
#######################################################
#                                                     #
#                        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 T0299TS168_2-D1
# Molecule2: number of CA atoms   91 (  726),  selected   91 , name T0299_D1.pdb
# PARAMETERS: T0299TS168_2-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    -       -      N      12           -
LGA    Y       4      V      13          5.093
LGA    A       5      G      14          2.650
LGA    -       -      G      15           -
LGA    L       6      K      16          5.148
LGA    L       7      N      17          2.970
LGA    V       8      K      18          4.606
LGA    R       9      V      19          3.137
LGA    -       -      V      20           -
LGA    G      10      M      21          3.184
LGA    -       -      A      22           -
LGA    -       -      E      23           -
LGA    I      11      L      24          4.436
LGA    N      12      -       -           -
LGA    V      13      R      25          5.129
LGA    -       -      Q      26           -
LGA    -       -      E      27           -
LGA    G      14      L      28          0.571
LGA    -       -      T      29           -
LGA    -       -      N      30           -
LGA    G      15      L      31          3.188
LGA    K      16      G      32          0.414
LGA    N      17      L      33          2.859
LGA    K      18      E      34          1.693
LGA    V      19      K      35          3.721
LGA    V      20      V      36          4.270
LGA    M      21      E      37           #
LGA    A      22      S      38           -
LGA    E      23      Y      39           -
LGA    L      24      I      40           -
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      -       -           -
LGA    N      41      -       -           -
LGA    S      42      -       -           -
LGA    G      43      -       -           -
LGA    N      44      -       -           -
LGA    I      45      N      41          3.732
LGA    F      46      S      42          4.052
LGA    F      47      G      43          3.591
LGA    T      48      N      44          3.470
LGA    S      49      I      45          3.564
LGA    I      50      F      46          3.822
LGA    D      51      F      47          2.967
LGA    S      52      T      48           #
LGA    -       -      S      49           -
LGA    -       -      I      50           -
LGA    -       -      D      51           -
LGA    -       -      S      52           -
LGA    K      53      K      53           #
LGA    -       -      A      54           -
LGA    A      54      Q      55           #
LGA    Q      55      L      56          3.069
LGA    L      56      -       -           -
LGA    V      57      V      57          3.521
LGA    E      58      E      58          4.209
LGA    K      59      K      59          4.692
LGA    L      60      L      60          3.053
LGA    E      61      E      61          1.419
LGA    T      62      T      62          2.892
LGA    F      63      F      63          2.745
LGA    F      64      F      64          1.849
LGA    A      65      A      65          2.263
LGA    V      66      V      66          1.457
LGA    H      67      H      67          3.179
LGA    Y      68      Y      68           #
LGA    P      69      -       -           -
LGA    F      70      P      69          1.650
LGA    I      71      F      70          3.660
LGA    Q      72      I      71          2.184
LGA    S      73      Q      72          2.244
LGA    F      74      S      73          2.586
LGA    S      75      F      74          3.483
LGA    L      76      S      75          2.298
LGA    L      77      L      76          1.696
LGA    S      78      L      77          4.594
LGA    A     168      S      78           -
LGA    K     169      A     168           -
LGA    -       -      K     169           -
LGA    T     170      T     170          4.115
LGA    F     171      F     171           -
LGA    D     172      D     172           -
LGA    K     173      K     173           #
LGA    I     174      I     174           -
LGA    G     175      G     175           -
LGA    Q     176      Q     176           -
LGA    M     177      M     177           -
LGA    L     178      L     178           -
LGA    K     179      K     179           -
LGA    K     180      K     180           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   91   91    5.0     45    3.34    31.11     28.232     1.309

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.280575 * X  +  -0.548048 * Y  +   0.787985 * Z  +  -1.140576
  Y_new =   0.455285 * X  +   0.798718 * Y  +   0.393401 * Z  +  43.171230
  Z_new =  -0.844981 * X  +   0.248379 * Y  +   0.473619 * Z  +  -2.438108 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.482999   -2.658594  [ DEG:    27.6738   -152.3262 ]
  Theta =   1.006530    2.135063  [ DEG:    57.6699    122.3301 ]
  Phi   =   1.018504   -2.123088  [ DEG:    58.3560   -121.6440 ]
 
# 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: T0299TS168_2-D1                               
REMARK     2: T0299_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0299TS168_2-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   45   3.34   31.11  28.232
REMARK  ---------------------------------------------------------- 
MOLECULE T0299TS168_2-D1
PFRMAT TS
TARGET T0299
MODEL 2
PARENT N/A
ATOM      1  CA  MET     1      22.090  35.219  -3.174  1.00 25.00           C
ATOM      2  CA  THR     2      18.322  34.950  -2.933  1.00 25.00           C
ATOM      3  CA  ARG     3      14.835  34.980  -4.559  1.00 25.00           C
ATOM      4  CA  TYR     4      11.947  33.643  -6.590  1.00 25.00           C
ATOM      5  CA  ALA     5       8.480  34.062  -4.943  1.00 25.00           C
ATOM      6  CA  LEU     6       6.474  35.476  -1.997  1.00 25.00           C
ATOM      7  CA  LEU     7       2.847  34.553  -2.192  1.00 25.00           C
ATOM      8  CA  VAL     8      -0.424  35.592  -0.457  1.00 25.00           C
ATOM      9  CA  ARG     9      -4.125  34.947  -1.055  1.00 25.00           C
ATOM     10  CA  GLY    10      -6.089  35.966  -4.149  1.00 25.00           C
ATOM     11  CA  ILE    11      -6.423  38.996  -1.971  1.00 25.00           C
ATOM     12  CA  ASN    12      -8.533  40.547  -4.705  1.00 25.00           C
ATOM     13  CA  VAL    13     -11.100  41.367  -1.982  1.00 25.00           C
ATOM     14  CA  GLY    14     -13.906  39.089  -0.739  1.00 25.00           C
ATOM     15  CA  GLY    15     -16.088  40.905   1.877  1.00 25.00           C
ATOM     16  CA  LYS    16     -19.825  40.316   1.412  1.00 25.00           C
ATOM     17  CA  ASN    17     -19.827  43.949   0.276  1.00 25.00           C
ATOM     18  CA  LYS    18     -17.651  43.416  -2.773  1.00 25.00           C
ATOM     19  CA  VAL    19     -14.962  42.511  -5.329  1.00 25.00           C
ATOM     20  CA  VAL    20     -17.338  39.688  -6.193  1.00 25.00           C
ATOM     21  CA  MET    21     -14.508  37.793  -7.925  1.00 25.00           C
ATOM     22  CA  ALA    22     -15.982  34.259  -7.859  1.00 25.00           C
ATOM     23  CA  GLU    23     -12.619  32.854  -6.682  1.00 25.00           C
ATOM     24  CA  LEU    24     -12.451  35.500  -3.919  1.00 25.00           C
ATOM     25  CA  ARG    25     -16.010  34.611  -2.817  1.00 25.00           C
ATOM     26  CA  GLN    26     -15.079  30.897  -2.725  1.00 25.00           C
ATOM     27  CA  GLU    27     -11.981  31.701  -0.620  1.00 25.00           C
ATOM     28  CA  LEU    28     -14.125  33.760   1.794  1.00 25.00           C
ATOM     29  CA  THR    29     -16.616  30.865   2.090  1.00 25.00           C
ATOM     30  CA  ASN    30     -13.745  28.436   2.810  1.00 25.00           C
ATOM     31  CA  LEU    31     -12.389  30.798   5.503  1.00 25.00           C
ATOM     32  CA  GLY    32      -9.149  31.353   3.495  1.00 25.00           C
ATOM     33  CA  LEU    33      -7.765  27.848   4.227  1.00 25.00           C
ATOM     34  CA  GLU    34      -7.307  25.881   0.974  1.00 25.00           C
ATOM     35  CA  LYS    35      -6.950  29.154  -0.983  1.00 25.00           C
ATOM     36  CA  VAL    36      -4.338  30.398   1.527  1.00 25.00           C
ATOM     37  CA  GLU    37      -2.409  27.107   1.188  1.00 25.00           C
ATOM     38  CA  SER    38      -2.497  27.419  -2.628  1.00 25.00           C
ATOM     39  CA  TYR    39      -1.203  31.016  -2.388  1.00 25.00           C
ATOM     40  CA  ILE    40       1.629  29.869  -0.079  1.00 25.00           C
ATOM     41  CA  ASN    41       2.545  27.084  -2.545  1.00 25.00           C
ATOM     42  CA  SER    42       4.459  29.914  -4.241  1.00 25.00           C
ATOM     43  CA  GLY    43       3.918  32.401  -7.119  1.00 25.00           C
ATOM     44  CA  ASN    44       4.251  36.181  -6.839  1.00 25.00           C
ATOM     45  CA  ILE    45       0.454  36.203  -6.511  1.00 25.00           C
ATOM     46  CA  PHE    46      -0.899  38.728  -4.054  1.00 25.00           C
ATOM     47  CA  PHE    47      -1.703  40.976  -1.144  1.00 25.00           C
ATOM     48  CA  THR    48      -3.801  43.647  -2.825  1.00 25.00           C
ATOM     49  CA  SER    49      -7.273  44.655  -1.753  1.00 25.00           C
ATOM     50  CA  ILE    50      -8.195  48.118  -3.144  1.00 25.00           C
ATOM     51  CA  ASP    51     -11.978  48.619  -3.563  1.00 25.00           C
ATOM     52  CA  SER    52     -11.272  52.125  -2.264  1.00 25.00           C
ATOM     53  CA  LYS    53     -10.754  50.646   1.233  1.00 25.00           C
ATOM     54  CA  ALA    54     -11.932  49.913   4.801  1.00 25.00           C
ATOM     55  CA  GLN    55     -13.857  46.842   3.561  1.00 25.00           C
ATOM     56  CA  LEU    56     -10.744  45.613   1.698  1.00 25.00           C
ATOM     57  CA  VAL    57      -8.636  46.081   4.860  1.00 25.00           C
ATOM     58  CA  GLU    58     -11.216  44.120   6.901  1.00 25.00           C
ATOM     59  CA  LYS    59     -11.164  41.304   4.305  1.00 25.00           C
ATOM     60  CA  LEU    60      -7.337  41.216   4.441  1.00 25.00           C
ATOM     61  CA  GLU    61      -7.454  41.033   8.265  1.00 25.00           C
ATOM     62  CA  THR    62      -9.975  38.157   8.075  1.00 25.00           C
ATOM     63  CA  PHE    63      -7.718  36.310   5.592  1.00 25.00           C
ATOM     64  CA  PHE    64      -4.716  36.799   7.919  1.00 25.00           C
ATOM     65  CA  ALA    65      -6.751  35.448  10.869  1.00 25.00           C
ATOM     66  CA  VAL    66      -7.782  32.399   8.793  1.00 25.00           C
ATOM     67  CA  HIS    67      -4.124  31.781   7.839  1.00 25.00           C
ATOM     68  CA  TYR    68      -2.438  32.628  11.150  1.00 25.00           C
ATOM     69  CA  PRO    69       1.074  31.967   9.933  1.00 25.00           C
ATOM     70  CA  PHE    70       0.334  35.078   7.783  1.00 25.00           C
ATOM     71  CA  ILE    71      -1.414  34.976   4.413  1.00 25.00           C
ATOM     72  CA  GLN    72      -1.692  38.628   3.372  1.00 25.00           C
ATOM     73  CA  SER    73      -0.709  40.871   6.349  1.00 25.00           C
ATOM     74  CA  PHE    74      -1.666  44.346   5.110  1.00 25.00           C
ATOM     75  CA  SER    75      -4.051  43.980   2.192  1.00 25.00           C
ATOM     76  CA  LEU    76      -4.158  47.749   1.806  1.00 25.00           C
ATOM     77  CA  LEU    77      -5.489  50.994   0.364  1.00 25.00           C
ATOM     78  CA  SER    78      -2.387  53.118  -0.045  1.00 25.00           C
ATOM    168  CA  ALA   168      -5.929  43.700 -12.912  1.00 25.00           C
ATOM    169  CA  LYS   169      -4.314  46.811 -14.454  1.00 25.00           C
ATOM    170  CA  THR   170      -1.082  46.122 -12.520  1.00 25.00           C
ATOM    171  CA  PHE   171      -1.093  42.494 -13.746  1.00 25.00           C
ATOM    172  CA  ASP   172      -1.596  43.687 -17.349  1.00 25.00           C
ATOM    173  CA  LYS   173       1.317  46.144 -16.969  1.00 25.00           C
ATOM    174  CA  ILE   174       3.534  43.342 -15.593  1.00 25.00           C
ATOM    175  CA  GLY   175       2.578  41.102 -18.548  1.00 25.00           C
ATOM    176  CA  GLN   176       3.418  43.926 -20.994  1.00 25.00           C
ATOM    177  CA  MET   177       6.809  44.430 -19.285  1.00 25.00           C
ATOM    178  CA  LEU   178       7.517  40.674 -19.529  1.00 25.00           C
ATOM    179  CA  LYS   179       9.554  39.184 -22.430  1.00 25.00           C
ATOM    180  CA  LYS   180      10.372  35.652 -21.244  1.00 25.00           C
TER
END
