
#######################################################
#                                                     #
#                        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_5-D1
# Molecule2: number of CA atoms   91 (  726),  selected   91 , name T0299_D1.pdb
# PARAMETERS: T0299TS393_5-D1.T0299_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      -       -           -
LGA    T       2      -       -           -
LGA    R       3      -       -           -
LGA    Y       4      -       -           -
LGA    A       5      -       -           -
LGA    L       6      -       -           -
LGA    L       7      M       1           #
LGA    V       8      T       2           -
LGA    R       9      R       3           #
LGA    -       -      Y       4           -
LGA    -       -      A       5           -
LGA    G      10      L       6           #
LGA    I      11      L       7           -
LGA    N      12      -       -           -
LGA    V      13      V       8           #
LGA    G      14      R       9           -
LGA    -       -      G      10           -
LGA    -       -      I      11           -
LGA    -       -      N      12           -
LGA    -       -      V      13           -
LGA    -       -      G      14           -
LGA    -       -      G      15           -
LGA    -       -      K      16           -
LGA    G      15      N      17           #
LGA    K      16      K      18          2.949
LGA    N      17      V      19          3.024
LGA    K      18      V      20          3.682
LGA    V      19      M      21          4.526
LGA    -       -      A      22           -
LGA    -       -      E      23           -
LGA    V      20      L      24          2.737
LGA    M      21      R      25          2.650
LGA    A      22      Q      26          4.721
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    E      23      K      35           #
LGA    L      24      V      36          3.744
LGA    R      25      E      37          4.622
LGA    Q      26      S      38          2.747
LGA    E      27      Y      39           -
LGA    -       -      I      40           -
LGA    -       -      N      41           -
LGA    -       -      S      42           -
LGA    L      28      G      43           #
LGA    T      29      N      44          4.115
LGA    N      30      I      45           #
LGA    L      31      F      46          3.793
LGA    G      32      F      47          3.106
LGA    L      33      -       -           -
LGA    E      34      -       -           -
LGA    K      35      T      48          2.340
LGA    V      36      S      49          4.138
LGA    E      37      -       -           -
LGA    S      38      I      50          2.766
LGA    Y      39      D      51          1.767
LGA    I      40      S      52          1.615
LGA    N      41      K      53           #
LGA    S      42      -       -           -
LGA    G      43      -       -           -
LGA    N      44      A      54          4.850
LGA    I      45      Q      55          0.700
LGA    F      46      L      56          0.381
LGA    F      47      V      57          3.551
LGA    -       -      E      58           -
LGA    -       -      K      59           -
LGA    T      48      L      60          1.025
LGA    S      49      E      61          2.876
LGA    I      50      T      62          4.368
LGA    -       -      F      63           -
LGA    -       -      F      64           -
LGA    -       -      A      65           -
LGA    D      51      V      66          1.767
LGA    S      52      H      67           #
LGA    K      53      Y      68           -
LGA    A      54      -       -           -
LGA    Q      55      P      69          2.659
LGA    L      56      -       -           -
LGA    V      57      -       -           -
LGA    E      58      F      70          5.172
LGA    K      59      I      71          1.829
LGA    L      60      Q      72           #
LGA    E      61      S      73          2.073
LGA    T      62      F      74          3.290
LGA    F      63      -       -           -
LGA    F      64      S      75          1.963
LGA    A      65      -       -           -
LGA    V      66      -       -           -
LGA    H      67      -       -           -
LGA    Y      68      -       -           -
LGA    P      69      -       -           -
LGA    F      70      L      76          2.627
LGA    I      71      L      77          2.802
LGA    Q      72      S      78           -
LGA    S      73      A     168           -
LGA    F      74      K     169           -
LGA    S      75      T     170           -
LGA    L      76      F     171           -
LGA    L      77      D     172           -
LGA    S      78      K     173           -
LGA    A     168      I     174           -
LGA    K     169      G     175           -
LGA    T     170      Q     176           -
LGA    F     171      M     177           -
LGA    D     172      L     178           -
LGA    K     173      K     179           -
LGA    I     174      K     180           -
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     34    3.20     2.94     21.933     1.031

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.492684 * X  +   0.608006 * Y  +  -0.622569 * Z  + -13.195743
  Y_new =  -0.866373 * X  +   0.275622 * Y  +  -0.416449 * Z  +  42.631561
  Z_new =  -0.081610 * X  +   0.744555 * Y  +   0.662554 * Z  +   9.059348 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.843608   -2.297985  [ DEG:    48.3352   -131.6648 ]
  Theta =   0.081700    3.059892  [ DEG:     4.6811    175.3189 ]
  Phi   =  -1.053729    2.087863  [ DEG:   -60.3742    119.6258 ]
 
# 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_5-D1                               
REMARK     2: T0299_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0299TS393_5-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   34   3.20    2.94  21.933
REMARK  ---------------------------------------------------------- 
MOLECULE T0299TS393_5-D1
PFRMAT TS
TARGET T0299
MODEL 5
PARENT N/A
ATOM      1  CA  MET     1     -31.245  59.485  11.051  1.00 25.00           C
ATOM      2  CA  THR     2     -27.731  58.095  10.710  1.00 25.00           C
ATOM      3  CA  ARG     3     -28.218  54.546   9.582  1.00 25.00           C
ATOM      4  CA  TYR     4     -26.991  51.457   7.809  1.00 25.00           C
ATOM      5  CA  ALA     5     -25.283  48.886   5.583  1.00 25.00           C
ATOM      6  CA  LEU     6     -22.907  46.134   4.460  1.00 25.00           C
ATOM      7  CA  LEU     7     -19.391  45.323   3.417  1.00 25.00           C
ATOM      8  CA  VAL     8     -17.180  42.950   1.351  1.00 25.00           C
ATOM      9  CA  ARG     9     -14.014  45.067   1.764  1.00 25.00           C
ATOM     10  CA  GLY    10     -11.348  42.780   0.194  1.00 25.00           C
ATOM     11  CA  ILE    11     -13.362  39.686   0.986  1.00 25.00           C
ATOM     12  CA  ASN    12     -10.388  38.262   2.993  1.00 25.00           C
ATOM     13  CA  VAL    13      -6.912  39.473   1.913  1.00 25.00           C
ATOM     14  CA  GLY    14      -6.158  35.804   1.800  1.00 25.00           C
ATOM     15  CA  GLY    15      -3.780  32.898   0.966  1.00 25.00           C
ATOM     16  CA  LYS    16      -1.974  31.050  -1.826  1.00 25.00           C
ATOM     17  CA  ASN    17      -4.819  31.964  -4.182  1.00 25.00           C
ATOM     18  CA  LYS    18      -4.091  35.633  -4.363  1.00 25.00           C
ATOM     19  CA  VAL    19      -7.587  36.229  -3.037  1.00 25.00           C
ATOM     20  CA  VAL    20      -9.814  33.473  -1.581  1.00 25.00           C
ATOM     21  CA  MET    21     -11.864  34.953  -4.447  1.00 25.00           C
ATOM     22  CA  ALA    22     -11.360  35.881  -8.128  1.00 25.00           C
ATOM     23  CA  GLU    23     -13.942  38.690  -7.799  1.00 25.00           C
ATOM     24  CA  LEU    24     -12.163  39.992  -4.668  1.00 25.00           C
ATOM     25  CA  ARG    25      -8.812  39.938  -6.520  1.00 25.00           C
ATOM     26  CA  GLN    26     -10.368  41.861  -9.444  1.00 25.00           C
ATOM     27  CA  GLU    27     -11.792  44.454  -7.012  1.00 25.00           C
ATOM     28  CA  LEU    28      -8.354  44.837  -5.369  1.00 25.00           C
ATOM     29  CA  THR    29      -6.737  45.318  -8.807  1.00 25.00           C
ATOM     30  CA  ASN    30      -9.350  47.974  -9.692  1.00 25.00           C
ATOM     31  CA  LEU    31      -8.673  49.778  -6.383  1.00 25.00           C
ATOM     32  CA  GLY    32     -11.527  48.537  -4.097  1.00 25.00           C
ATOM     33  CA  LEU    33     -12.695  52.160  -4.301  1.00 25.00           C
ATOM     34  CA  GLU    34     -16.191  53.674  -3.910  1.00 25.00           C
ATOM     35  CA  LYS    35     -17.466  50.399  -2.390  1.00 25.00           C
ATOM     36  CA  VAL    36     -14.517  50.356   0.054  1.00 25.00           C
ATOM     37  CA  GLU    37     -15.255  53.980   1.047  1.00 25.00           C
ATOM     38  CA  SER    38     -18.938  53.098   1.621  1.00 25.00           C
ATOM     39  CA  TYR    39     -17.910  50.115   3.791  1.00 25.00           C
ATOM     40  CA  ILE    40     -15.575  52.367   5.825  1.00 25.00           C
ATOM     41  CA  ASN    41     -18.403  54.903   6.311  1.00 25.00           C
ATOM     42  CA  SER    42     -21.393  52.595   6.782  1.00 25.00           C
ATOM     43  CA  GLY    43     -19.487  51.269   9.770  1.00 25.00           C
ATOM     44  CA  ASN    44     -16.557  50.497  12.093  1.00 25.00           C
ATOM     45  CA  ILE    45     -15.043  48.562   9.208  1.00 25.00           C
ATOM     46  CA  PHE    46     -12.744  46.922   6.634  1.00 25.00           C
ATOM     47  CA  PHE    47     -11.214  44.222   8.914  1.00 25.00           C
ATOM     48  CA  THR    48      -8.559  42.466   6.771  1.00 25.00           C
ATOM     49  CA  SER    49      -7.093  39.259   8.224  1.00 25.00           C
ATOM     50  CA  ILE    50      -7.755  35.515   8.782  1.00 25.00           C
ATOM     51  CA  ASP    51      -5.287  32.638   9.091  1.00 25.00           C
ATOM     52  CA  SER    52      -1.985  32.647  10.996  1.00 25.00           C
ATOM     53  CA  LYS    53      -1.787  35.782  13.088  1.00 25.00           C
ATOM     54  CA  ALA    54       1.439  37.483  11.921  1.00 25.00           C
ATOM     55  CA  GLN    55       0.954  36.048   8.405  1.00 25.00           C
ATOM     56  CA  LEU    56      -2.657  37.324   8.354  1.00 25.00           C
ATOM     57  CA  VAL    57      -1.470  40.797   9.450  1.00 25.00           C
ATOM     58  CA  GLU    58       1.176  40.793   6.682  1.00 25.00           C
ATOM     59  CA  LYS    59      -1.482  39.801   4.109  1.00 25.00           C
ATOM     60  CA  LEU    60      -3.757  42.629   5.333  1.00 25.00           C
ATOM     61  CA  GLU    61      -0.860  45.117   5.042  1.00 25.00           C
ATOM     62  CA  THR    62      -0.144  43.905   1.481  1.00 25.00           C
ATOM     63  CA  PHE    63      -3.841  44.317   0.571  1.00 25.00           C
ATOM     64  CA  PHE    64      -3.826  47.866   2.010  1.00 25.00           C
ATOM     65  CA  ALA    65      -0.686  48.701  -0.018  1.00 25.00           C
ATOM     66  CA  VAL    66      -2.343  47.340  -3.191  1.00 25.00           C
ATOM     67  CA  HIS    67      -5.460  49.458  -2.501  1.00 25.00           C
ATOM     68  CA  TYR    68      -5.649  53.025  -3.680  1.00 25.00           C
ATOM     69  CA  PRO    69      -3.072  54.333  -1.228  1.00 25.00           C
ATOM     70  CA  PHE    70      -5.257  52.662   1.351  1.00 25.00           C
ATOM     71  CA  ILE    71      -8.537  51.058   0.148  1.00 25.00           C
ATOM     72  CA  GLN    72      -8.908  48.944   3.329  1.00 25.00           C
ATOM     73  CA  SER    73      -8.639  50.500   6.790  1.00 25.00           C
ATOM     74  CA  PHE    74      -7.251  47.189   8.126  1.00 25.00           C
ATOM     75  CA  SER    75      -5.700  45.399  11.112  1.00 25.00           C
ATOM     76  CA  LEU    76      -5.315  42.017  12.744  1.00 25.00           C
ATOM     77  CA  LEU    77      -5.539  40.548  16.300  1.00 25.00           C
ATOM     78  CA  SER    78      -6.845  43.917  17.468  1.00 25.00           C
ATOM    168  CA  ALA   168     -17.790  31.804   8.136  1.00 25.00           C
ATOM    169  CA  LYS   169     -19.477  32.123  11.561  1.00 25.00           C
ATOM    170  CA  THR   170     -20.385  35.765  10.802  1.00 25.00           C
ATOM    171  CA  PHE   171     -21.856  34.721   7.423  1.00 25.00           C
ATOM    172  CA  ASP   172     -23.909  31.980   9.137  1.00 25.00           C
ATOM    173  CA  LYS   173     -25.198  34.515  11.702  1.00 25.00           C
ATOM    174  CA  ILE   174     -26.169  36.914   8.880  1.00 25.00           C
ATOM    175  CA  GLY   175     -28.016  34.085   7.076  1.00 25.00           C
ATOM    176  CA  GLN   176     -29.876  33.207  10.307  1.00 25.00           C
ATOM    177  CA  MET   177     -30.857  36.880  10.771  1.00 25.00           C
ATOM    178  CA  LEU   178     -32.128  37.021   7.161  1.00 25.00           C
ATOM    179  CA  LYS   179     -35.804  36.363   7.697  1.00 25.00           C
ATOM    180  CA  LYS   180     -36.186  40.147   7.533  1.00 25.00           C
TER
END
