
#######################################################
#                                                     #
#                        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   82 (   82),  selected   82 , name T0340TS168_3-D1
# Molecule2: number of CA atoms   82 (  626),  selected   82 , name T0340_D1.pdb
# PARAMETERS: T0340TS168_3-D1.T0340_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    R       4      R       4          0.229
LGA    P       5      P       5          1.859
LGA    R       6      R       6          0.862
LGA    L       7      L       7          1.845
LGA    C       8      C       8          1.373
LGA    H       9      H       9          0.832
LGA    L      10      L      10          1.082
LGA    R      11      R      11          0.279
LGA    K      12      K      12          0.436
LGA    G      13      G      13          2.781
LGA    P      14      P      14          1.624
LGA    Q      15      Q      15          1.776
LGA    G      16      G      16          0.990
LGA    Y      17      Y      17          0.901
LGA    G      18      G      18          1.416
LGA    F      19      F      19          1.401
LGA    N      20      N      20          1.669
LGA    L      21      L      21          0.667
LGA    H      22      H      22          1.127
LGA    S      23      S      23          1.721
LGA    D      24      D      24          2.138
LGA    K      25      K      25          4.158
LGA    S      26      S      26          5.819
LGA    R      27      R      27          1.780
LGA    P      28      P      28          1.672
LGA    G      29      G      29          1.468
LGA    Q      30      Q      30          0.646
LGA    Y      31      Y      31          0.549
LGA    I      32      I      32          0.617
LGA    R      33      R      33          0.688
LGA    S      34      S      34          2.473
LGA    V      35      V      35          1.098
LGA    D      36      D      36          1.646
LGA    P      37      P      37          2.001
LGA    G      38      G      38          0.997
LGA    S      39      S      39          1.674
LGA    P      40      P      40          1.358
LGA    -       -      A      41           -
LGA    A      41      A      42           #
LGA    A      42      R      43          1.397
LGA    R      43      S      44           #
LGA    S      44      -       -           -
LGA    G      45      G      45          1.654
LGA    L      46      L      46          1.157
LGA    R      47      R      47          1.924
LGA    A      48      A      48          1.115
LGA    Q      49      Q      49          0.628
LGA    D      50      D      50          0.646
LGA    R      51      R      51          0.717
LGA    L      52      L      52          1.614
LGA    I      53      I      53          1.642
LGA    E      54      E      54          0.830
LGA    V      55      V      55          1.487
LGA    N      56      N      56          1.647
LGA    G      57      G      57          1.893
LGA    Q      58      Q      58          2.109
LGA    N      59      N      59          3.434
LGA    V      60      V      60          1.686
LGA    E      61      E      61          0.361
LGA    G      62      G      62          0.615
LGA    L      63      L      63          2.699
LGA    R      64      R      64          2.883
LGA    H      65      H      65          1.428
LGA    A      66      A      66          1.563
LGA    E      67      E      67          1.127
LGA    V      68      V      68          1.034
LGA    V      69      V      69          1.476
LGA    A      70      A      70          1.817
LGA    S      71      S      71          1.635
LGA    I      72      I      72          1.680
LGA    K      73      K      73          2.336
LGA    A      74      A      74          2.541
LGA    R      75      R      75          1.933
LGA    E      76      E      76          1.239
LGA    D      77      D      77          2.114
LGA    E      78      E      78          1.780
LGA    A      79      A      79          0.599
LGA    R      80      R      80          0.832
LGA    L      81      L      81          1.122
LGA    L      82      L      82          1.341
LGA    V      83      V      83          1.743
LGA    V      84      V      84          1.770
LGA    G      85      G      85          1.813

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   82   82    5.0     79    1.75    98.73     88.136     4.272

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.479514 * X  +  -0.264729 * Y  +   0.836651 * Z  +   9.985994
  Y_new =   0.785391 * X  +  -0.554757 * Y  +   0.274601 * Z  +  25.983574
  Z_new =   0.391443 * X  +   0.788773 * Y  +   0.473929 * Z  +   9.155940 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.029757   -2.111836  [ DEG:    59.0007   -120.9993 ]
  Theta =  -0.402199   -2.739393  [ DEG:   -23.0443   -156.9557 ]
  Phi   =   2.118931   -1.022662  [ DEG:   121.4058    -58.5942 ]
 
# 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: T0340TS168_3-D1                               
REMARK     2: T0340_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0340TS168_3-D1.T0340_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   82   82   5.0   79   1.75   98.73  88.136
REMARK  ---------------------------------------------------------- 
MOLECULE T0340TS168_3-D1
PFRMAT TS
TARGET T0340
MODEL 3
PARENT N/A
ATOM      4  CA  ARG     4      14.606  40.074   8.281  1.00 25.00           C
ATOM      5  CA  PRO     5      14.062  37.257  10.780  1.00 25.00           C
ATOM      6  CA  ARG     6      10.364  36.716  10.529  1.00 25.00           C
ATOM      7  CA  LEU     7       8.701  34.595  13.188  1.00 25.00           C
ATOM      8  CA  CYS     8       5.934  31.946  13.208  1.00 25.00           C
ATOM      9  CA  HIS     9       5.826  31.098  16.933  1.00 25.00           C
ATOM     10  CA  LEU    10       3.457  28.051  17.022  1.00 25.00           C
ATOM     11  CA  ARG    11       1.596  25.491  19.148  1.00 25.00           C
ATOM     12  CA  LYS    12       1.528  21.739  18.520  1.00 25.00           C
ATOM     13  CA  GLY    13      -1.749  21.719  20.408  1.00 25.00           C
ATOM     14  CA  PRO    14      -3.289  18.625  18.783  1.00 25.00           C
ATOM     15  CA  GLN    15      -2.430  15.995  16.195  1.00 25.00           C
ATOM     16  CA  GLY    16       0.987  17.603  15.614  1.00 25.00           C
ATOM     17  CA  TYR    17       1.908  20.609  13.389  1.00 25.00           C
ATOM     18  CA  GLY    18       0.763  22.276  10.127  1.00 25.00           C
ATOM     19  CA  PHE    19       4.040  22.022   8.193  1.00 25.00           C
ATOM     20  CA  ASN    20       5.953  19.228   6.375  1.00 25.00           C
ATOM     21  CA  LEU    21       9.434  19.885   4.990  1.00 25.00           C
ATOM     22  CA  HIS    22      10.074  19.514   1.251  1.00 25.00           C
ATOM     23  CA  SER    23      13.500  20.134  -0.212  1.00 25.00           C
ATOM     24  CA  ASP    24      16.798  19.484  -1.902  1.00 25.00           C
ATOM     25  CA  LYS    25      20.070  17.908  -2.987  1.00 25.00           C
ATOM     26  CA  SER    26      22.823  20.467  -2.684  1.00 25.00           C
ATOM     27  CA  ARG    27      20.486  23.493  -2.284  1.00 25.00           C
ATOM     28  CA  PRO    28      21.206  23.507   1.486  1.00 25.00           C
ATOM     29  CA  GLY    29      18.159  25.163   3.052  1.00 25.00           C
ATOM     30  CA  GLN    30      14.952  23.265   3.942  1.00 25.00           C
ATOM     31  CA  TYR    31      11.350  24.063   2.992  1.00 25.00           C
ATOM     32  CA  ILE    32       7.699  24.973   3.316  1.00 25.00           C
ATOM     33  CA  ARG    33       5.648  22.821   0.863  1.00 25.00           C
ATOM     34  CA  SER    34       2.859  21.309   2.951  1.00 25.00           C
ATOM     35  CA  VAL    35       0.628  23.905   4.620  1.00 25.00           C
ATOM     36  CA  ASP    36      -2.346  21.749   5.791  1.00 25.00           C
ATOM     37  CA  PRO    37      -5.276  24.024   6.663  1.00 25.00           C
ATOM     38  CA  GLY    38      -6.023  25.936   9.844  1.00 25.00           C
ATOM     39  CA  SER    39      -3.866  23.418  11.679  1.00 25.00           C
ATOM     40  CA  PRO    40      -1.410  26.126  12.687  1.00 25.00           C
ATOM     41  CA  ALA    41      -1.420  28.288  15.847  1.00 25.00           C
ATOM     42  CA  ALA    42      -0.789  31.421  13.736  1.00 25.00           C
ATOM     43  CA  ARG    43      -3.671  30.459  11.405  1.00 25.00           C
ATOM     44  CA  SER    44      -1.175  30.958   8.608  1.00 25.00           C
ATOM     45  CA  GLY    45       1.635  33.440   9.304  1.00 25.00           C
ATOM     46  CA  LEU    46       4.023  31.042   7.624  1.00 25.00           C
ATOM     47  CA  ARG    47       4.279  32.082   3.924  1.00 25.00           C
ATOM     48  CA  ALA    48       4.552  28.865   1.936  1.00 25.00           C
ATOM     49  CA  GLN    49       7.833  28.778  -0.061  1.00 25.00           C
ATOM     50  CA  ASP    50      10.147  29.324   2.961  1.00 25.00           C
ATOM     51  CA  ARG    51      13.775  28.468   3.532  1.00 25.00           C
ATOM     52  CA  LEU    52      12.645  27.312   7.007  1.00 25.00           C
ATOM     53  CA  ILE    53      15.656  28.129   9.125  1.00 25.00           C
ATOM     54  CA  GLU    54      16.140  27.415  12.812  1.00 25.00           C
ATOM     55  CA  VAL    55      15.839  25.183  15.898  1.00 25.00           C
ATOM     56  CA  ASN    56      15.576  27.442  18.987  1.00 25.00           C
ATOM     57  CA  GLY    57      18.906  28.917  17.802  1.00 25.00           C
ATOM     58  CA  GLN    58      20.950  26.880  15.319  1.00 25.00           C
ATOM     59  CA  ASN    59      20.157  23.581  13.562  1.00 25.00           C
ATOM     60  CA  VAL    60      18.547  23.801  10.061  1.00 25.00           C
ATOM     61  CA  GLU    61      21.300  24.755   7.590  1.00 25.00           C
ATOM     62  CA  GLY    62      23.868  21.925   7.684  1.00 25.00           C
ATOM     63  CA  LEU    63      20.963  19.797   6.459  1.00 25.00           C
ATOM     64  CA  ARG    64      19.509  17.010   4.320  1.00 25.00           C
ATOM     65  CA  HIS    65      16.156  17.568   5.960  1.00 25.00           C
ATOM     66  CA  ALA    66      15.376  14.444   8.033  1.00 25.00           C
ATOM     67  CA  GLU    67      17.038  16.033  11.096  1.00 25.00           C
ATOM     68  CA  VAL    68      14.981  19.223  10.588  1.00 25.00           C
ATOM     69  CA  VAL    69      11.774  17.145  10.330  1.00 25.00           C
ATOM     70  CA  ALA    70      12.685  15.294  13.557  1.00 25.00           C
ATOM     71  CA  SER    71      13.316  18.633  15.323  1.00 25.00           C
ATOM     72  CA  ILE    72       9.927  19.942  14.111  1.00 25.00           C
ATOM     73  CA  LYS    73       8.214  16.765  15.395  1.00 25.00           C
ATOM     74  CA  ALA    74       9.939  17.178  18.789  1.00 25.00           C
ATOM     75  CA  ARG    75       9.443  20.451  20.572  1.00 25.00           C
ATOM     76  CA  GLU    76       6.160  19.121  22.086  1.00 25.00           C
ATOM     77  CA  ASP    77       5.903  22.401  23.909  1.00 25.00           C
ATOM     78  CA  GLU    78       6.529  25.234  21.456  1.00 25.00           C
ATOM     79  CA  ALA    79       7.876  25.148  17.883  1.00 25.00           C
ATOM     80  CA  ARG    80      10.178  28.090  17.955  1.00 25.00           C
ATOM     81  CA  LEU    81      10.096  28.232  14.180  1.00 25.00           C
ATOM     82  CA  LEU    82      12.337  31.135  13.255  1.00 25.00           C
ATOM     83  CA  VAL    83      12.996  32.469   9.720  1.00 25.00           C
ATOM     84  CA  VAL    84      14.350  32.840   6.197  1.00 25.00           C
ATOM     85  CA  GLY    85      11.823  34.337   3.780  1.00 25.00           C
TER
END
