
#######################################################
#                                                     #
#                        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   27 (  207),  selected   27 , name T0348TS389_4
# Molecule2: number of CA atoms   61 (  465),  selected   61 , name T0348.pdb
# PARAMETERS: T0348TS389_4.T0348.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      D       2           -
LGA    -       -      A       3           -
LGA    -       -      K       4           -
LGA    -       -      F       5           -
LGA    -       -      L       6           -
LGA    -       -      E       7           -
LGA    -       -      I       8           -
LGA    -       -      L       9           -
LGA    -       -      V      10           -
LGA    C      11      C      11          1.050
LGA    P      12      P      12          1.681
LGA    L      13      L      13          1.300
LGA    C      14      C      14          1.154
LGA    K      15      K      15          4.778
LGA    G      16      G      16          1.513
LGA    P      17      P      17          1.540
LGA    L      18      L      18          2.020
LGA    V      19      V      19          1.401
LGA    F      20      F      20          0.986
LGA    D      21      D      21          1.271
LGA    K      22      K      22          1.909
LGA    S      23      S      23          3.005
LGA    K      24      K      24          2.103
LGA    D      25      D      25          4.465
LGA    E      26      E      26          1.440
LGA    L      27      L      27          1.375
LGA    I      28      I      28          1.055
LGA    C      29      C      29          0.329
LGA    K      30      K      30          1.491
LGA    G      31      G      31          1.248
LGA    D      32      D      32          0.930
LGA    R      33      R      33          0.983
LGA    L      34      L      34          0.502
LGA    A      35      A      35          0.933
LGA    F      36      F      36          1.012
LGA    P      37      P      37          0.921
LGA    -       -      I      38           -
LGA    -       -      K      39           -
LGA    -       -      D      40           -
LGA    -       -      G      41           -
LGA    -       -      I      42           -
LGA    -       -      P      43           -
LGA    -       -      M      44           -
LGA    -       -      M      45           -
LGA    -       -      L      46           -
LGA    -       -      E      47           -
LGA    -       -      S      48           -
LGA    -       -      E      49           -
LGA    -       -      A      50           -
LGA    -       -      R      51           -
LGA    -       -      E      52           -
LGA    -       -      L      53           -
LGA    -       -      A      54           -
LGA    -       -      P      55           -
LGA    -       -      E      56           -
LGA    -       -      E      57           -
LGA    -       -      E      58           -
LGA    -       -      V      59           -
LGA    -       -      K      60           -
LGA    -       -      L      61           -
LGA    -       -      E      62           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   27   61    5.0     27    1.86   100.00     40.789     1.374

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.447878 * X  +   0.679449 * Y  +   0.581167 * Z  +  12.032256
  Y_new =   0.545764 * X  +  -0.307104 * Y  +   0.779634 * Z  +  27.499804
  Z_new =   0.708200 * X  +   0.666360 * Y  +  -0.233274 * Z  +  39.647381 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.907535   -1.234058  [ DEG:   109.2937    -70.7063 ]
  Theta =  -0.786945   -2.354647  [ DEG:   -45.0886   -134.9114 ]
  Phi   =   2.257998   -0.883594  [ DEG:   129.3738    -50.6262 ]
 
# 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: T0348TS389_4                                  
REMARK     2: T0348.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0348TS389_4.T0348.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   27   61   5.0   27   1.86  100.00  40.789
REMARK  ---------------------------------------------------------- 
MOLECULE T0348TS389_4
PFRMAT TS
TARGET T0348
MODEL  4
PARENT N/A
ATOM      2  N   CYS    11       7.084  30.954  60.675  1.00  0.00
ATOM      3  CA  CYS    11       6.209  29.796  60.805  1.00  0.00
ATOM      4  CB  CYS    11       6.962  28.625  61.442  1.00  0.00
ATOM      5  SG  CYS    11       8.233  27.891  60.387  1.00  0.00
ATOM      6  O   CYS    11       5.153  30.699  62.765  1.00  0.00
ATOM      7  C   CYS    11       5.002  30.128  61.686  1.00  0.00
ATOM      8  N   PRO    12       3.783  29.774  61.236  1.00  0.00
ATOM      9  CA  PRO    12       2.556  30.044  61.994  1.00  0.00
ATOM     10  CB  PRO    12       1.454  29.382  61.161  1.00  0.00
ATOM     11  CG  PRO    12       1.975  29.412  59.763  1.00  0.00
ATOM     12  CD  PRO    12       3.451  29.147  59.863  1.00  0.00
ATOM     13  O   PRO    12       2.092  30.062  64.349  1.00  0.00
ATOM     14  C   PRO    12       2.595  29.460  63.400  1.00  0.00
ATOM     15  N   LEU    13       3.194  28.283  63.528  1.00  0.00
ATOM     16  CA  LEU    13       3.294  27.611  64.819  1.00  0.00
ATOM     17  CB  LEU    13       3.012  26.114  64.669  1.00  0.00
ATOM     18  CG  LEU    13       1.624  25.735  64.143  1.00  0.00
ATOM     19  CD1 LEU    13       1.514  24.231  63.952  1.00  0.00
ATOM     20  CD2 LEU    13       0.542  26.172  65.119  1.00  0.00
ATOM     21  O   LEU    13       5.018  27.096  66.409  1.00  0.00
ATOM     22  C   LEU    13       4.687  27.763  65.430  1.00  0.00
ATOM     23  N   CYS    14       5.501  28.643  64.852  1.00  0.00
ATOM     24  CA  CYS    14       6.852  28.872  65.356  1.00  0.00
ATOM     25  CB  CYS    14       7.832  27.877  64.731  1.00  0.00
ATOM     26  SG  CYS    14       9.480  27.885  65.475  1.00  0.00
ATOM     27  O   CYS    14       7.940  30.510  63.977  1.00  0.00
ATOM     28  C   CYS    14       7.328  30.284  65.020  1.00  0.00
ATOM     29  N   LYS    15       9.554  32.249  66.859  1.00  0.00
ATOM     30  CA  LYS    15      10.991  32.348  67.084  1.00  0.00
ATOM     31  CB  LYS    15      11.374  31.674  68.402  1.00  0.00
ATOM     32  CG  LYS    15      10.905  32.422  69.640  1.00  0.00
ATOM     33  CD  LYS    15      11.321  31.700  70.911  1.00  0.00
ATOM     34  CE  LYS    15      10.830  32.433  72.149  1.00  0.00
ATOM     35  NZ  LYS    15      11.203  31.720  73.403  1.00  0.00
ATOM     36  O   LYS    15      12.810  32.150  65.529  1.00  0.00
ATOM     37  C   LYS    15      11.762  31.668  65.958  1.00  0.00
ATOM     38  N   GLY    16      11.235  30.543  65.484  1.00  0.00
ATOM     39  CA  GLY    16      11.873  29.794  64.407  1.00  0.00
ATOM     40  O   GLY    16      10.105  30.123  62.818  1.00  0.00
ATOM     41  C   GLY    16      11.310  30.205  63.052  1.00  0.00
ATOM     42  N   PRO    17      12.190  30.650  62.161  1.00  0.00
ATOM     43  CA  PRO    17      11.777  31.074  60.829  1.00  0.00
ATOM     44  CB  PRO    17      12.542  32.380  60.605  1.00  0.00
ATOM     45  CG  PRO    17      13.801  32.216  61.387  1.00  0.00
ATOM     46  CD  PRO    17      13.468  31.285  62.520  1.00  0.00
ATOM     47  O   PRO    17      13.250  29.502  59.772  1.00  0.00
ATOM     48  C   PRO    17      12.139  30.032  59.779  1.00  0.00
ATOM     49  N   LEU    18      11.193  29.744  58.891  1.00  0.00
ATOM     50  CA  LEU    18      11.415  28.767  57.830  1.00  0.00
ATOM     51  CB  LEU    18      10.174  28.648  56.943  1.00  0.00
ATOM     52  CG  LEU    18       8.910  28.103  57.614  1.00  0.00
ATOM     53  CD1 LEU    18       7.721  28.184  56.670  1.00  0.00
ATOM     54  CD2 LEU    18       9.100  26.649  58.019  1.00  0.00
ATOM     55  O   LEU    18      12.523  30.184  56.241  1.00  0.00
ATOM     56  C   LEU    18      12.593  29.183  56.954  1.00  0.00
ATOM     57  N   VAL    19      13.675  28.414  57.011  1.00  0.00
ATOM     58  CA  VAL    19      14.863  28.711  56.220  1.00  0.00
ATOM     59  CB  VAL    19      16.090  27.934  56.733  1.00  0.00
ATOM     60  CG1 VAL    19      16.383  28.296  58.180  1.00  0.00
ATOM     61  CG2 VAL    19      15.842  26.435  56.653  1.00  0.00
ATOM     62  O   VAL    19      13.797  27.503  54.447  1.00  0.00
ATOM     63  C   VAL    19      14.649  28.332  54.762  1.00  0.00
ATOM     64  N   PHE    20      15.425  28.942  53.872  1.00  0.00
ATOM     65  CA  PHE    20      15.314  28.664  52.445  1.00  0.00
ATOM     66  CB  PHE    20      14.881  29.920  51.687  1.00  0.00
ATOM     67  CG  PHE    20      15.876  31.043  51.754  1.00  0.00
ATOM     68  CD1 PHE    20      16.876  31.158  50.804  1.00  0.00
ATOM     69  CD2 PHE    20      15.814  31.982  52.768  1.00  0.00
ATOM     70  CE1 PHE    20      17.793  32.191  50.866  1.00  0.00
ATOM     71  CE2 PHE    20      16.730  33.016  52.831  1.00  0.00
ATOM     72  CZ  PHE    20      17.716  33.123  51.884  1.00  0.00
ATOM     73  O   PHE    20      17.711  28.656  52.295  1.00  0.00
ATOM     74  C   PHE    20      16.648  28.199  51.873  1.00  0.00
ATOM     75  N   ASP    21      16.587  27.291  50.904  1.00  0.00
ATOM     76  CA  ASP    21      17.790  26.764  50.271  1.00  0.00
ATOM     77  CB  ASP    21      17.498  25.417  49.608  1.00  0.00
ATOM     78  CG  ASP    21      17.122  24.342  50.609  1.00  0.00
ATOM     79  OD1 ASP    21      17.793  24.248  51.659  1.00  0.00
ATOM     80  OD2 ASP    21      16.156  23.597  50.346  1.00  0.00
ATOM     81  O   ASP    21      17.911  28.888  49.158  1.00  0.00
ATOM     82  C   ASP    21      18.303  27.723  49.199  1.00  0.00
ATOM     83  N   LYS    22      19.186  27.226  48.337  1.00  0.00
ATOM     84  CA  LYS    22      19.754  28.041  47.271  1.00  0.00
ATOM     85  CB  LYS    22      21.197  27.622  46.985  1.00  0.00
ATOM     86  CG  LYS    22      22.157  27.878  48.137  1.00  0.00
ATOM     87  CD  LYS    22      23.577  27.481  47.771  1.00  0.00
ATOM     88  CE  LYS    22      24.531  27.712  48.932  1.00  0.00
ATOM     89  NZ  LYS    22      25.922  27.299  48.597  1.00  0.00
ATOM     90  O   LYS    22      18.891  28.814  45.167  1.00  0.00
ATOM     91  C   LYS    22      18.952  27.891  45.981  1.00  0.00
ATOM     92  N   SER    23      18.338  26.723  45.800  1.00  0.00
ATOM     93  CA  SER    23      17.538  26.445  44.617  1.00  0.00
ATOM     94  CB  SER    23      18.333  26.747  43.346  1.00  0.00
ATOM     95  OG  SER    23      17.586  26.425  42.187  1.00  0.00
ATOM     96  O   SER    23      17.963  24.080  44.604  1.00  0.00
ATOM     97  C   SER    23      17.123  24.981  44.589  1.00  0.00
ATOM     98  N   LYS    24      15.821  24.757  44.549  1.00  0.00
ATOM     99  CA  LYS    24      15.261  23.408  44.519  1.00  0.00
ATOM    100  CB  LYS    24      16.029  22.532  43.528  1.00  0.00
ATOM    101  CG  LYS    24      16.025  23.057  42.103  1.00  0.00
ATOM    102  CD  LYS    24      16.589  22.030  41.134  1.00  0.00
ATOM    103  CE  LYS    24      16.689  22.597  39.727  1.00  0.00
ATOM    104  NZ  LYS    24      17.263  21.609  38.770  1.00  0.00
ATOM    105  O   LYS    24      15.405  21.525  46.000  1.00  0.00
ATOM    106  C   LYS    24      15.336  22.748  45.893  1.00  0.00
ATOM    107  N   ASP    25      15.323  23.567  46.940  1.00  0.00
ATOM    108  CA  ASP    25      15.389  23.044  48.292  1.00  0.00
ATOM    109  CB  ASP    25      16.605  23.613  49.028  1.00  0.00
ATOM    110  CG  ASP    25      17.918  23.152  48.426  1.00  0.00
ATOM    111  OD1 ASP    25      18.289  23.665  47.349  1.00  0.00
ATOM    112  OD2 ASP    25      18.575  22.280  49.029  1.00  0.00
ATOM    113  O   ASP    25      13.923  22.787  50.164  1.00  0.00
ATOM    114  C   ASP    25      14.163  23.389  49.116  1.00  0.00
ATOM    115  N   GLU    26      13.380  24.360  48.647  1.00  0.00
ATOM    116  CA  GLU    26      12.174  24.781  49.350  1.00  0.00
ATOM    117  CB  GLU    26      11.280  23.576  49.649  1.00  0.00
ATOM    118  CG  GLU    26      11.895  22.570  50.610  1.00  0.00
ATOM    119  CD  GLU    26      11.015  21.355  50.825  1.00  0.00
ATOM    120  OE1 GLU    26       9.936  21.284  50.199  1.00  0.00
ATOM    121  OE2 GLU    26      11.402  20.472  51.620  1.00  0.00
ATOM    122  O   GLU    26      13.692  25.703  50.966  1.00  0.00
ATOM    123  C   GLU    26      12.521  25.457  50.672  1.00  0.00
ATOM    124  N   LEU    27      11.497  25.754  51.465  1.00  0.00
ATOM    125  CA  LEU    27      11.692  26.400  52.758  1.00  0.00
ATOM    126  CB  LEU    27      10.906  27.710  52.827  1.00  0.00
ATOM    127  CG  LEU    27      11.270  28.774  51.791  1.00  0.00
ATOM    128  CD1 LEU    27      10.331  29.966  51.889  1.00  0.00
ATOM    129  CD2 LEU    27      12.693  29.271  52.007  1.00  0.00
ATOM    130  O   LEU    27      10.039  25.138  53.956  1.00  0.00
ATOM    131  C   LEU    27      11.215  25.494  53.890  1.00  0.00
ATOM    132  N   ILE    28      12.134  25.114  54.773  1.00  0.00
ATOM    133  CA  ILE    28      11.813  24.244  55.882  1.00  0.00
ATOM    134  CB  ILE    28      12.777  23.047  55.959  1.00  0.00
ATOM    135  CG1 ILE    28      14.214  23.532  56.161  1.00  0.00
ATOM    136  CG2 ILE    28      12.716  22.231  54.677  1.00  0.00
ATOM    137  CD1 ILE    28      15.200  22.418  56.445  1.00  0.00
ATOM    138  O   ILE    28      12.599  25.976  57.347  1.00  0.00
ATOM    139  C   ILE    28      11.894  24.978  57.218  1.00  0.00
ATOM    140  N   CYS    29      11.170  24.470  58.215  1.00  0.00
ATOM    141  CA  CYS    29      11.168  25.077  59.541  1.00  0.00
ATOM    142  CB  CYS    29       9.756  25.072  60.131  1.00  0.00
ATOM    143  SG  CYS    29       8.557  26.057  59.204  1.00  0.00
ATOM    144  O   CYS    29      12.086  23.075  60.493  1.00  0.00
ATOM    145  C   CYS    29      12.088  24.304  60.488  1.00  0.00
ATOM    146  N   LYS    30      12.896  25.014  61.296  1.00  0.00
ATOM    147  CA  LYS    30      13.826  24.376  62.235  1.00  0.00
ATOM    148  CB  LYS    30      14.868  25.385  62.728  1.00  0.00
ATOM    149  CG  LYS    30      15.802  25.892  61.640  1.00  0.00
ATOM    150  CD  LYS    30      16.806  26.887  62.195  1.00  0.00
ATOM    151  CE  LYS    30      17.716  27.423  61.102  1.00  0.00
ATOM    152  NZ  LYS    30      18.691  28.417  61.629  1.00  0.00
ATOM    153  O   LYS    30      13.790  23.273  64.368  1.00  0.00
ATOM    154  C   LYS    30      13.134  23.808  63.474  1.00  0.00
ATOM    155  N   GLY    31      11.808  23.925  63.526  1.00  0.00
ATOM    156  CA  GLY    31      11.044  23.420  64.660  1.00  0.00
ATOM    157  O   GLY    31      10.424  21.110  64.470  1.00  0.00
ATOM    158  C   GLY    31      10.120  22.279  64.233  1.00  0.00
ATOM    159  N   ASP    32       8.994  22.615  63.600  1.00  0.00
ATOM    160  CA  ASP    32       8.054  21.591  63.148  1.00  0.00
ATOM    161  CB  ASP    32       6.761  22.236  62.644  1.00  0.00
ATOM    162  CG  ASP    32       5.915  22.801  63.767  1.00  0.00
ATOM    163  OD1 ASP    32       6.196  22.481  64.941  1.00  0.00
ATOM    164  OD2 ASP    32       4.972  23.566  63.474  1.00  0.00
ATOM    165  O   ASP    32       8.123  19.712  61.657  1.00  0.00
ATOM    166  C   ASP    32       8.650  20.768  62.012  1.00  0.00
ATOM    167  N   ARG    33       9.750  21.252  61.439  1.00  0.00
ATOM    168  CA  ARG    33      10.386  20.540  60.349  1.00  0.00
ATOM    169  CB  ARG    33      10.800  19.135  60.793  1.00  0.00
ATOM    170  CG  ARG    33      11.766  19.116  61.966  1.00  0.00
ATOM    171  CD  ARG    33      12.100  17.693  62.383  1.00  0.00
ATOM    172  NE  ARG    33      12.963  17.026  61.412  1.00  0.00
ATOM    173  CZ  ARG    33      14.285  17.155  61.375  1.00  0.00
ATOM    174  NH1 ARG    33      14.990  16.510  60.455  1.00  0.00
ATOM    175  NH2 ARG    33      14.901  17.928  62.259  1.00  0.00
ATOM    176  O   ARG    33       9.246  19.279  58.670  1.00  0.00
ATOM    177  C   ARG    33       9.468  20.389  59.154  1.00  0.00
ATOM    178  N   LEU    34       8.933  21.508  58.676  1.00  0.00
ATOM    179  CA  LEU    34       8.035  21.486  57.530  1.00  0.00
ATOM    180  CB  LEU    34       6.910  22.510  57.712  1.00  0.00
ATOM    181  CG  LEU    34       6.037  22.342  58.956  1.00  0.00
ATOM    182  CD1 LEU    34       5.002  23.454  59.041  1.00  0.00
ATOM    183  CD2 LEU    34       5.301  21.010  58.922  1.00  0.00
ATOM    184  O   LEU    34       9.992  22.090  56.288  1.00  0.00
ATOM    185  C   LEU    34       8.791  21.826  56.251  1.00  0.00
ATOM    186  N   ALA    35       8.081  21.815  55.129  1.00  0.00
ATOM    187  CA  ALA    35       8.683  22.117  53.837  1.00  0.00
ATOM    188  CB  ALA    35       9.128  20.838  53.146  1.00  0.00
ATOM    189  O   ALA    35       6.921  22.192  52.209  1.00  0.00
ATOM    190  C   ALA    35       7.691  22.831  52.923  1.00  0.00
ATOM    191  N   PHE    36       7.716  24.161  52.951  1.00  0.00
ATOM    192  CA  PHE    36       6.818  24.956  52.124  1.00  0.00
ATOM    193  CB  PHE    36       6.329  26.186  52.892  1.00  0.00
ATOM    194  CG  PHE    36       5.432  25.859  54.052  1.00  0.00
ATOM    195  CD1 PHE    36       5.954  25.692  55.323  1.00  0.00
ATOM    196  CD2 PHE    36       4.067  25.717  53.872  1.00  0.00
ATOM    197  CE1 PHE    36       5.130  25.391  56.390  1.00  0.00
ATOM    198  CE2 PHE    36       3.243  25.417  54.938  1.00  0.00
ATOM    199  CZ  PHE    36       3.769  25.253  56.194  1.00  0.00
ATOM    200  O   PHE    36       8.621  25.980  50.910  1.00  0.00
ATOM    201  C   PHE    36       7.517  25.438  50.855  1.00  0.00
ATOM    202  N   PRO    37       6.866  25.234  49.715  1.00  0.00
ATOM    203  CA  PRO    37       7.441  25.654  48.449  1.00  0.00
ATOM    204  CB  PRO    37       8.377  26.802  48.828  1.00  0.00
ATOM    205  CG  PRO    37       8.858  26.453  50.198  1.00  0.00
ATOM    206  CD  PRO    37       7.692  25.817  50.899  1.00  0.00
ATOM    207  O   PRO    37       9.424  24.621  47.601  1.00  0.00
ATOM    208  C   PRO    37       8.205  24.540  47.762  1.00  0.00
TER
END
