
#######################################################
#                                                     #
#                        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 T0340TS393_5-D1
# Molecule2: number of CA atoms   82 (  626),  selected   82 , name T0340_D1.pdb
# PARAMETERS: T0340TS393_5-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          1.571
LGA    P       5      P       5          2.047
LGA    R       6      R       6          2.228
LGA    L       7      L       7          1.991
LGA    C       8      C       8          1.368
LGA    H       9      H       9          0.735
LGA    L      10      L      10          0.449
LGA    R      11      R      11          1.943
LGA    K      12      K      12          0.979
LGA    G      13      G      13          2.065
LGA    P      14      P      14          2.477
LGA    Q      15      Q      15          1.363
LGA    G      16      G      16          0.638
LGA    Y      17      Y      17          1.000
LGA    G      18      G      18          0.999
LGA    F      19      F      19          2.080
LGA    N      20      N      20          1.550
LGA    L      21      L      21          1.310
LGA    H      22      H      22          1.302
LGA    S      23      S      23          1.669
LGA    D      24      D      24          2.661
LGA    K      25      K      25          4.221
LGA    S      26      S      26          6.490
LGA    R      27      R      27          2.768
LGA    P      28      P      28          2.169
LGA    G      29      G      29          0.882
LGA    Q      30      Q      30          1.171
LGA    Y      31      Y      31          0.385
LGA    I      32      I      32          0.644
LGA    R      33      R      33          0.921
LGA    S      34      S      34          1.124
LGA    V      35      V      35          1.328
LGA    D      36      D      36          1.212
LGA    P      37      P      37          1.184
LGA    G      38      G      38          1.818
LGA    S      39      S      39          1.165
LGA    P      40      P      40          1.460
LGA    A      41      A      41          1.094
LGA    A      42      A      42          1.029
LGA    R      43      R      43          1.498
LGA    S      44      S      44          2.404
LGA    G      45      G      45          0.850
LGA    L      46      L      46          0.318
LGA    R      47      R      47          1.212
LGA    A      48      A      48          1.083
LGA    Q      49      Q      49          2.498
LGA    D      50      D      50          1.698
LGA    R      51      R      51          1.344
LGA    L      52      L      52          1.474
LGA    I      53      I      53          1.692
LGA    E      54      E      54          1.924
LGA    V      55      V      55          1.798
LGA    N      56      N      56          1.937
LGA    G      57      G      57          1.790
LGA    Q      58      Q      58          1.925
LGA    N      59      N      59          2.911
LGA    V      60      V      60          1.066
LGA    E      61      E      61          1.491
LGA    G      62      G      62          1.574
LGA    L      63      L      63          2.446
LGA    R      64      R      64          3.255
LGA    H      65      H      65          2.391
LGA    A      66      A      66          1.957
LGA    E      67      E      67          2.111
LGA    V      68      V      68          2.311
LGA    V      69      V      69          1.767
LGA    A      70      A      70          1.558
LGA    S      71      S      71          1.932
LGA    I      72      I      72          1.862
LGA    K      73      K      73          1.308
LGA    A      74      A      74          1.792
LGA    R      75      R      75          3.358
LGA    E      76      E      76          3.220
LGA    D      77      D      77          1.631
LGA    E      78      E      78          2.328
LGA    A      79      A      79          1.541
LGA    R      80      R      80          1.045
LGA    L      81      L      81          1.787
LGA    L      82      L      82          1.764
LGA    V      83      V      83          1.473
LGA    V      84      V      84          1.810
LGA    G      85      G      85          2.463

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   82   82    5.0     82    1.95   100.00     88.409     3.997

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.212347 * X  +   0.976413 * Y  +  -0.039065 * Z  +  10.070713
  Y_new =  -0.466712 * X  +   0.066214 * Y  +  -0.881927 * Z  +  25.934959
  Z_new =  -0.858539 * X  +   0.205506 * Y  +   0.469764 * Z  +   9.108504 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.412383   -2.729210  [ DEG:    23.6278   -156.3722 ]
  Theta =   1.032413    2.109179  [ DEG:    59.1529    120.8471 ]
  Phi   =  -1.143805    1.997788  [ DEG:   -65.5352    114.4648 ]
 
# 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: T0340TS393_5-D1                               
REMARK     2: T0340_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0340TS393_5-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   82   1.95  100.00  88.409
REMARK  ---------------------------------------------------------- 
MOLECULE T0340TS393_5-D1
PFRMAT TS
TARGET T0340
MODEL 5
PARENT N/A
ATOM      4  CA  ARG     4      14.518  40.673   9.883  1.00 25.00           C
ATOM      5  CA  PRO     5      12.516  37.420  10.236  1.00 25.00           C
ATOM      6  CA  ARG     6       8.857  36.734   9.808  1.00 25.00           C
ATOM      7  CA  LEU     7       8.659  34.424  12.878  1.00 25.00           C
ATOM      8  CA  CYS     8       5.902  32.128  14.139  1.00 25.00           C
ATOM      9  CA  HIS     9       5.306  30.071  17.284  1.00 25.00           C
ATOM     10  CA  LEU    10       3.724  26.815  16.318  1.00 25.00           C
ATOM     11  CA  ARG    11       0.367  25.874  17.792  1.00 25.00           C
ATOM     12  CA  LYS    12       2.020  22.551  18.744  1.00 25.00           C
ATOM     13  CA  GLY    13      -1.146  20.593  19.608  1.00 25.00           C
ATOM     14  CA  PRO    14      -1.474  16.806  18.930  1.00 25.00           C
ATOM     15  CA  GLN    15      -1.655  15.826  15.251  1.00 25.00           C
ATOM     16  CA  GLY    16       0.699  18.749  14.616  1.00 25.00           C
ATOM     17  CA  TYR    17       1.156  22.312  13.430  1.00 25.00           C
ATOM     18  CA  GLY    18       1.029  21.313   9.747  1.00 25.00           C
ATOM     19  CA  PHE    19       4.569  22.070   8.623  1.00 25.00           C
ATOM     20  CA  ASN    20       6.101  19.533   6.213  1.00 25.00           C
ATOM     21  CA  LEU    21       9.807  20.583   6.159  1.00 25.00           C
ATOM     22  CA  HIS    22      11.638  19.213   3.075  1.00 25.00           C
ATOM     23  CA  SER    23      13.343  19.680  -0.304  1.00 25.00           C
ATOM     24  CA  ASP    24      16.728  18.674  -1.819  1.00 25.00           C
ATOM     25  CA  LYS    25      20.099  17.484  -3.121  1.00 25.00           C
ATOM     26  CA  SER    26      23.116  19.680  -2.349  1.00 25.00           C
ATOM     27  CA  ARG    27      21.400  23.024  -1.995  1.00 25.00           C
ATOM     28  CA  PRO    28      21.714  24.101   1.597  1.00 25.00           C
ATOM     29  CA  GLY    29      18.042  23.282   2.060  1.00 25.00           C
ATOM     30  CA  GLN    30      15.016  23.842   4.239  1.00 25.00           C
ATOM     31  CA  TYR    31      11.399  24.554   3.149  1.00 25.00           C
ATOM     32  CA  ILE    32       7.757  24.951   4.289  1.00 25.00           C
ATOM     33  CA  ARG    33       6.609  22.571   1.551  1.00 25.00           C
ATOM     34  CA  SER    34       2.883  22.567   2.452  1.00 25.00           C
ATOM     35  CA  VAL    35       0.393  23.624   5.134  1.00 25.00           C
ATOM     36  CA  ASP    36      -3.046  22.276   5.917  1.00 25.00           C
ATOM     37  CA  PRO    37      -5.588  25.036   6.795  1.00 25.00           C
ATOM     38  CA  GLY    38      -7.136  25.380  10.246  1.00 25.00           C
ATOM     39  CA  SER    39      -3.852  23.931  11.517  1.00 25.00           C
ATOM     40  CA  PRO    40      -2.069  26.756  13.440  1.00 25.00           C
ATOM     41  CA  ALA    41       0.876  27.327  11.061  1.00 25.00           C
ATOM     42  CA  ALA    42      -1.343  29.462   8.785  1.00 25.00           C
ATOM     43  CA  ARG    43      -2.500  31.517  11.802  1.00 25.00           C
ATOM     44  CA  SER    44       0.825  33.030  12.887  1.00 25.00           C
ATOM     45  CA  GLY    45       2.503  32.886   9.495  1.00 25.00           C
ATOM     46  CA  LEU    46       4.473  29.978   8.072  1.00 25.00           C
ATOM     47  CA  ARG    47       3.941  31.404   4.599  1.00 25.00           C
ATOM     48  CA  ALA    48       4.938  28.793   2.051  1.00 25.00           C
ATOM     49  CA  GLN    49       8.062  30.694   0.971  1.00 25.00           C
ATOM     50  CA  ASP    50       9.383  30.850   4.506  1.00 25.00           C
ATOM     51  CA  ARG    51      12.772  29.444   3.329  1.00 25.00           C
ATOM     52  CA  LEU    52      13.062  27.771   6.719  1.00 25.00           C
ATOM     53  CA  ILE    53      15.921  27.644   9.282  1.00 25.00           C
ATOM     54  CA  GLU    54      15.674  26.370  12.901  1.00 25.00           C
ATOM     55  CA  VAL    55      15.662  24.661  16.262  1.00 25.00           C
ATOM     56  CA  ASN    56      15.366  27.956  18.196  1.00 25.00           C
ATOM     57  CA  GLY    57      18.724  29.670  18.116  1.00 25.00           C
ATOM     58  CA  GLN    58      20.832  27.512  15.828  1.00 25.00           C
ATOM     59  CA  ASN    59      20.448  24.155  14.045  1.00 25.00           C
ATOM     60  CA  VAL    60      20.054  24.040  10.232  1.00 25.00           C
ATOM     61  CA  GLU    61      21.585  24.043   6.722  1.00 25.00           C
ATOM     62  CA  GLY    62      23.424  20.839   7.647  1.00 25.00           C
ATOM     63  CA  LEU    63      20.995  17.952   7.043  1.00 25.00           C
ATOM     64  CA  ARG    64      18.231  17.045   4.505  1.00 25.00           C
ATOM     65  CA  HIS    65      14.795  15.453   5.000  1.00 25.00           C
ATOM     66  CA  ALA    66      14.577  13.016   7.947  1.00 25.00           C
ATOM     67  CA  GLU    67      16.861  15.283  10.022  1.00 25.00           C
ATOM     68  CA  VAL    68      14.675  18.310   9.166  1.00 25.00           C
ATOM     69  CA  VAL    69      11.541  16.368  10.200  1.00 25.00           C
ATOM     70  CA  ALA    70      13.205  15.393  13.509  1.00 25.00           C
ATOM     71  CA  SER    71      14.152  19.050  14.138  1.00 25.00           C
ATOM     72  CA  ILE    72      10.548  20.132  13.424  1.00 25.00           C
ATOM     73  CA  LYS    73       9.243  17.477  15.855  1.00 25.00           C
ATOM     74  CA  ALA    74      11.690  18.694  18.537  1.00 25.00           C
ATOM     75  CA  ARG    75      11.369  21.887  20.614  1.00 25.00           C
ATOM     76  CA  GLU    76       8.784  19.931  22.603  1.00 25.00           C
ATOM     77  CA  ASP    77       5.660  22.095  22.775  1.00 25.00           C
ATOM     78  CA  GLU    78       4.956  25.697  21.899  1.00 25.00           C
ATOM     79  CA  ALA    79       7.477  25.092  19.176  1.00 25.00           C
ATOM     80  CA  ARG    80       9.804  27.993  18.175  1.00 25.00           C
ATOM     81  CA  LEU    81       9.900  27.289  14.480  1.00 25.00           C
ATOM     82  CA  LEU    82      11.922  29.995  12.740  1.00 25.00           C
ATOM     83  CA  VAL    83      13.124  31.873   9.640  1.00 25.00           C
ATOM     84  CA  VAL    84      14.061  34.106   6.794  1.00 25.00           C
ATOM     85  CA  GLY    85      13.068  34.748   3.205  1.00 25.00           C
TER
END
