0.752556 * Z  +  13.707006 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.609959   -0.531633  [ DEG:   149.5397    -30.4603 ]
  Theta =   0.509365    2.632228  [ DEG:    29.1844    150.8156 ]
  Phi   =  -2.186219    0.955374  [ DEG:  -125.2611     54.7389 ]
 
# 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: T0311TS393_3-D1                               
REMARK     2: T0311_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0311TS393_3-D1.T0311_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   64   64   5.0   48   2.64   56.25  49.911
REMARK  ---------------------------------------------------------- 
MOLECULE T0311TS393_3-D1
PFRMAT TS
TARGET T0311
MODEL 3
PARENT N/A
ATOM      8  CA  ARG     8      38.792  -0.812  23.340  1.00 25.00           C
ATOM      9  CA  PRO     9      38.228  -0.589  19.549  1.00 25.00           C
ATOM     10  CA  GLY    10      35.442  -1.945  17.297  1.00 25.00           C
ATOM     11  CA  ASP    11      32.798  -0.654  19.748  1.00 25.00           C
ATOM     12  CA  ILE    12      34.476   2.789  19.783  1.00 25.00           C
ATOM     13  CA  ILE    13      34.512   2.837  15.954  1.00 25.00           C
ATOM     14  CA  GLN    14      30.796   1.914  15.882  1.00 25.00           C
ATOM     15  CA  GLU    15      30.025   4.721  18.370  1.00 25.00           C
ATOM     16  CA  SER    16      31.983   7.205  16.211  1.00 25.00           C
ATOM     17  CA  LEU    17      30.048   6.070  13.107  1.00 25.00           C
ATOM     18  CA  ASP    18      26.737   6.516  14.978  1.00 25.00           C
ATOM     19  CA  GLU    19      27.796  10.031  16.066  1.00 25.00           C
ATOM     20  CA  LEU    20      24.289   9.999  17.677  1.00 25.00           C
ATOM     21  CA  ASN    21      23.232   6.423  18.609  1.00 25.00           C
ATOM     22  CA  VAL    22      24.038   3.023  20.183  1.00 25.00           C
ATOM     23  CA  SER    23      27.039   0.729  19.971  1.00 25.00           C
ATOM     24  CA  LEU    24      25.769   0.101  16.435  1.00 25.00           C
ATOM     25  CA  ARG    25      24.771  -3.446  17.478  1.00 25.00           C
ATOM     26  CA  GLU    26      21.069  -2.540  17.107  1.00 25.00           C
ATOM     27  CA  PHE    27      21.745  -1.100  13.624  1.00 25.00           C
ATOM     28  CA  ALA    28      23.605  -4.298  12.635  1.00 25.00           C
ATOM     29  CA  ARG    29      20.674  -6.420  13.893  1.00 25.00           C
ATOM     30  CA  ALA    30      18.224  -4.276  11.875  1.00 25.00           C
ATOM     31  CA  MET    31      20.398  -4.691   8.750  1.00 25.00           C
ATOM     32  CA  GLU    32      21.402  -7.103   5.951  1.00 25.00           C
ATOM     33  CA  ILE    33      24.916  -6.752   7.350  1.00 25.00           C
ATOM     34  CA  ALA    34      24.212 -10.148   9.001  1.00 25.00           C
ATOM     35  CA  PRO    35      25.187  -9.392  12.613  1.00 25.00           C
ATOM     36  CA  SER    36      28.433 -11.419  12.444  1.00 25.00           C
ATOM     37  CA  THR    37      29.357  -9.711   9.143  1.00 25.00           C
ATOM     38  CA  ALA    38      28.680  -6.279  10.701  1.00 25.00           C
ATOM     39  CA  SER    39      30.879  -7.180  13.703  1.00 25.00           C
ATOM     40  CA  ARG    40      33.681  -8.301  11.345  1.00 25.00           C
ATOM     41  CA  LEU    41      33.396  -5.012   9.404  1.00 25.00           C
ATOM     42  CA  LEU    42      33.583  -3.035  12.679  1.00 25.00           C
ATOM     43  CA  THR    43      36.691  -5.012  13.725  1.00 25.00           C
ATOM     44  CA  GLY    44      39.855  -7.061  13.235  1.00 25.00           C
ATOM     45  CA  LYS    45      38.130 -10.379  12.867  1.00 25.00           C
ATOM     46  CA  ALA    46      38.033  -9.467   9.213  1.00 25.00           C
ATOM     47  CA  ALA    47      37.919  -6.159   7.335  1.00 25.00           C
ATOM     48  CA  LEU    48      37.658  -2.822   5.526  1.00 25.00           C
ATOM     49  CA  THR    49      37.059   0.261   3.467  1.00 25.00           C
ATOM     50  CA  PRO    50      34.860   0.041   0.319  1.00 25.00           C
ATOM     51  CA  GLU    51      32.411  -2.895   0.533  1.00 25.00           C
ATOM     52  CA  MET    52      32.800  -2.973   4.343  1.00 25.00           C
ATOM     53  CA  ALA    53      32.142   0.796   4.510  1.00 25.00           C
ATOM     54  CA  ILE    54      29.009   0.371   2.349  1.00 25.00           C
ATOM     55  CA  LYS    55      27.783  -2.444   4.637  1.00 25.00           C
ATOM     56  CA  LEU    56      28.368  -0.235   7.711  1.00 25.00           C
ATOM     57  CA  SER    57      26.419   2.619   6.061  1.00 25.00           C
ATOM     58  CA  VAL    58      23.537   0.225   5.267  1.00 25.00           C
ATOM     59  CA  VAL    59      23.515  -0.992   8.899  1.00 25.00           C
ATOM     60  CA  ILE    60      23.432   2.631  10.138  1.00 25.00           C
ATOM     61  CA  GLY    61      19.675   2.164   9.556  1.00 25.00           C
ATOM     62  CA  SER    62      19.369   3.022   5.817  1.00 25.00           C
ATOM     63  CA  SER    63      20.394   4.851   2.678  1.00 25.00           C
ATOM     64  CA  PRO    64      18.662   7.594   4.768  1.00 25.00           C
ATOM     65  CA  GLN    65      19.572  10.579   6.988  1.00 25.00           C
ATOM     66  CA  MET    66      21.595   8.282   9.289  1.00 25.00           C
ATOM     67  CA  TRP    67      23.427   6.821   6.261  1.00 25.00           C
ATOM     68  CA  LEU    68      24.213  10.351   5.001  1.00 25.00           C
ATOM     69  CA  ASN    69      25.554  11.312   8.458  1.00 25.00           C
ATOM     70  CA  LEU    70      27.747   8.174   8.507  1.00 25.00           C
ATOM     71  CA  GLN    71      29.090   9.027   5.024  1.00 25.00           C
TER
END
