
#######################################################
#                                                     #
#                        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   94 (   94),  selected   94 , name T0359TS168_3-D1
# Molecule2: number of CA atoms   90 (  669),  selected   90 , name T0359_D1.pdb
# PARAMETERS: T0359TS168_3-D1.T0359_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    S       1      S       1           -
LGA    M       2      M       2           -
LGA    S       3      S       3          4.291
LGA    E       4      E       4          2.109
LGA    T       5      T       5          1.044
LGA    F       6      F       6          1.066
LGA    D       7      D       7          0.893
LGA    V       8      V       8          1.610
LGA    E       9      E       9          2.328
LGA    L      10      L      10          1.220
LGA    T      11      T      11          2.125
LGA    K      12      K      12          0.266
LGA    N      13      N      13          1.628
LGA    V      14      V      14          3.035
LGA    Q      15      Q      15          2.959
LGA    G      16      G      16          2.282
LGA    L      17      L      17          1.802
LGA    G      18      G      18          1.377
LGA    I      19      I      19          0.752
LGA    T      20      T      20          1.020
LGA    I      21      I      21          2.064
LGA    A      22      A      22          1.484
LGA    G      23      G      23          2.209
LGA    Y      24      Y      24          2.916
LGA    I      25      I      25          5.440
LGA    G      26      G      26          4.648
LGA    D      27      D      27           #
LGA    K      28      -       -           -
LGA    K      29      -       -           -
LGA    L      30      -       -           -
LGA    E      31      P      32          0.908
LGA    P      32      S      33          1.591
LGA    S      33      G      34          2.807
LGA    G      34      -       -           -
LGA    I      35      I      35          2.418
LGA    F      36      F      36          1.180
LGA    V      37      V      37          1.137
LGA    K      38      K      38          1.286
LGA    S      39      S      39          0.931
LGA    I      40      I      40          1.830
LGA    T      41      T      41          1.431
LGA    K      42      K      42          1.745
LGA    S      43      S      43          2.331
LGA    S      44      S      44          0.888
LGA    A      45      A      45          1.153
LGA    V      46      V      46          0.782
LGA    E      47      E      47          0.674
LGA    H      48      H      48          1.596
LGA    D      49      D      49          1.296
LGA    G      50      G      50          0.974
LGA    R      51      R      51          1.713
LGA    I      52      I      52          1.751
LGA    Q      53      Q      53          0.639
LGA    I      54      I      54          0.901
LGA    G      55      G      55          1.504
LGA    D      56      D      56          0.913
LGA    Q      57      Q      57          1.208
LGA    I      58      I      58          1.320
LGA    I      59      I      59          1.970
LGA    A      60      A      60          3.651
LGA    V      61      V      61          1.918
LGA    D      62      D      62          0.692
LGA    G      63      G      63          0.604
LGA    T      64      T      64          1.090
LGA    N      65      N      65          1.195
LGA    L      66      L      66          1.556
LGA    Q      67      Q      67          1.515
LGA    G      68      G      68          0.745
LGA    F      69      F      69          1.085
LGA    T      70      T      70          1.211
LGA    N      71      N      71          1.854
LGA    Q      72      Q      72          1.874
LGA    Q      73      Q      73          2.192
LGA    A      74      A      74          1.919
LGA    V      75      V      75          1.834
LGA    E      76      E      76          1.980
LGA    V      77      V      77          1.834
LGA    L      78      L      78          1.377
LGA    R      79      R      79          1.959
LGA    H      80      H      80          2.037
LGA    T      81      T      81          1.850
LGA    G      82      G      82          2.693
LGA    Q      83      Q      83          1.678
LGA    T      84      T      84          1.383
LGA    V      85      V      85          1.466
LGA    L      86      L      86          1.263
LGA    L      87      L      87          0.746
LGA    T      88      T      88          1.589
LGA    L      89      L      89          2.358
LGA    M      90      M      90          1.233
LGA    R      91      R      91          0.342
LGA    R      92      R      92          1.270
LGA    G      93      G      93          1.373
LGA    E      94      E      94          2.238

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   94   90    5.0     87    1.88    96.55     86.637     4.392

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.291567 * X  +  -0.365588 * Y  +  -0.883931 * Z  +  -4.541382
  Y_new =  -0.662531 * X  +   0.589356 * Y  +  -0.462291 * Z  +  13.720727
  Z_new =   0.689958 * X  +   0.720420 * Y  +  -0.070377 * Z  +  -7.119132 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.668176   -1.473417  [ DEG:    95.5794    -84.4206 ]
  Theta =  -0.761431   -2.380162  [ DEG:   -43.6268   -136.3732 ]
  Phi   =  -1.156222    1.985371  [ DEG:   -66.2466    113.7534 ]
 
# 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: T0359TS168_3-D1                               
REMARK     2: T0359_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0359TS168_3-D1.T0359_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   94   90   5.0   87   1.88   96.55  86.637
REMARK  ---------------------------------------------------------- 
MOLECULE T0359TS168_3-D1
PFRMAT TS
TARGET T0359
MODEL 3
PARENT N/A
ATOM      1  CA  SER     1       9.115  -0.231   1.435  1.00 25.00           C
ATOM      2  CA  MET     2       6.055   1.740   2.572  1.00 25.00           C
ATOM      3  CA  SER     3       7.138   4.094  -0.148  1.00 25.00           C
ATOM      4  CA  GLU     4       5.616   7.492   0.427  1.00 25.00           C
ATOM      5  CA  THR     5       1.864   7.439  -0.205  1.00 25.00           C
ATOM      6  CA  PHE     6       0.392  10.506   1.497  1.00 25.00           C
ATOM      7  CA  ASP     7      -2.533  12.388   2.915  1.00 25.00           C
ATOM      8  CA  VAL     8      -2.329  15.840   1.232  1.00 25.00           C
ATOM      9  CA  GLU     9      -5.024  18.436   2.045  1.00 25.00           C
ATOM     10  CA  LEU    10      -6.855  21.619   0.896  1.00 25.00           C
ATOM     11  CA  THR    11      -8.450  24.981   1.535  1.00 25.00           C
ATOM     12  CA  LYS    12     -11.143  25.003  -1.230  1.00 25.00           C
ATOM     13  CA  ASN    13     -11.842  28.642  -0.243  1.00 25.00           C
ATOM     14  CA  VAL    14     -14.569  30.119  -2.346  1.00 25.00           C
ATOM     15  CA  GLN    15     -12.936  28.623  -5.492  1.00 25.00           C
ATOM     16  CA  GLY    16     -12.461  25.567  -7.705  1.00 25.00           C
ATOM     17  CA  LEU    17      -9.460  23.800  -6.174  1.00 25.00           C
ATOM     18  CA  GLY    18      -7.130  25.115  -8.797  1.00 25.00           C
ATOM     19  CA  ILE    19      -5.643  21.634  -8.808  1.00 25.00           C
ATOM     20  CA  THR    20      -6.083  19.815 -12.150  1.00 25.00           C
ATOM     21  CA  ILE    21      -7.880  16.584 -13.117  1.00 25.00           C
ATOM     22  CA  ALA    22      -7.271  13.861 -15.785  1.00 25.00           C
ATOM     23  CA  GLY    23      -5.889  11.816 -18.691  1.00 25.00           C
ATOM     24  CA  TYR    24      -7.479   8.474 -17.804  1.00 25.00           C
ATOM     25  CA  ILE    25      -4.406   6.897 -19.349  1.00 25.00           C
ATOM     26  CA  GLY    26      -6.933   4.998 -21.492  1.00 25.00           C
ATOM     27  CA  ASP    27      -8.172   2.494 -18.933  1.00 25.00           C
ATOM     28  CA  LYS    28      -4.779   0.822 -18.401  1.00 25.00           C
ATOM     29  CA  LYS    29      -5.389  -2.159 -16.039  1.00 25.00           C
ATOM     30  CA  LEU    30      -3.526  -0.123 -13.371  1.00 25.00           C
ATOM     31  CA  GLU    31      -0.549   0.335 -15.711  1.00 25.00           C
ATOM     32  CA  PRO    32      -1.803   3.966 -15.828  1.00 25.00           C
ATOM     33  CA  SER    33      -5.369   4.696 -14.723  1.00 25.00           C
ATOM     34  CA  GLY    34      -4.298   6.890 -11.796  1.00 25.00           C
ATOM     35  CA  ILE    35      -3.780   9.506 -14.469  1.00 25.00           C
ATOM     36  CA  PHE    36      -3.110  12.830 -12.836  1.00 25.00           C
ATOM     37  CA  VAL    37      -2.559  15.937 -10.737  1.00 25.00           C
ATOM     38  CA  LYS    38      -2.000  17.608 -14.071  1.00 25.00           C
ATOM     39  CA  SER    39      -0.925  21.064 -12.775  1.00 25.00           C
ATOM     40  CA  ILE    40       0.510  23.463 -10.146  1.00 25.00           C
ATOM     41  CA  THR    41      -2.069  26.255 -10.282  1.00 25.00           C
ATOM     42  CA  LYS    42      -0.169  28.944  -8.323  1.00 25.00           C
ATOM     43  CA  SER    43      -3.092  31.137  -7.245  1.00 25.00           C
ATOM     44  CA  SER    44      -4.593  28.108  -5.564  1.00 25.00           C
ATOM     45  CA  ALA    45      -5.504  25.887  -2.549  1.00 25.00           C
ATOM     46  CA  VAL    46      -3.147  23.102  -3.600  1.00 25.00           C
ATOM     47  CA  GLU    47      -0.254  25.611  -3.588  1.00 25.00           C
ATOM     48  CA  HIS    48      -0.939  26.419   0.093  1.00 25.00           C
ATOM     49  CA  ASP    49       0.416  23.059   1.263  1.00 25.00           C
ATOM     50  CA  GLY    50       3.411  22.618  -1.125  1.00 25.00           C
ATOM     51  CA  ARG    51       2.277  19.097  -2.041  1.00 25.00           C
ATOM     52  CA  ILE    52       0.259  18.549  -5.197  1.00 25.00           C
ATOM     53  CA  GLN    53       3.232  18.958  -7.511  1.00 25.00           C
ATOM     54  CA  ILE    54       3.262  18.759 -11.298  1.00 25.00           C
ATOM     55  CA  GLY    55       2.300  15.261 -12.363  1.00 25.00           C
ATOM     56  CA  ASP    56       1.487  13.423  -9.122  1.00 25.00           C
ATOM     57  CA  GLN    57      -0.236  10.082  -9.484  1.00 25.00           C
ATOM     58  CA  ILE    58      -3.676  10.801  -7.906  1.00 25.00           C
ATOM     59  CA  ILE    59      -6.181   9.179  -5.568  1.00 25.00           C
ATOM     60  CA  ALA    60      -9.942   9.876  -5.203  1.00 25.00           C
ATOM     61  CA  VAL    61     -11.794  12.156  -2.723  1.00 25.00           C
ATOM     62  CA  ASP    62     -12.039  11.067   0.880  1.00 25.00           C
ATOM     63  CA  GLY    63     -11.858   7.403   1.987  1.00 25.00           C
ATOM     64  CA  THR    64     -11.500   6.386  -1.625  1.00 25.00           C
ATOM     65  CA  ASN    65      -8.595   4.694  -3.367  1.00 25.00           C
ATOM     66  CA  LEU    66      -8.167   4.812  -7.161  1.00 25.00           C
ATOM     67  CA  GLN    67      -5.784   2.043  -8.329  1.00 25.00           C
ATOM     68  CA  GLY    68      -8.951   0.311  -9.608  1.00 25.00           C
ATOM     69  CA  PHE    69     -10.704   3.149 -11.443  1.00 25.00           C
ATOM     70  CA  THR    70     -10.812   4.833 -14.870  1.00 25.00           C
ATOM     71  CA  ASN    71     -10.879   8.608 -14.062  1.00 25.00           C
ATOM     72  CA  GLN    72     -14.196  10.366 -14.820  1.00 25.00           C
ATOM     73  CA  GLN    73     -15.593   9.242 -11.436  1.00 25.00           C
ATOM     74  CA  ALA    74     -12.456  10.560  -9.676  1.00 25.00           C
ATOM     75  CA  VAL    75     -12.815  13.912 -11.494  1.00 25.00           C
ATOM     76  CA  GLU    76     -16.493  14.116 -10.445  1.00 25.00           C
ATOM     77  CA  VAL    77     -15.523  13.379  -6.814  1.00 25.00           C
ATOM     78  CA  LEU    78     -12.848  16.117  -6.947  1.00 25.00           C
ATOM     79  CA  ARG    79     -15.414  18.588  -8.354  1.00 25.00           C
ATOM     80  CA  HIS    80     -17.864  17.677  -5.555  1.00 25.00           C
ATOM     81  CA  THR    81     -16.036  18.072  -2.224  1.00 25.00           C
ATOM     82  CA  GLY    82     -16.249  21.881  -1.977  1.00 25.00           C
ATOM     83  CA  GLN    83     -15.042  21.454   1.605  1.00 25.00           C
ATOM     84  CA  THR    84     -11.962  19.423   2.527  1.00 25.00           C
ATOM     85  CA  VAL    85      -9.837  16.753   0.918  1.00 25.00           C
ATOM     86  CA  LEU    86      -8.010  13.829   2.417  1.00 25.00           C
ATOM     87  CA  LEU    87      -6.195  13.153  -0.913  1.00 25.00           C
ATOM     88  CA  THR    88      -3.178  11.202  -2.026  1.00 25.00           C
ATOM     89  CA  LEU    89      -0.157  13.153  -3.255  1.00 25.00           C
ATOM     90  CA  MET    90       1.553  10.027  -4.628  1.00 25.00           C
ATOM     91  CA  ARG    91       4.967   9.856  -6.135  1.00 25.00           C
ATOM     92  CA  ARG    92       7.976   7.856  -7.246  1.00 25.00           C
ATOM     93  CA  GLY    93      11.674   8.602  -6.990  1.00 25.00           C
ATOM     94  CA  GLU    94      13.107   5.052  -7.223  1.00 25.00           C
TER
END
