
#######################################################
#                                                     #
#                        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_5-D1
# Molecule2: number of CA atoms   64 (  486),  selected   64 , name T0311_D1.pdb
# PARAMETERS: T0311TS393_5-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      P       9          4.700
LGA    G      10      G      10          1.748
LGA    D      11      D      11          1.884
LGA    I      12      I      12          2.247
LGA    I      13      I      13          2.936
LGA    Q      14      Q      14          3.011
LGA    E      15      E      15          2.164
LGA    S      16      S      16          2.871
LGA    L      17      -       -           -
LGA    D      18      -       -           -
LGA    E      19      L      17          5.503
LGA    L      20      D      18           -
LGA    -       -      E      19           -
LGA    N      21      L      20          2.242
LGA    V      22      N      21          4.038
LGA    S      23      V      22          3.498
LGA    L      24      S      23          5.458
LGA    R      25      L      24          1.134
LGA    -       -      R      25           -
LGA    E      26      E      26          2.040
LGA    F      27      F      27          1.714
LGA    A      28      A      28          1.266
LGA    R      29      R      29          2.056
LGA    A      30      A      30          2.222
LGA    M      31      M      31          2.627
LGA    E      32      E      32          1.589
LGA    I      33      I      33          1.731
LGA    A      34      A      34          2.167
LGA    P      35      P      35          2.314
LGA    S      36      S      36          2.280
LGA    T      37      T      37          2.031
LGA    A      38      A      38          1.692
LGA    S      39      S      39          1.609
LGA    R      40      R      40          1.609
LGA    L      41      L      41          1.287
LGA    L      42      L      42          0.932
LGA    T      43      T      43          1.556
LGA    -       -      G      44           -
LGA    G      44      K      45          0.507
LGA    K      45      A      46          3.347
LGA    A      46      -       -           -
LGA    A      47      A      47          2.941
LGA    L      48      -       -           -
LGA    T      49      L      48          1.014
LGA    P      50      T      49          4.448
LGA    E      51      P      50          3.730
LGA    -       -      E      51           -
LGA    M      52      M      52          2.888
LGA    A      53      A      53          4.544
LGA    I      54      I      54          3.686
LGA    K      55      K      55          2.161
LGA    L      56      L      56          3.543
LGA    S      57      S      57          4.052
LGA    V      58      V      58          2.586
LGA    V      59      V      59          3.034
LGA    I      60      I      60          3.919
LGA    G      61      -       -           -
LGA    S      62      -       -           -
LGA    S      63      -       -           -
LGA    P      64      -       -           -
LGA    Q      65      -       -           -
LGA    M      66      -       -           -
LGA    W      67      -       -           -
LGA    L      68      G      61           #
LGA    N      69      -       -           -
LGA    L      70      -       -           -
LGA    Q      71      S      62          3.178
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    2.87    75.00     49.113     1.618

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.007363 * X  +   0.977464 * Y  +   0.210972 * Z  +  32.426857
  Y_new =   0.955717 * X  +   0.055191 * Y  +  -0.289067 * Z  +   4.111284
  Z_new =  -0.294197 * X  +   0.203758 * Y  +  -0.933773 * Z  +  11.336295 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.926751   -0.214841  [ DEG:   167.6905    -12.3095 ]
  Theta =   0.298615    2.842978  [ DEG:    17.1094    162.8906 ]
  Phi   =   1.563092   -1.578501  [ DEG:    89.5586    -90.4414 ]
 
# 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_5-D1                               
REMARK     2: T0311_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0311TS393_5-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   2.87   75.00  49.113
REMARK  ---------------------------------------------------------- 
MOLECULE T0311TS393_5-D1
PFRMAT TS
TARGET T0311
MODEL 5
PARENT N/A
ATOM      8  CA  ARG     8      40.500   2.338  19.324  1.00 25.00           C
ATOM      9  CA  PRO     9      40.104   2.462  15.571  1.00 25.00           C
ATOM     10  CA  GLY    10      37.424  -0.015  14.408  1.00 25.00           C
ATOM     11  CA  ASP    11      35.238   0.899  17.416  1.00 25.00           C
ATOM     12  CA  ILE    12      35.657   4.622  16.621  1.00 25.00           C
ATOM     13  CA  ILE    13      34.679   3.979  12.974  1.00 25.00           C
ATOM     14  CA  GLN    14      31.579   2.043  14.122  1.00 25.00           C
ATOM     15  CA  GLU    15      30.615   4.922  16.456  1.00 25.00           C
ATOM     16  CA  SER    16      31.030   7.422  13.585  1.00 25.00           C
ATOM     17  CA  LEU    17      28.831   5.238  11.334  1.00 25.00           C
ATOM     18  CA  ASP    18      26.161   5.061  14.073  1.00 25.00           C
ATOM     19  CA  GLU    19      26.267   8.870  14.458  1.00 25.00           C
ATOM     20  CA  LEU    20      22.752   8.941  12.866  1.00 25.00           C
ATOM     21  CA  ASN    21      21.804   7.065  16.075  1.00 25.00           C
ATOM     22  CA  VAL    22      22.278   3.465  17.001  1.00 25.00           C
ATOM     23  CA  SER    23      25.694   2.106  18.135  1.00 25.00           C
ATOM     24  CA  LEU    24      26.872  -0.398  15.526  1.00 25.00           C
ATOM     25  CA  ARG    25      24.881  -3.513  16.527  1.00 25.00           C
ATOM     26  CA  GLU    26      21.598  -1.670  15.822  1.00 25.00           C
ATOM     27  CA  PHE    27      22.912  -0.588  12.391  1.00 25.00           C
ATOM     28  CA  ALA    28      23.922  -4.200  11.613  1.00 25.00           C
ATOM     29  CA  ARG    29      20.440  -5.420  12.639  1.00 25.00           C
ATOM     30  CA  ALA    30      18.823  -2.779  10.387  1.00 25.00           C
ATOM     31  CA  MET    31      21.049  -3.869   7.467  1.00 25.00           C
ATOM     32  CA  GLU    32      20.694  -7.264   5.789  1.00 25.00           C
ATOM     33  CA  ILE    33      24.435  -7.338   5.975  1.00 25.00           C
ATOM     34  CA  ALA    34      23.825 -10.355   8.178  1.00 25.00           C
ATOM     35  CA  PRO    35      24.814  -9.169  11.683  1.00 25.00           C
ATOM     36  CA  SER    36      27.915 -11.414  11.607  1.00 25.00           C
ATOM     37  CA  THR    37      29.383  -9.331   8.749  1.00 25.00           C
ATOM     38  CA  ALA    38      28.724  -6.115  10.722  1.00 25.00           C
ATOM     39  CA  SER    39      30.436  -7.622  13.798  1.00 25.00           C
ATOM     40  CA  ARG    40      33.453  -8.621  11.661  1.00 25.00           C
ATOM     41  CA  LEU    41      33.644  -5.073  10.231  1.00 25.00           C
ATOM     42  CA  LEU    42      33.513  -3.613  13.768  1.00 25.00           C
ATOM     43  CA  THR    43      36.318  -5.974  14.874  1.00 25.00           C
ATOM     44  CA  GLY    44      38.422  -8.613  13.081  1.00 25.00           C
ATOM     45  CA  LYS    45      40.433  -7.471   9.989  1.00 25.00           C
ATOM     46  CA  ALA    46      37.569  -9.217   8.179  1.00 25.00           C
ATOM     47  CA  ALA    47      38.627  -7.844   4.790  1.00 25.00           C
ATOM     48  CA  LEU    48      35.410  -5.876   4.491  1.00 25.00           C
ATOM     49  CA  THR    49      36.609  -2.879   6.532  1.00 25.00           C
ATOM     50  CA  PRO    50      35.777  -0.035   4.172  1.00 25.00           C
ATOM     51  CA  GLU    51      32.874  -1.963   2.584  1.00 25.00           C
ATOM     52  CA  MET    52      31.620  -2.984   6.055  1.00 25.00           C
ATOM     53  CA  ALA    53      31.807   0.660   7.222  1.00 25.00           C
ATOM     54  CA  ILE    54      29.844   1.776   4.129  1.00 25.00           C
ATOM     55  CA  LYS    55      27.188  -0.895   4.821  1.00 25.00           C
ATOM     56  CA  LEU    56      26.921   0.277   8.456  1.00 25.00           C
ATOM     57  CA  SER    57      26.519   3.901   7.287  1.00 25.00           C
ATOM     58  CA  VAL    58      23.773   2.832   4.840  1.00 25.00           C
ATOM     59  CA  VAL    59      21.978   0.940   7.644  1.00 25.00           C
ATOM     60  CA  ILE    60      22.196   4.026   9.900  1.00 25.00           C
ATOM     61  CA  GLY    61      19.916   6.956   8.993  1.00 25.00           C
ATOM     62  CA  SER    62      19.300   5.805   5.369  1.00 25.00           C
ATOM     63  CA  SER    63      18.826   2.841   2.977  1.00 25.00           C
ATOM     64  CA  PRO    64      21.273   4.138   0.354  1.00 25.00           C
ATOM     65  CA  GLN    65      24.039   3.421  -2.196  1.00 25.00           C
ATOM     66  CA  MET    66      24.780   7.168  -2.481  1.00 25.00           C
ATOM     67  CA  TRP    67      24.963   7.447   1.335  1.00 25.00           C
ATOM     68  CA  LEU    68      27.366   4.467   1.461  1.00 25.00           C
ATOM     69  CA  ASN    69      29.556   6.087  -1.231  1.00 25.00           C
ATOM     70  CA  LEU    70      29.600   9.368   0.744  1.00 25.00           C
ATOM     71  CA  GLN    71      30.603   7.472   3.918  1.00 25.00           C
TER
END
