
#######################################################
#                                                     #
#                        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  123 (  123),  selected  123 , name T0307TS599_4-D1
# Molecule2: number of CA atoms  123 (  939),  selected  123 , name T0307_D1.pdb
# PARAMETERS: T0307TS599_4-D1.T0307_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    I      10      I      10          3.978
LGA    -       -      M      11           -
LGA    M      11      T      12          0.600
LGA    T      12      F      13          2.949
LGA    F      13      S      14          1.523
LGA    S      14      G      15          3.524
LGA    G      15      Q      16          1.979
LGA    Q      16      -       -           -
LGA    E      17      E      17          1.175
LGA    L      18      L      18          2.044
LGA    T      19      T      19          2.082
LGA    A      20      A      20          1.288
LGA    I      21      I      21          1.252
LGA    I      22      I      22          1.889
LGA    K      23      K      23          1.032
LGA    M      24      M      24          1.884
LGA    A      25      A      25          2.542
LGA    K      26      K      26          2.105
LGA    S      27      S      27          2.924
LGA    -       -      M      28           -
LGA    M      28      V      29          2.302
LGA    -       -      M      30           -
LGA    -       -      A      31           -
LGA    -       -      D      32           -
LGA    -       -      G      33           -
LGA    -       -      K      34           -
LGA    -       -      I      35           -
LGA    -       -      K      36           -
LGA    -       -      P      37           -
LGA    V      29      A      38           #
LGA    M      30      E      39          2.986
LGA    A      31      I      40          3.939
LGA    D      32      A      41          4.158
LGA    G      33      V      42          3.214
LGA    K      34      M      43          3.975
LGA    I      35      T      44          2.830
LGA    K      36      R      45          4.736
LGA    -       -      E      46           -
LGA    -       -      F      47           -
LGA    -       -      M      48           -
LGA    -       -      R      49           -
LGA    -       -      F      50           -
LGA    -       -      G      51           -
LGA    -       -      I      52           -
LGA    -       -      L      53           -
LGA    -       -      Q      54           -
LGA    -       -      D      55           -
LGA    -       -      Q      56           -
LGA    P      37      V      57          4.641
LGA    A      38      D      58           #
LGA    E      39      L      59           -
LGA    I      40      L      60           -
LGA    A      41      L      61           -
LGA    -       -      K      62           -
LGA    -       -      A      63           -
LGA    -       -      S      64           -
LGA    -       -      D      65           -
LGA    -       -      S      66           -
LGA    -       -      I      67           -
LGA    -       -      E      68           -
LGA    -       -      A      69           -
LGA    -       -      S      70           -
LGA    -       -      Q      71           -
LGA    -       -      A      72           -
LGA    -       -      V      73           -
LGA    -       -      A      74           -
LGA    V      42      L      75           #
LGA    -       -      I      76           -
LGA    -       -      A      77           -
LGA    -       -      R      78           -
LGA    M      43      M      79          6.261
LGA    T      44      -       -           -
LGA    R      45      -       -           -
LGA    E      46      -       -           -
LGA    F      47      -       -           -
LGA    M      48      -       -           -
LGA    R      49      -       -           -
LGA    F      50      -       -           -
LGA    G      51      -       -           -
LGA    I      52      -       -           -
LGA    L      53      -       -           -
LGA    Q      54      -       -           -
LGA    D      55      -       -           -
LGA    Q      56      -       -           -
LGA    V      57      D      80          5.401
LGA    D      58      E      81          2.610
LGA    L      59      -       -           -
LGA    L      60      E      82          1.521
LGA    L      61      R      83          1.329
LGA    K      62      K      84          2.077
LGA    A      63      K      85          1.096
LGA    S      64      Y      86          0.898
LGA    D      65      V      87          2.001
LGA    S      66      A      88          1.819
LGA    I      67      S      89          1.331
LGA    E      68      Y      90          1.446
LGA    A      69      L      91          1.709
LGA    S      70      G      92          1.693
LGA    Q      71      V      93          1.351
LGA    A      72      I      94          1.221
LGA    V      73      M      95          2.160
LGA    A      74      A      96          2.567
LGA    L      75      S      97          4.097
LGA    I      76      -       -           -
LGA    A      77      -       -           -
LGA    R      78      D      98           #
LGA    M      79      G      99           -
LGA    D      80      D     100           -
LGA    E      81      I     101           -
LGA    E      82      D     102           -
LGA    R      83      D     103           -
LGA    K      84      N     104           -
LGA    K      85      E     105           -
LGA    Y      86      L     106           -
LGA    V      87      A     107           -
LGA    A      88      L     108           -
LGA    S      89      W     109           -
LGA    Y      90      T     110           -
LGA    L      91      L     111           -
LGA    G      92      I     112           -
LGA    V      93      S     113           -
LGA    I      94      T     114           -
LGA    M      95      L     115           -
LGA    A      96      C     116           -
LGA    S      97      G     117           -
LGA    D      98      L     118           -
LGA    G      99      P     119           -
LGA    D     100      T     120           -
LGA    I     101      M     121           -
LGA    D     102      T     122           -
LGA    D     103      V     123           -
LGA    N     104      M     124           -
LGA    E     105      E     125           -
LGA    L     106      A     126           -
LGA    A     107      I     127           -
LGA    L     108      N     128           -
LGA    W     109      N     129           -
LGA    T     110      M     130           -
LGA    L     111      K     131           -
LGA    I     112      N     132           -
LGA    S     113      -       -           -
LGA    T     114      -       -           -
LGA    L     115      -       -           -
LGA    C     116      -       -           -
LGA    G     117      -       -           -
LGA    L     118      -       -           -
LGA    P     119      -       -           -
LGA    T     120      -       -           -
LGA    M     121      -       -           -
LGA    T     122      -       -           -
LGA    V     123      -       -           -
LGA    M     124      -       -           -
LGA    E     125      -       -           -
LGA    A     126      -       -           -
LGA    I     127      -       -           -
LGA    N     128      -       -           -
LGA    N     129      -       -           -
LGA    M     130      -       -           -
LGA    K     131      -       -           -
LGA    N     132      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  123  123    5.0     45    2.76    33.33     24.345     1.572

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.224481 * X  +   0.795479 * Y  +  -0.562868 * Z  +  20.722023
  Y_new =  -0.841820 * X  +   0.449254 * Y  +   0.299180 * Z  +  14.877566
  Z_new =   0.490863 * X  +   0.406674 * Y  +   0.770500 * Z  +  19.178391 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.485643   -2.655949  [ DEG:    27.8253   -152.1747 ]
  Theta =  -0.513080   -2.628513  [ DEG:   -29.3973   -150.6027 ]
  Phi   =  -1.310198    1.831394  [ DEG:   -75.0688    104.9312 ]
 
# 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: T0307TS599_4-D1                               
REMARK     2: T0307_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0307TS599_4-D1.T0307_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  123  123   5.0   45   2.76   33.33  24.345
REMARK  ---------------------------------------------------------- 
MOLECULE T0307TS599_4-D1
PFRMAT TS                                                                       
TARGET T0307                                                                    
MODEL  4                                                                        
PARENT N/A                                                                      
ATOM     10  CA  ILE    10      10.146  15.929  43.275  1.00  0.00              
ATOM     11  CA  MET    11      13.073  15.499  40.828  1.00  0.00              
ATOM     12  CA  THR    12      16.539  15.691  42.271  1.00  0.00              
ATOM     13  CA  PHE    13      19.630  16.208  40.205  1.00  0.00              
ATOM     14  CA  SER    14      22.435  14.741  42.231  1.00  0.00              
ATOM     15  CA  GLY    15      25.894  14.700  40.754  1.00  0.00              
ATOM     16  CA  GLN    16      25.916  10.997  39.835  1.00  0.00              
ATOM     17  CA  GLU    17      22.565  10.974  38.031  1.00  0.00              
ATOM     18  CA  LEU    18      23.499  14.012  35.951  1.00  0.00              
ATOM     19  CA  THR    19      26.869  12.490  34.915  1.00  0.00              
ATOM     20  CA  ALA    20      25.211   9.209  33.901  1.00  0.00              
ATOM     21  CA  ILE    21      22.621  11.096  31.811  1.00  0.00              
ATOM     22  CA  ILE    22      25.426  13.094  30.107  1.00  0.00              
ATOM     23  CA  LYS    23      27.376   9.962  29.310  1.00  0.00              
ATOM     24  CA  MET    24      24.195   8.436  27.800  1.00  0.00              
ATOM     25  CA  ALA    25      23.490  11.552  25.707  1.00  0.00              
ATOM     26  CA  LYS    26      26.958  11.693  24.247  1.00  0.00              
ATOM     27  CA  SER    27      27.026   7.975  23.229  1.00  0.00              
ATOM     28  CA  MET    28      23.597   8.481  21.533  1.00  0.00              
ATOM     29  CA  VAL    29      24.279  11.733  19.626  1.00  0.00              
ATOM     30  CA  MET    30      21.519  14.327  19.379  1.00  0.00              
ATOM     31  CA  ALA    31      21.243  16.326  16.079  1.00  0.00              
ATOM     32  CA  ASP    32      17.597  17.522  16.192  1.00  0.00              
ATOM     33  CA  GLY    33      18.107  18.943  19.691  1.00  0.00              
ATOM     34  CA  LYS    34      16.530  16.164  21.698  1.00  0.00              
ATOM     35  CA  ILE    35      19.320  15.628  24.213  1.00  0.00              
ATOM     36  CA  LYS    36      20.926  18.544  25.988  1.00  0.00              
ATOM     37  CA  PRO    37      24.222  18.116  27.827  1.00  0.00              
ATOM     38  CA  ALA    38      22.750  19.098  31.199  1.00  0.00              
ATOM     39  CA  GLU    39      19.790  16.756  31.222  1.00  0.00              
ATOM     40  CA  ILE    40      19.807  15.518  34.843  1.00  0.00              
ATOM     41  CA  ALA    41      16.668  14.496  36.831  1.00  0.00              
ATOM     42  CA  VAL    42      16.704  11.383  38.991  1.00  0.00              
ATOM     43  CA  MET    43      15.017  11.139  42.429  1.00  0.00              
ATOM     44  CA  THR    44      13.127   7.906  42.887  1.00  0.00              
ATOM     45  CA  ARG    45      14.079   7.117  46.476  1.00  0.00              
ATOM     46  CA  GLU    46      13.199  10.607  47.620  1.00  0.00              
ATOM     47  CA  PHE    47       9.778  10.544  45.938  1.00  0.00              
ATOM     48  CA  MET    48       8.970   7.133  47.522  1.00  0.00              
ATOM     49  CA  ARG    49      10.149   8.477  50.886  1.00  0.00              
ATOM     50  CA  PHE    50       7.641  11.410  50.689  1.00  0.00              
ATOM     51  CA  GLY    51       4.839   9.054  49.833  1.00  0.00              
ATOM     52  CA  ILE    52       3.563  10.400  46.575  1.00  0.00              
ATOM     53  CA  LEU    53       2.543   7.034  45.067  1.00  0.00              
ATOM     54  CA  GLN    54       5.579   4.786  45.661  1.00  0.00              
ATOM     55  CA  ASP    55       4.712   2.444  42.761  1.00  0.00              
ATOM     56  CA  GLN    56       3.992   5.579  40.708  1.00  0.00              
ATOM     57  CA  VAL    57       7.438   7.192  41.210  1.00  0.00              
ATOM     58  CA  ASP    58       9.930   4.374  40.492  1.00  0.00              
ATOM     59  CA  LEU    59       7.686   3.414  37.505  1.00  0.00              
ATOM     60  CA  LEU    60       7.732   6.942  35.974  1.00  0.00              
ATOM     61  CA  LEU    61      11.532   6.977  36.336  1.00  0.00              
ATOM     62  CA  LYS    62      12.008   3.563  34.677  1.00  0.00              
ATOM     63  CA  ALA    63       9.735   4.711  31.831  1.00  0.00              
ATOM     64  CA  SER    64      11.628   7.990  31.328  1.00  0.00              
ATOM     65  CA  ASP    65      14.859   6.099  30.652  1.00  0.00              
ATOM     66  CA  SER    66      13.086   3.839  28.120  1.00  0.00              
ATOM     67  CA  ILE    67      11.342   6.418  25.943  1.00  0.00              
ATOM     68  CA  GLU    68      14.482   8.559  25.804  1.00  0.00              
ATOM     69  CA  ALA    69      16.772   5.762  24.610  1.00  0.00              
ATOM     70  CA  SER    70      14.583   4.618  21.791  1.00  0.00              
ATOM     71  CA  GLN    71      14.026   8.130  20.417  1.00  0.00              
ATOM     72  CA  ALA    72      17.693   9.060  20.425  1.00  0.00              
ATOM     73  CA  VAL    73      19.229   6.171  18.483  1.00  0.00              
ATOM     74  CA  ALA    74      16.506   6.578  15.872  1.00  0.00              
ATOM     75  CA  LEU    75      17.061  10.317  15.537  1.00  0.00              
ATOM     76  CA  ILE    76      20.808   9.950  15.060  1.00  0.00              
ATOM     77  CA  ALA    77      20.356   7.336  12.416  1.00  0.00              
ATOM     78  CA  ARG    78      17.889   9.549  10.455  1.00  0.00              
ATOM     79  CA  MET    79      20.104  12.675  10.515  1.00  0.00              
ATOM     80  CA  ASP    80      23.130  10.661   9.271  1.00  0.00              
ATOM     81  CA  GLU    81      21.150   9.047   6.408  1.00  0.00              
ATOM     82  CA  GLU    82      19.850  12.472   5.284  1.00  0.00              
ATOM     83  CA  ARG    83      23.399  13.890   5.365  1.00  0.00              
ATOM     84  CA  LYS    84      24.622  10.902   3.295  1.00  0.00              
ATOM     85  CA  LYS    85      21.898  11.331   0.693  1.00  0.00              
ATOM     86  CA  TYR    86      22.684  15.064   0.366  1.00  0.00              
ATOM     87  CA  VAL    87      26.396  14.348   0.012  1.00  0.00              
ATOM     88  CA  ALA    88      25.914  11.707  -2.764  1.00  0.00              
ATOM     89  CA  SER    89      23.686  14.076  -4.697  1.00  0.00              
ATOM     90  CA  TYR    90      26.174  16.917  -4.381  1.00  0.00              
ATOM     91  CA  LEU    91      29.220  14.817  -5.421  1.00  0.00              
ATOM     92  CA  GLY    92      27.205  13.452  -8.319  1.00  0.00              
ATOM     93  CA  VAL    93      26.533  17.071  -9.418  1.00  0.00              
ATOM     94  CA  ILE    94      29.766  19.019  -8.834  1.00  0.00              
ATOM     95  CA  MET    95      29.232  22.678  -8.180  1.00  0.00              
ATOM     96  CA  ALA    96      32.048  25.159  -8.202  1.00  0.00              
ATOM     97  CA  SER    97      31.338  28.905  -7.860  1.00  0.00              
ATOM     98  CA  ASP    98      31.845  30.216 -11.422  1.00  0.00              
ATOM     99  CA  GLY    99      29.639  27.576 -12.989  1.00  0.00              
ATOM    100  CA  ASP   100      32.268  25.763 -15.063  1.00  0.00              
ATOM    101  CA  ILE   101      31.884  22.372 -13.581  1.00  0.00              
ATOM    102  CA  ASP   102      31.363  19.292 -15.646  1.00  0.00              
ATOM    103  CA  ASP   103      28.410  17.151 -14.638  1.00  0.00              
ATOM    104  CA  ASN   104      30.495  14.431 -12.883  1.00  0.00              
ATOM    105  CA  GLU   105      32.928  16.773 -11.248  1.00  0.00              
ATOM    106  CA  LEU   106      33.955  19.564  -9.081  1.00  0.00              
ATOM    107  CA  ALA   107      32.267  20.717  -5.938  1.00  0.00              
ATOM    108  CA  LEU   108      33.462  24.015  -4.406  1.00  0.00              
ATOM    109  CA  TRP   109      32.137  23.845  -0.841  1.00  0.00              
ATOM    110  CA  THR   110      33.225  20.195  -0.966  1.00  0.00              
ATOM    111  CA  LEU   111      36.821  21.201  -1.707  1.00  0.00              
ATOM    112  CA  ILE   112      36.885  23.826   1.050  1.00  0.00              
ATOM    113  CA  SER   113      35.160  21.457   3.465  1.00  0.00              
ATOM    114  CA  THR   114      37.797  18.855   2.873  1.00  0.00              
ATOM    115  CA  LEU   115      40.673  21.207   3.440  1.00  0.00              
ATOM    116  CA  CYS   116      39.057  22.808   6.530  1.00  0.00              
ATOM    117  CA  GLY   117      37.685  19.687   8.077  1.00  0.00              
ATOM    118  CA  LEU   118      34.027  20.777   7.621  1.00  0.00              
ATOM    119  CA  PRO   119      31.845  17.747   7.777  1.00  0.00              
ATOM    120  CA  THR   120      30.085  16.872   4.599  1.00  0.00              
ATOM    121  CA  MET   121      26.426  17.054   5.863  1.00  0.00              
ATOM    122  CA  THR   122      27.165  20.628   7.033  1.00  0.00              
ATOM    123  CA  VAL   123      28.952  21.811   3.860  1.00  0.00              
ATOM    124  CA  MET   124      26.223  20.476   1.620  1.00  0.00              
ATOM    125  CA  GLU   125      23.620  22.364   3.708  1.00  0.00              
ATOM    126  CA  ALA   126      25.612  25.561   3.462  1.00  0.00              
ATOM    127  CA  ILE   127      25.976  25.328  -0.310  1.00  0.00              
ATOM    128  CA  ASN   128      22.232  24.696  -0.661  1.00  0.00              
ATOM    129  CA  ASN   129      21.417  27.721   1.409  1.00  0.00              
ATOM    130  CA  MET   130      23.719  30.058  -0.606  1.00  0.00              
ATOM    131  CA  LYS   131      21.833  28.543  -4.065  1.00  0.00              
ATOM    132  CA  ASN   132      23.220  31.130  -2.009  1.00  0.00              
TER                                                                             
END
