
#######################################################
#                                                     #
#                        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_4-D1
# Molecule2: number of CA atoms   91 (  726),  selected   91 , name T0299_D1.pdb
# PARAMETERS: T0299TS393_4-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      -       -           -
LGA    Y       4      -       -           -
LGA    A       5      -       -           -
LGA    L       6      R       3           #
LGA    L       7      Y       4          3.832
LGA    V       8      A       5          3.355
LGA    R       9      L       6           #
LGA    G      10      -       -           -
LGA    I      11      L       7           #
LGA    N      12      V       8           -
LGA    -       -      R       9           -
LGA    -       -      G      10           -
LGA    -       -      I      11           -
LGA    -       -      N      12           -
LGA    -       -      V      13           -
LGA    -       -      G      14           -
LGA    -       -      G      15           -
LGA    -       -      K      16           -
LGA    -       -      N      17           -
LGA    -       -      K      18           -
LGA    -       -      V      19           -
LGA    -       -      V      20           -
LGA    -       -      M      21           -
LGA    -       -      A      22           -
LGA    -       -      E      23           -
LGA    -       -      L      24           -
LGA    V      13      R      25           #
LGA    G      14      Q      26           -
LGA    G      15      E      27           -
LGA    K      16      -       -           -
LGA    N      17      -       -           -
LGA    K      18      -       -           -
LGA    V      19      -       -           -
LGA    V      20      -       -           -
LGA    M      21      L      28          5.197
LGA    -       -      T      29           -
LGA    A      22      N      30          3.691
LGA    E      23      L      31          3.482
LGA    L      24      G      32          4.514
LGA    R      25      L      33           #
LGA    Q      26      E      34           #
LGA    E      27      K      35          5.253
LGA    L      28      V      36          3.888
LGA    T      29      -       -           -
LGA    N      30      -       -           -
LGA    L      31      E      37           #
LGA    G      32      -       -           -
LGA    L      33      -       -           -
LGA    E      34      -       -           -
LGA    K      35      -       -           -
LGA    V      36      S      38          4.495
LGA    E      37      Y      39           #
LGA    S      38      I      40          5.418
LGA    Y      39      N      41          2.270
LGA    I      40      S      42          3.020
LGA    N      41      -       -           -
LGA    S      42      -       -           -
LGA    G      43      -       -           -
LGA    N      44      G      43          4.110
LGA    I      45      N      44          2.381
LGA    F      46      I      45           #
LGA    F      47      F      46           #
LGA    T      48      F      47           #
LGA    S      49      T      48           -
LGA    I      50      S      49           #
LGA    -       -      I      50           -
LGA    -       -      D      51           -
LGA    -       -      S      52           -
LGA    D      51      K      53          1.834
LGA    S      52      A      54          2.445
LGA    -       -      Q      55           -
LGA    -       -      L      56           -
LGA    K      53      V      57          2.487
LGA    A      54      E      58          1.867
LGA    Q      55      K      59          2.042
LGA    L      56      L      60          2.370
LGA    V      57      E      61          1.595
LGA    E      58      T      62          1.469
LGA    K      59      F      63          2.110
LGA    L      60      F      64          3.165
LGA    E      61      A      65          2.961
LGA    T      62      V      66          3.486
LGA    F      63      H      67          4.353
LGA    F      64      Y      68          2.010
LGA    A      65      P      69          3.613
LGA    V      66      -       -           -
LGA    H      67      -       -           -
LGA    Y      68      -       -           -
LGA    P      69      F      70          3.271
LGA    F      70      I      71          3.276
LGA    I      71      Q      72          2.793
LGA    Q      72      S      73          4.835
LGA    S      73      F      74          3.018
LGA    F      74      S      75          4.616
LGA    S      75      -       -           -
LGA    L      76      L      76          3.681
LGA    L      77      L      77          2.673
LGA    S      78      S      78          3.515
LGA    A     168      -       -           -
LGA    K     169      -       -           -
LGA    T     170      -       -           -
LGA    F     171      -       -           -
LGA    D     172      -       -           -
LGA    K     173      A     168          1.732
LGA    I     174      K     169          2.677
LGA    G     175      T     170           #
LGA    Q     176      F     171           -
LGA    M     177      D     172           -
LGA    L     178      K     173           -
LGA    K     179      I     174           -
LGA    K     180      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    3.39    10.00     26.506     1.147

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.175306 * X  +  -0.219394 * Y  +   0.959757 * Z  +  -3.469641
  Y_new =   0.857191 * X  +   0.445478 * Y  +   0.258405 * Z  +  49.473789
  Z_new =  -0.484244 * X  +   0.867995 * Y  +   0.109968 * Z  +  -0.835962 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.444776   -1.696817  [ DEG:    82.7796    -97.2204 ]
  Theta =   0.505498    2.636094  [ DEG:    28.9629    151.0371 ]
  Phi   =   1.772526   -1.369066  [ DEG:   101.5583    -78.4417 ]
 
# 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_4-D1                               
REMARK     2: T0299_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0299TS393_4-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   3.39   10.00  26.506
REMARK  ---------------------------------------------------------- 
MOLECULE T0299TS393_4-D1
PFRMAT TS
TARGET T0299
MODEL 4
PARENT N/A
ATOM      1  CA  MET     1     -19.760  66.109  -8.963  1.00 25.00           C
ATOM      2  CA  THR     2     -17.119  63.395  -8.181  1.00 25.00           C
ATOM      3  CA  ARG     3     -13.935  61.428  -8.996  1.00 25.00           C
ATOM      4  CA  TYR     4     -11.494  60.231 -11.719  1.00 25.00           C
ATOM      5  CA  ALA     5     -10.702  57.286  -9.492  1.00 25.00           C
ATOM      6  CA  LEU     6     -10.522  53.833  -7.779  1.00 25.00           C
ATOM      7  CA  LEU     7      -9.205  50.691  -6.015  1.00 25.00           C
ATOM      8  CA  VAL     8      -8.650  46.993  -5.775  1.00 25.00           C
ATOM      9  CA  ARG     9      -7.364  43.506  -6.771  1.00 25.00           C
ATOM     10  CA  GLY    10      -6.972  42.792  -3.057  1.00 25.00           C
ATOM     11  CA  ILE    11      -8.209  42.344   0.513  1.00 25.00           C
ATOM     12  CA  ASN    12     -11.294  44.243   1.471  1.00 25.00           C
ATOM     13  CA  VAL    13     -11.805  44.498  -2.272  1.00 25.00           C
ATOM     14  CA  GLY    14     -15.279  46.100  -2.066  1.00 25.00           C
ATOM     15  CA  GLY    15     -18.645  46.994  -3.640  1.00 25.00           C
ATOM     16  CA  LYS    16     -21.576  44.732  -2.540  1.00 25.00           C
ATOM     17  CA  ASN    17     -21.868  47.076   0.452  1.00 25.00           C
ATOM     18  CA  LYS    18     -20.385  44.126   2.345  1.00 25.00           C
ATOM     19  CA  VAL    19     -17.103  45.704   3.370  1.00 25.00           C
ATOM     20  CA  VAL    20     -17.151  43.167   6.224  1.00 25.00           C
ATOM     21  CA  MET    21     -15.208  40.968   3.826  1.00 25.00           C
ATOM     22  CA  ALA    22     -16.997  37.723   2.858  1.00 25.00           C
ATOM     23  CA  GLU    23     -19.093  39.622   0.275  1.00 25.00           C
ATOM     24  CA  LEU    24     -15.921  41.207  -1.171  1.00 25.00           C
ATOM     25  CA  ARG    25     -14.272  37.758  -1.398  1.00 25.00           C
ATOM     26  CA  GLN    26     -17.362  36.371  -3.185  1.00 25.00           C
ATOM     27  CA  GLU    27     -17.284  39.301  -5.650  1.00 25.00           C
ATOM     28  CA  LEU    28     -13.566  38.671  -6.318  1.00 25.00           C
ATOM     29  CA  THR    29     -14.280  34.959  -6.934  1.00 25.00           C
ATOM     30  CA  ASN    30     -17.095  35.879  -9.363  1.00 25.00           C
ATOM     31  CA  LEU    31     -14.747  38.272 -11.215  1.00 25.00           C
ATOM     32  CA  GLY    32     -11.216  37.237 -10.187  1.00 25.00           C
ATOM     33  CA  LEU    33      -9.244  35.496  -7.375  1.00 25.00           C
ATOM     34  CA  GLU    34      -6.312  33.897  -9.253  1.00 25.00           C
ATOM     35  CA  LYS    35      -5.372  37.302 -10.732  1.00 25.00           C
ATOM     36  CA  VAL    36      -5.491  38.878  -7.244  1.00 25.00           C
ATOM     37  CA  GLU    37      -3.253  36.087  -5.880  1.00 25.00           C
ATOM     38  CA  SER    38      -0.773  36.640  -8.745  1.00 25.00           C
ATOM     39  CA  TYR    39      -0.734  40.401  -8.018  1.00 25.00           C
ATOM     40  CA  ILE    40      -0.090  39.701  -4.308  1.00 25.00           C
ATOM     41  CA  ASN    41       2.786  37.345  -5.227  1.00 25.00           C
ATOM     42  CA  SER    42       5.004  40.142  -3.815  1.00 25.00           C
ATOM     43  CA  GLY    43       3.673  43.109  -5.809  1.00 25.00           C
ATOM     44  CA  ASN    44       0.329  44.993  -5.639  1.00 25.00           C
ATOM     45  CA  ILE    45      -3.136  46.537  -5.358  1.00 25.00           C
ATOM     46  CA  PHE    46      -4.924  48.477  -2.608  1.00 25.00           C
ATOM     47  CA  PHE    47      -7.789  47.362  -0.417  1.00 25.00           C
ATOM     48  CA  THR    48      -9.797  50.529  -0.721  1.00 25.00           C
ATOM     49  CA  SER    49     -10.599  50.108   2.959  1.00 25.00           C
ATOM     50  CA  ILE    50     -12.780  48.508   5.587  1.00 25.00           C
ATOM     51  CA  ASP    51     -14.450  51.613   7.114  1.00 25.00           C
ATOM     52  CA  SER    52     -14.024  49.552  10.324  1.00 25.00           C
ATOM     53  CA  LYS    53     -10.380  48.499  10.032  1.00 25.00           C
ATOM     54  CA  ALA    54      -9.770  45.613  12.475  1.00 25.00           C
ATOM     55  CA  GLN    55     -12.148  43.380  10.468  1.00 25.00           C
ATOM     56  CA  LEU    56     -10.314  44.293   7.231  1.00 25.00           C
ATOM     57  CA  VAL    57      -6.955  43.460   8.872  1.00 25.00           C
ATOM     58  CA  GLU    58      -8.338  40.087  10.047  1.00 25.00           C
ATOM     59  CA  LYS    59      -9.598  39.342   6.509  1.00 25.00           C
ATOM     60  CA  LEU    60      -6.160  40.224   5.072  1.00 25.00           C
ATOM     61  CA  GLU    61      -4.476  37.914   7.619  1.00 25.00           C
ATOM     62  CA  THR    62      -6.880  35.085   6.681  1.00 25.00           C
ATOM     63  CA  PHE    63      -6.112  35.629   2.969  1.00 25.00           C
ATOM     64  CA  PHE    64      -2.355  35.519   3.705  1.00 25.00           C
ATOM     65  CA  ALA    65      -2.811  32.265   5.671  1.00 25.00           C
ATOM     66  CA  VAL    66      -4.792  30.756   2.761  1.00 25.00           C
ATOM     67  CA  HIS    67      -2.030  31.786   0.316  1.00 25.00           C
ATOM     68  CA  TYR    68       0.936  34.214   0.322  1.00 25.00           C
ATOM     69  CA  PRO    69       2.133  33.233   3.805  1.00 25.00           C
ATOM     70  CA  PHE    70       2.523  36.965   4.229  1.00 25.00           C
ATOM     71  CA  ILE    71       0.061  39.621   5.544  1.00 25.00           C
ATOM     72  CA  GLN    72      -1.826  41.818   3.087  1.00 25.00           C
ATOM     73  CA  SER    73      -2.609  44.910   1.007  1.00 25.00           C
ATOM     74  CA  PHE    74      -5.165  45.933   3.705  1.00 25.00           C
ATOM     75  CA  SER    75      -7.059  48.238   6.077  1.00 25.00           C
ATOM     76  CA  LEU    76      -5.981  51.729   5.088  1.00 25.00           C
ATOM     77  CA  LEU    77      -7.478  54.029   2.473  1.00 25.00           C
ATOM     78  CA  SER    78     -10.768  55.720   1.642  1.00 25.00           C
ATOM    168  CA  ALA   168      -3.815  53.984 -10.457  1.00 25.00           C
ATOM    169  CA  LYS   169      -0.953  56.502 -10.830  1.00 25.00           C
ATOM    170  CA  THR   170       1.501  53.973  -9.331  1.00 25.00           C
ATOM    171  CA  PHE   171       0.255  51.287 -11.761  1.00 25.00           C
ATOM    172  CA  ASP   172       0.702  53.703 -14.699  1.00 25.00           C
ATOM    173  CA  LYS   173       4.261  54.504 -13.531  1.00 25.00           C
ATOM    174  CA  ILE   174       5.047  50.763 -13.282  1.00 25.00           C
ATOM    175  CA  GLY   175       3.684  50.217 -16.818  1.00 25.00           C
ATOM    176  CA  GLN   176       5.840  53.100 -18.122  1.00 25.00           C
ATOM    177  CA  MET   177       8.922  51.601 -16.415  1.00 25.00           C
ATOM    178  CA  LEU   178       8.164  48.191 -17.987  1.00 25.00           C
ATOM    179  CA  LYS   179      11.887  47.783 -18.293  1.00 25.00           C
ATOM    180  CA  LYS   180      12.022  44.280 -16.901  1.00 25.00           C
TER
END
