
#######################################################
#                                                     #
#                        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   91 (   91),  selected   91 , name T0299TS393_1-D1
# Molecule2: number of CA atoms   91 (  726),  selected   91 , name T0299_D1.pdb
# PARAMETERS: T0299TS393_1-D1.T0299_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    T       2      T       2           -
LGA    R       3      R       3           -
LGA    -       -      Y       4           -
LGA    -       -      A       5           -
LGA    -       -      L       6           -
LGA    -       -      L       7           -
LGA    -       -      V       8           -
LGA    -       -      R       9           -
LGA    -       -      G      10           -
LGA    -       -      I      11           -
LGA    Y       4      N      12           #
LGA    -       -      V      13           -
LGA    -       -      G      14           -
LGA    -       -      G      15           -
LGA    -       -      K      16           -
LGA    -       -      N      17           -
LGA    -       -      K      18           -
LGA    A       5      V      19           #
LGA    L       6      V      20           #
LGA    L       7      M      21          2.993
LGA    -       -      A      22           -
LGA    -       -      E      23           -
LGA    -       -      L      24           -
LGA    V       8      R      25          0.941
LGA    R       9      Q      26          4.198
LGA    G      10      E      27           -
LGA    I      11      L      28           -
LGA    -       -      T      29           -
LGA    -       -      N      30           -
LGA    N      12      L      31           #
LGA    V      13      G      32          1.119
LGA    G      14      -       -           -
LGA    G      15      -       -           -
LGA    K      16      -       -           -
LGA    N      17      L      33          2.579
LGA    K      18      E      34           #
LGA    -       -      K      35           -
LGA    V      19      V      36           #
LGA    V      20      E      37           -
LGA    M      21      S      38           -
LGA    A      22      Y      39           -
LGA    E      23      -       -           -
LGA    L      24      -       -           -
LGA    R      25      -       -           -
LGA    Q      26      -       -           -
LGA    E      27      -       -           -
LGA    L      28      -       -           -
LGA    T      29      -       -           -
LGA    N      30      -       -           -
LGA    L      31      -       -           -
LGA    G      32      -       -           -
LGA    L      33      -       -           -
LGA    E      34      -       -           -
LGA    K      35      -       -           -
LGA    V      36      -       -           -
LGA    E      37      -       -           -
LGA    S      38      -       -           -
LGA    Y      39      -       -           -
LGA    I      40      I      40           #
LGA    N      41      -       -           -
LGA    S      42      N      41           #
LGA    G      43      S      42          1.889
LGA    N      44      G      43          2.909
LGA    I      45      N      44          3.761
LGA    F      46      I      45          4.331
LGA    F      47      -       -           -
LGA    T      48      F      46           #
LGA    S      49      F      47          2.366
LGA    I      50      T      48          3.775
LGA    D      51      S      49          2.870
LGA    S      52      I      50          2.172
LGA    K      53      D      51          3.637
LGA    A      54      S      52          3.029
LGA    -       -      K      53           -
LGA    -       -      A      54           -
LGA    Q      55      Q      55          4.300
LGA    L      56      L      56          2.479
LGA    V      57      V      57          2.180
LGA    E      58      E      58          3.215
LGA    K      59      K      59          2.736
LGA    L      60      L      60          1.046
LGA    E      61      E      61          1.434
LGA    T      62      T      62          2.020
LGA    F      63      F      63          2.378
LGA    F      64      F      64          2.411
LGA    A      65      A      65          1.242
LGA    V      66      V      66          1.666
LGA    -       -      H      67           -
LGA    H      67      Y      68          2.292
LGA    Y      68      P      69          2.526
LGA    P      69      F      70          2.154
LGA    F      70      I      71          0.899
LGA    I      71      Q      72          4.362
LGA    Q      72      S      73          5.536
LGA    S      73      F      74          3.039
LGA    F      74      S      75          2.028
LGA    S      75      L      76          1.834
LGA    L      76      L      77          3.545
LGA    L      77      S      78          2.390
LGA    -       -      A     168           -
LGA    -       -      K     169           -
LGA    -       -      T     170           -
LGA    -       -      F     171           -
LGA    -       -      D     172           -
LGA    -       -      K     173           -
LGA    -       -      I     174           -
LGA    -       -      G     175           -
LGA    -       -      Q     176           -
LGA    -       -      M     177           -
LGA    S      78      L     178          3.928
LGA    -       -      K     179           -
LGA    A     168      K     180          1.698
LGA    K     169      -       -           -
LGA    T     170      -       -           -
LGA    F     171      -       -           -
LGA    D     172      -       -           -
LGA    K     173      -       -           -
LGA    I     174      -       -           -
LGA    G     175      -       -           -
LGA    Q     176      -       -           -
LGA    M     177      -       -           -
LGA    L     178      -       -           -
LGA    K     179      -       -           -
LGA    K     180      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   91   91    5.0     40    2.85    32.50     28.761     1.354

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.686705 * X  +  -0.683650 * Y  +   0.247099 * Z  +  -7.135216
  Y_new =  -0.641097 * X  +  -0.409317 * Y  +   0.649195 * Z  +  45.105587
  Z_new =  -0.342680 * X  +  -0.604220 * Y  +  -0.719366 * Z  +  -4.659216 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.442971    0.698621  [ DEG:  -139.9720     40.0280 ]
  Theta =   0.349769    2.791824  [ DEG:    20.0403    159.9597 ]
  Phi   =  -0.751063    2.390530  [ DEG:   -43.0327    136.9673 ]
 
# 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: T0299TS393_1-D1                               
REMARK     2: T0299_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0299TS393_1-D1.T0299_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   91   91   5.0   40   2.85   32.50  28.761
REMARK  ---------------------------------------------------------- 
MOLECULE T0299TS393_1-D1
PFRMAT TS
TARGET T0299
MODEL 1
PARENT N/A
ATOM      1  CA  MET     1       3.566  26.299 -15.327  1.00 25.00           C
ATOM      2  CA  THR     2       3.345  29.097 -12.775  1.00 25.00           C
ATOM      3  CA  ARG     3       0.702  31.755 -11.855  1.00 25.00           C
ATOM      4  CA  TYR     4      -1.733  34.095 -10.021  1.00 25.00           C
ATOM      5  CA  ALA     5      -3.109  37.341  -8.514  1.00 25.00           C
ATOM      6  CA  LEU     6      -6.844  37.533  -9.079  1.00 25.00           C
ATOM      7  CA  LEU     7      -8.085  37.124  -5.500  1.00 25.00           C
ATOM      8  CA  VAL     8     -11.741  37.222  -4.370  1.00 25.00           C
ATOM      9  CA  ARG     9     -14.714  38.432  -6.402  1.00 25.00           C
ATOM     10  CA  GLY    10     -15.132  41.941  -4.899  1.00 25.00           C
ATOM     11  CA  ILE    11     -18.408  43.659  -3.958  1.00 25.00           C
ATOM     12  CA  ASN    12     -20.690  41.267  -2.081  1.00 25.00           C
ATOM     13  CA  VAL    13     -20.639  40.177   1.514  1.00 25.00           C
ATOM     14  CA  GLY    14     -19.046  40.987   4.830  1.00 25.00           C
ATOM     15  CA  GLY    15     -21.849  43.549   4.574  1.00 25.00           C
ATOM     16  CA  LYS    16     -21.963  45.692   1.431  1.00 25.00           C
ATOM     17  CA  ASN    17     -18.367  44.739   0.916  1.00 25.00           C
ATOM     18  CA  LYS    18     -15.972  41.762   0.477  1.00 25.00           C
ATOM     19  CA  VAL    19     -16.292  38.578  -1.628  1.00 25.00           C
ATOM     20  CA  VAL    20     -18.884  36.676  -3.740  1.00 25.00           C
ATOM     21  CA  MET    21     -19.388  34.588  -6.846  1.00 25.00           C
ATOM     22  CA  ALA    22     -21.121  31.721  -4.989  1.00 25.00           C
ATOM     23  CA  GLU    23     -17.759  29.942  -4.547  1.00 25.00           C
ATOM     24  CA  LEU    24     -16.203  33.166  -3.188  1.00 25.00           C
ATOM     25  CA  ARG    25     -19.115  33.566  -0.733  1.00 25.00           C
ATOM     26  CA  GLN    26     -18.669  29.943   0.424  1.00 25.00           C
ATOM     27  CA  GLU    27     -14.922  30.541   0.936  1.00 25.00           C
ATOM     28  CA  LEU    28     -15.679  33.697   2.969  1.00 25.00           C
ATOM     29  CA  THR    29     -18.172  31.743   5.120  1.00 25.00           C
ATOM     30  CA  ASN    30     -15.559  29.006   5.708  1.00 25.00           C
ATOM     31  CA  LEU    31     -12.982  31.651   6.723  1.00 25.00           C
ATOM     32  CA  GLY    32      -9.504  30.528   5.482  1.00 25.00           C
ATOM     33  CA  LEU    33     -10.628  32.113   2.175  1.00 25.00           C
ATOM     34  CA  GLU    34      -7.863  29.699   1.083  1.00 25.00           C
ATOM     35  CA  LYS    35      -7.839  31.267  -2.411  1.00 25.00           C
ATOM     36  CA  VAL    36      -7.584  34.763  -0.866  1.00 25.00           C
ATOM     37  CA  GLU    37      -4.668  33.606   1.330  1.00 25.00           C
ATOM     38  CA  SER    38      -2.907  32.139  -1.737  1.00 25.00           C
ATOM     39  CA  TYR    39      -3.406  35.431  -3.629  1.00 25.00           C
ATOM     40  CA  ILE    40      -1.964  37.382  -0.665  1.00 25.00           C
ATOM     41  CA  ASN    41       1.063  35.039  -0.563  1.00 25.00           C
ATOM     42  CA  SER    42       1.620  35.572  -4.231  1.00 25.00           C
ATOM     43  CA  GLY    43       1.764  39.115  -5.725  1.00 25.00           C
ATOM     44  CA  ASN    44       1.001  42.342  -3.865  1.00 25.00           C
ATOM     45  CA  ILE    45      -2.609  41.266  -4.402  1.00 25.00           C
ATOM     46  CA  PHE    46      -5.900  40.829  -2.665  1.00 25.00           C
ATOM     47  CA  PHE    47      -7.865  42.653   0.007  1.00 25.00           C
ATOM     48  CA  THR    48     -10.586  45.345   0.169  1.00 25.00           C
ATOM     49  CA  SER    49     -13.646  46.287  -1.918  1.00 25.00           C
ATOM     50  CA  ILE    50     -14.940  49.483  -0.180  1.00 25.00           C
ATOM     51  CA  ASP    51     -18.155  51.438  -0.800  1.00 25.00           C
ATOM     52  CA  SER    52     -18.662  51.673   2.964  1.00 25.00           C
ATOM     53  CA  LYS    53     -15.419  51.243   4.864  1.00 25.00           C
ATOM     54  CA  ALA    54     -15.801  49.586   8.296  1.00 25.00           C
ATOM     55  CA  GLN    55     -16.909  46.323   6.624  1.00 25.00           C
ATOM     56  CA  LEU    56     -13.880  46.464   4.285  1.00 25.00           C
ATOM     57  CA  VAL    57     -11.563  47.029   7.281  1.00 25.00           C
ATOM     58  CA  GLU    58     -13.134  44.042   9.092  1.00 25.00           C
ATOM     59  CA  LYS    59     -12.645  41.866   5.979  1.00 25.00           C
ATOM     60  CA  LEU    60      -8.981  42.959   5.761  1.00 25.00           C
ATOM     61  CA  GLU    61      -8.481  42.107   9.462  1.00 25.00           C
ATOM     62  CA  THR    62     -10.057  38.661   8.906  1.00 25.00           C
ATOM     63  CA  PHE    63      -7.746  38.060   5.911  1.00 25.00           C
ATOM     64  CA  PHE    64      -4.711  39.066   8.019  1.00 25.00           C
ATOM     65  CA  ALA    65      -5.813  36.667  10.794  1.00 25.00           C
ATOM     66  CA  VAL    66      -6.204  33.845   8.234  1.00 25.00           C
ATOM     67  CA  HIS    67      -2.704  34.575   6.860  1.00 25.00           C
ATOM     68  CA  TYR    68      -0.686  36.642   9.358  1.00 25.00           C
ATOM     69  CA  PRO    69       2.080  37.593   6.949  1.00 25.00           C
ATOM     70  CA  PHE    70      -0.726  38.358   4.472  1.00 25.00           C
ATOM     71  CA  ILE    71       1.320  41.467   3.482  1.00 25.00           C
ATOM     72  CA  GLN    72       1.658  44.293   0.906  1.00 25.00           C
ATOM     73  CA  SER    73       0.389  47.685   2.102  1.00 25.00           C
ATOM     74  CA  PHE    74      -3.147  48.124   3.543  1.00 25.00           C
ATOM     75  CA  SER    75      -6.716  48.574   2.307  1.00 25.00           C
ATOM     76  CA  LEU    76      -9.155  50.589   0.182  1.00 25.00           C
ATOM     77  CA  LEU    77     -11.423  52.877  -1.786  1.00 25.00           C
ATOM     78  CA  SER    78     -10.653  54.186  -5.230  1.00 25.00           C
ATOM    168  CA  ALA   168     -15.501  49.968 -12.289  1.00 25.00           C
ATOM    169  CA  LYS   169     -14.613  53.062 -14.364  1.00 25.00           C
ATOM    170  CA  THR   170     -11.055  51.736 -14.863  1.00 25.00           C
ATOM    171  CA  PHE   171     -12.447  48.346 -15.974  1.00 25.00           C
ATOM    172  CA  ASP   172     -14.790  50.094 -18.449  1.00 25.00           C
ATOM    173  CA  LYS   173     -11.853  52.120 -19.838  1.00 25.00           C
ATOM    174  CA  ILE   174      -9.800  48.913 -20.241  1.00 25.00           C
ATOM    175  CA  GLY   175     -12.719  47.244 -22.073  1.00 25.00           C
ATOM    176  CA  GLN   176     -13.028  50.275 -24.394  1.00 25.00           C
ATOM    177  CA  MET   177      -9.270  50.135 -25.116  1.00 25.00           C
ATOM    178  CA  LEU   178      -9.535  46.396 -25.904  1.00 25.00           C
ATOM    179  CA  LYS   179      -9.559  47.609 -29.509  1.00 25.00           C
ATOM    180  CA  LYS   180     -11.733  50.602 -30.340  1.00 25.00           C
TER
END
