
#######################################################
#                                                     #
#                        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   76 (   76),  selected   76 , name T0309TS393_4
# Molecule2: number of CA atoms   62 (  501),  selected   62 , name T0309.pdb
# PARAMETERS: T0309TS393_4.T0309.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      A       2           -
LGA    -       -      S       3           -
LGA    M       1      K       4          4.339
LGA    A       2      K       5          1.575
LGA    S       3      V       6          1.290
LGA    K       4      H       7          2.597
LGA    K       5      Q       8          1.527
LGA    V       6      I       9          1.581
LGA    H       7      N      10          0.977
LGA    Q       8      V      11          1.692
LGA    I       9      K      12          1.652
LGA    N      10      G      13          2.378
LGA    V      11      F      14          2.472
LGA    K      12      F      15          3.835
LGA    G      13      -       -           -
LGA    F      14      -       -           -
LGA    F      15      -       -           -
LGA    D      16      D      16           #
LGA    M      17      M      17          4.678
LGA    D      18      D      18          3.807
LGA    -       -      V      19           -
LGA    -       -      M      20           -
LGA    V      19      E      21          2.656
LGA    M      20      V      22          0.315
LGA    E      21      T      23          1.241
LGA    V      22      E      24          1.531
LGA    T      23      Q      25          4.306
LGA    E      24      T      26          2.796
LGA    Q      25      K      27          2.020
LGA    T      26      E      28          4.737
LGA    K      27      A      29           -
LGA    E      28      E      30           -
LGA    A      29      -       -           -
LGA    E      30      -       -           -
LGA    Y      31      -       -           -
LGA    T      32      -       -           -
LGA    Y      33      -       -           -
LGA    D      34      -       -           -
LGA    F      35      -       -           -
LGA    K      36      -       -           -
LGA    E      37      Y      31          4.097
LGA    I      38      T      32           #
LGA    L      39      Y      33          1.813
LGA    S      40      -       -           -
LGA    E      41      D      34          3.957
LGA    F      42      F      35          4.883
LGA    N      43      K      36           #
LGA    G      44      -       -           -
LGA    K      45      -       -           -
LGA    N      46      E      37          3.253
LGA    V      47      I      38          3.038
LGA    S      48      L      39           #
LGA    I      49      S      40           -
LGA    -       -      E      41           -
LGA    -       -      F      42           -
LGA    -       -      N      43           -
LGA    -       -      G      44           -
LGA    -       -      K      45           -
LGA    -       -      N      46           -
LGA    -       -      V      47           -
LGA    -       -      S      48           -
LGA    -       -      I      49           -
LGA    -       -      T      50           -
LGA    T      50      V      51           #
LGA    V      51      K      52          4.649
LGA    K      52      E      53          4.453
LGA    E      53      E      54          2.566
LGA    E      54      N      55          2.718
LGA    N      55      E      56           #
LGA    E      56      L      57           -
LGA    L      57      P      58           -
LGA    P      58      V      59           -
LGA    V      59      K      60           -
LGA    K      60      G      61           -
LGA    G      61      V      62           -
LGA    V      62      E      63           -
LGA    E      63      -       -           -
LGA    M      64      -       -           -
LGA    A      65      -       -           -
LGA    G      66      -       -           -
LGA    D      67      -       -           -
LGA    P      68      -       -           -
LGA    L      69      -       -           -
LGA    E      70      -       -           -
LGA    H      71      -       -           -
LGA    H      72      -       -           -
LGA    H      73      -       -           -
LGA    H      74      -       -           -
LGA    H      75      -       -           -
LGA    H      76      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   76   62    5.0     32    3.08    12.50     31.689     1.008

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.316215 * X  +   0.878292 * Y  +   0.358623 * Z  +  -0.849248
  Y_new =  -0.912933 * X  +  -0.178914 * Y  +  -0.366802 * Z  + -13.876863
  Z_new =  -0.257996 * X  +  -0.443387 * Y  +   0.858397 * Z  +  -5.356487 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.476783    2.664809  [ DEG:   -27.3177    152.6823 ]
  Theta =   0.260948    2.880645  [ DEG:    14.9512    165.0488 ]
  Phi   =  -1.904236    1.237357  [ DEG:  -109.1047     70.8953 ]
 
# 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: T0309TS393_4                                  
REMARK     2: T0309.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0309TS393_4.T0309.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   76   62   5.0   32   3.08   12.50  31.689
REMARK  ---------------------------------------------------------- 
MOLECULE T0309TS393_4
PFRMAT TS
TARGET T0309
MODEL 4
PARENT N/A
ATOM      1  CA  MET     1     -15.971 -27.285   3.592  1.00 25.00           C
ATOM      2  CA  ALA     2     -16.349 -23.491   3.144  1.00 25.00           C
ATOM      3  CA  SER     3     -12.903 -22.619   1.711  1.00 25.00           C
ATOM      4  CA  LYS     4     -10.243 -20.835  -0.276  1.00 25.00           C
ATOM      5  CA  LYS     5      -7.654 -18.608  -1.973  1.00 25.00           C
ATOM      6  CA  VAL     6      -5.901 -15.887  -3.958  1.00 25.00           C
ATOM      7  CA  HIS     7      -3.091 -18.231  -5.076  1.00 25.00           C
ATOM      8  CA  GLN     8      -1.031 -15.352  -6.286  1.00 25.00           C
ATOM      9  CA  ILE     9       1.416 -15.090  -9.120  1.00 25.00           C
ATOM     10  CA  ASN    10       4.603 -13.176  -9.845  1.00 25.00           C
ATOM     11  CA  VAL    11       6.068  -9.668  -9.824  1.00 25.00           C
ATOM     12  CA  LYS    12       8.255  -6.744  -8.721  1.00 25.00           C
ATOM     13  CA  GLY    13      10.595  -4.017  -7.525  1.00 25.00           C
ATOM     14  CA  PHE    14      11.121  -3.419 -11.244  1.00 25.00           C
ATOM     15  CA  PHE    15       8.091  -3.367 -13.483  1.00 25.00           C
ATOM     16  CA  ASP    16       7.183  -0.317 -11.431  1.00 25.00           C
ATOM     17  CA  MET    17       4.873  -2.671  -9.593  1.00 25.00           C
ATOM     18  CA  ASP    18       4.555  -4.188  -6.081  1.00 25.00           C
ATOM     19  CA  VAL    19       2.312  -6.800  -7.827  1.00 25.00           C
ATOM     20  CA  MET    20       0.954  -9.709  -9.938  1.00 25.00           C
ATOM     21  CA  GLU    21       2.514 -10.050 -13.423  1.00 25.00           C
ATOM     22  CA  VAL    22       1.055 -13.493 -13.995  1.00 25.00           C
ATOM     23  CA  THR    23       1.787 -17.007 -15.272  1.00 25.00           C
ATOM     24  CA  GLU    24       1.365 -19.591 -18.065  1.00 25.00           C
ATOM     25  CA  GLN    25       0.956 -18.473 -21.672  1.00 25.00           C
ATOM     26  CA  THR    26      -2.493 -20.143 -21.407  1.00 25.00           C
ATOM     27  CA  LYS    27      -5.533 -22.068 -20.131  1.00 25.00           C
ATOM     28  CA  GLU    28      -6.484 -22.281 -16.457  1.00 25.00           C
ATOM     29  CA  ALA    29      -3.025 -23.693 -16.060  1.00 25.00           C
ATOM     30  CA  GLU    30      -1.897 -23.807 -12.468  1.00 25.00           C
ATOM     31  CA  TYR    31      -0.024 -20.561 -11.682  1.00 25.00           C
ATOM     32  CA  THR    32      -2.692 -18.542 -13.547  1.00 25.00           C
ATOM     33  CA  TYR    33      -5.452 -20.327 -11.581  1.00 25.00           C
ATOM     34  CA  ASP    34      -6.238 -16.817 -10.338  1.00 25.00           C
ATOM     35  CA  PHE    35      -7.691 -14.123 -12.598  1.00 25.00           C
ATOM     36  CA  LYS    36      -4.152 -12.953 -13.481  1.00 25.00           C
ATOM     37  CA  GLU    37      -5.589  -9.910 -15.310  1.00 25.00           C
ATOM     38  CA  ILE    38      -7.766  -9.080 -12.272  1.00 25.00           C
ATOM     39  CA  LEU    39      -4.712  -9.353  -9.977  1.00 25.00           C
ATOM     40  CA  SER    40      -2.734  -7.032 -12.293  1.00 25.00           C
ATOM     41  CA  GLU    41      -5.613  -4.508 -12.263  1.00 25.00           C
ATOM     42  CA  PHE    42      -5.730  -4.649  -8.437  1.00 25.00           C
ATOM     43  CA  ASN    43      -8.826  -2.561  -8.837  1.00 25.00           C
ATOM     44  CA  GLY    44     -11.183  -5.402  -7.756  1.00 25.00           C
ATOM     45  CA  LYS    45      -8.928  -5.684  -4.672  1.00 25.00           C
ATOM     46  CA  ASN    46      -5.355  -6.559  -3.546  1.00 25.00           C
ATOM     47  CA  VAL    47      -4.598  -9.970  -4.979  1.00 25.00           C
ATOM     48  CA  SER    48      -0.780 -10.459  -5.269  1.00 25.00           C
ATOM     49  CA  ILE    49       2.996 -11.116  -5.396  1.00 25.00           C
ATOM     50  CA  THR    50       6.695 -11.713  -5.301  1.00 25.00           C
ATOM     51  CA  VAL    51       7.354 -15.437  -6.004  1.00 25.00           C
ATOM     52  CA  LYS    52       7.117 -18.349  -8.439  1.00 25.00           C
ATOM     53  CA  GLU    53       9.097 -20.973  -6.526  1.00 25.00           C
ATOM     54  CA  GLU    54      12.815 -20.885  -6.980  1.00 25.00           C
ATOM     55  CA  ASN    55      13.585 -20.748  -3.276  1.00 25.00           C
ATOM     56  CA  GLU    56      11.688 -24.067  -3.028  1.00 25.00           C
ATOM     57  CA  LEU    57       8.467 -24.024  -0.970  1.00 25.00           C
ATOM     58  CA  PRO    58       7.128 -27.248  -2.618  1.00 25.00           C
ATOM     59  CA  VAL    59       5.597 -24.825  -5.132  1.00 25.00           C
ATOM     60  CA  LYS    60       2.791 -24.088  -2.667  1.00 25.00           C
ATOM     61  CA  GLY    61       1.179 -20.819  -3.676  1.00 25.00           C
ATOM     62  CA  VAL    62       4.653 -19.284  -4.077  1.00 25.00           C
ATOM     63  CA  GLU    63       3.946 -15.985  -2.352  1.00 25.00           C
ATOM     64  CA  MET    64       3.869 -12.484  -0.825  1.00 25.00           C
ATOM     65  CA  ALA    65       0.052 -12.033  -0.574  1.00 25.00           C
ATOM     66  CA  GLY    66       0.454  -8.560   1.010  1.00 25.00           C
ATOM     67  CA  ASP    67      -0.253 -10.184   4.387  1.00 25.00           C
ATOM     68  CA  PRO    68       1.518 -11.263   7.622  1.00 25.00           C
ATOM     69  CA  LEU    69      -1.830 -12.210   9.160  1.00 25.00           C
ATOM     70  CA  GLU    70      -2.404 -12.905  12.864  1.00 25.00           C
ATOM     71  CA  HIS    71      -4.024 -13.274  16.253  1.00 25.00           C
ATOM     72  CA  HIS    72      -6.388 -10.366  15.902  1.00 25.00           C
ATOM     73  CA  HIS    73     -10.156 -10.637  16.210  1.00 25.00           C
ATOM     74  CA  HIS    74     -10.006  -6.889  16.602  1.00 25.00           C
ATOM     75  CA  HIS    75     -13.784  -6.629  17.256  1.00 25.00           C
ATOM     76  CA  HIS    76     -14.196  -8.195  13.825  1.00 25.00           C
TER
END
