
#######################################################
#                                                     #
#                        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  126 (  126),  selected  126 , name T0372TS393_4-D1
# Molecule2: number of CA atoms  126 ( 1027),  selected  126 , name T0372_D1.pdb
# PARAMETERS: T0372TS393_4-D1.T0372_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      M       1           -
LGA    I       2      I       2           -
LGA    P       3      P       3           -
LGA    F       4      F       4           -
LGA    K       5      K       5           -
LGA    D       6      D       6           -
LGA    I       7      I       7           -
LGA    T       8      T       8           -
LGA    L       9      L       9           -
LGA    A      10      A      10           -
LGA    D      11      D      11           -
LGA    R      12      R      12           -
LGA    D      13      D      13           -
LGA    T      14      T      14           -
LGA    I      15      I      15           -
LGA    T      16      T      16           -
LGA    A      17      A      17           -
LGA    F      18      F      18           -
LGA    T      19      T      19           -
LGA    M      20      M      20           -
LGA    K      21      -       -           -
LGA    S      22      -       -           -
LGA    D      23      -       -           -
LGA    R      24      K      21           #
LGA    R      25      S      22          3.783
LGA    N      26      D      23          1.652
LGA    C      27      R      24          2.799
LGA    D      28      R      25          4.344
LGA    L      29      N      26          1.654
LGA    S      30      C      27          3.301
LGA    F      31      D      28          3.281
LGA    S      32      -       -           -
LGA    N      33      -       -           -
LGA    L      34      L      29          3.704
LGA    C      35      S      30           -
LGA    S      36      -       -           -
LGA    W      37      -       -           -
LGA    R      38      -       -           -
LGA    F      39      -       -           -
LGA    L      40      -       -           -
LGA    Y      41      -       -           -
LGA    D      42      -       -           -
LGA    T      43      -       -           -
LGA    Q      44      -       -           -
LGA    F      45      -       -           -
LGA    A      46      F      31           #
LGA    -       -      S      32           -
LGA    -       -      N      33           -
LGA    V      47      L      34           #
LGA    I      48      C      35          4.591
LGA    D      49      S      36           #
LGA    D      50      W      37           -
LGA    F      51      -       -           -
LGA    L      52      -       -           -
LGA    V      53      R      38          5.144
LGA    -       -      F      39           -
LGA    -       -      L      40           -
LGA    -       -      Y      41           -
LGA    -       -      D      42           -
LGA    -       -      T      43           -
LGA    -       -      Q      44           -
LGA    -       -      F      45           -
LGA    -       -      A      46           -
LGA    -       -      V      47           -
LGA    -       -      I      48           -
LGA    -       -      D      49           -
LGA    -       -      D      50           -
LGA    -       -      F      51           -
LGA    -       -      L      52           -
LGA    -       -      V      53           -
LGA    -       -      F      54           -
LGA    F      54      K      55          2.127
LGA    K      55      F      56          2.335
LGA    F      56      W      57          1.787
LGA    W      57      A      58          2.707
LGA    A      58      G      59          4.342
LGA    G      59      E      60          4.341
LGA    E      60      -       -           -
LGA    Q      61      -       -           -
LGA    L      62      Q      61          2.123
LGA    A      63      L      62           #
LGA    Y      64      A      63          3.245
LGA    M      65      Y      64          3.992
LGA    M      66      M      65          4.220
LGA    P      67      M      66          3.171
LGA    V      68      -       -           -
LGA    G      69      P      67          2.948
LGA    N      70      V      68           #
LGA    G      71      G      69           -
LGA    D      72      N      70           #
LGA    L      73      G      71          4.708
LGA    K      74      D      72          3.168
LGA    A      75      -       -           -
LGA    V      76      L      73          1.876
LGA    L      77      K      74          1.449
LGA    R      78      A      75          0.674
LGA    K      79      V      76          0.557
LGA    L      80      L      77          1.690
LGA    I      81      R      78          2.019
LGA    E      82      K      79          1.353
LGA    D      83      L      80          1.472
LGA    A      84      I      81          2.536
LGA    D      85      E      82          2.527
LGA    K      86      D      83          1.615
LGA    E      87      A      84          3.517
LGA    -       -      D      85           -
LGA    -       -      K      86           -
LGA    -       -      E      87           -
LGA    -       -      K      88           -
LGA    -       -      H      89           -
LGA    -       -      N      90           -
LGA    -       -      F      91           -
LGA    K      88      C      92          4.886
LGA    H      89      M      93          3.700
LGA    N      90      L      94           #
LGA    -       -      G      95           -
LGA    F      91      V      96          4.843
LGA    -       -      C      97           -
LGA    -       -      S      98           -
LGA    -       -      N      99           -
LGA    C      92      M     100          4.991
LGA    M      93      R     101          4.421
LGA    L      94      A     102           -
LGA    G      95      D     103           -
LGA    V      96      L     104           -
LGA    C      97      -       -           -
LGA    S      98      -       -           -
LGA    N      99      -       -           -
LGA    M     100      -       -           -
LGA    R     101      -       -           -
LGA    A     102      -       -           -
LGA    D     103      -       -           -
LGA    L     104      -       -           -
LGA    E     105      -       -           -
LGA    A     106      -       -           -
LGA    I     107      -       -           -
LGA    L     108      E     105           #
LGA    P     109      -       -           -
LGA    E     110      -       -           -
LGA    R     111      A     106           #
LGA    F     112      I     107          3.136
LGA    I     113      L     108          1.424
LGA    -       -      P     109           -
LGA    -       -      E     110           -
LGA    F     114      R     111          4.577
LGA    T     115      F     112          3.646
LGA    -       -      I     113           -
LGA    -       -      F     114           -
LGA    -       -      T     115           -
LGA    -       -      E     116           -
LGA    -       -      D     117           -
LGA    -       -      K     290           -
LGA    -       -      Y     291           -
LGA    -       -      M     292           -
LGA    -       -      A     293           -
LGA    -       -      C     294           -
LGA    -       -      L     295           -
LGA    E     116      K     296          4.821
LGA    D     117      D     297          2.449
LGA    K     290      H     298           -
LGA    Y     291      -       -           -
LGA    M     292      -       -           -
LGA    A     293      -       -           -
LGA    C     294      -       -           -
LGA    L     295      -       -           -
LGA    K     296      -       -           -
LGA    D     297      -       -           -
LGA    H     298      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  126  126    5.0     47    3.30     8.51     21.362     1.381

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.035480 * X  +  -0.722037 * Y  +   0.690944 * Z  +  34.493073
  Y_new =   0.560568 * X  +  -0.586750 * Y  +  -0.584369 * Z  +  47.175694
  Z_new =   0.827348 * X  +   0.366587 * Y  +   0.425570 * Z  +   8.734093 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.711078   -2.430515  [ DEG:    40.7418   -139.2582 ]
  Theta =  -0.974369   -2.167223  [ DEG:   -55.8272   -124.1728 ]
  Phi   =   1.634006   -1.507587  [ DEG:    93.6216    -86.3784 ]
 
# 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: T0372TS393_4-D1                               
REMARK     2: T0372_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0372TS393_4-D1.T0372_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  126  126   5.0   47   3.30    8.51  21.362
REMARK  ---------------------------------------------------------- 
MOLECULE T0372TS393_4-D1
PFRMAT TS
TARGET T0372
MODEL 4
PARENT N/A
ATOM      1  CA  MET     1       2.342  65.969  -5.006  1.00 25.00           C
ATOM      2  CA  ILE     2       3.550  62.369  -5.419  1.00 25.00           C
ATOM      3  CA  PRO     3       0.340  60.388  -6.091  1.00 25.00           C
ATOM      4  CA  PHE     4       0.943  57.923  -3.274  1.00 25.00           C
ATOM      5  CA  LYS     5       1.050  56.050   0.023  1.00 25.00           C
ATOM      6  CA  ASP     6       2.716  57.448   3.102  1.00 25.00           C
ATOM      7  CA  ILE     7       4.983  55.336   5.288  1.00 25.00           C
ATOM      8  CA  THR     8       3.122  52.110   6.289  1.00 25.00           C
ATOM      9  CA  LEU     9       4.740  52.617   9.727  1.00 25.00           C
ATOM     10  CA  ALA    10       7.916  51.707   7.913  1.00 25.00           C
ATOM     11  CA  ASP    11      11.586  51.454   6.905  1.00 25.00           C
ATOM     12  CA  ARG    12      10.905  55.220   7.066  1.00 25.00           C
ATOM     13  CA  ASP    13      11.045  55.107  10.891  1.00 25.00           C
ATOM     14  CA  THR    14      14.371  53.214  10.738  1.00 25.00           C
ATOM     15  CA  ILE    15      15.769  55.816   8.301  1.00 25.00           C
ATOM     16  CA  THR    16      14.652  58.639  10.635  1.00 25.00           C
ATOM     17  CA  ALA    17      16.335  56.889  13.597  1.00 25.00           C
ATOM     18  CA  PHE    18      19.561  56.507  11.569  1.00 25.00           C
ATOM     19  CA  THR    19      19.450  60.223  10.647  1.00 25.00           C
ATOM     20  CA  MET    20      18.956  61.148  14.331  1.00 25.00           C
ATOM     21  CA  LYS    21      17.592  64.411  15.709  1.00 25.00           C
ATOM     22  CA  SER    22      20.865  65.347  17.455  1.00 25.00           C
ATOM     23  CA  ASP    23      24.556  64.771  17.644  1.00 25.00           C
ATOM     24  CA  ARG    24      27.977  63.838  16.411  1.00 25.00           C
ATOM     25  CA  ARG    25      30.585  62.607  13.956  1.00 25.00           C
ATOM     26  CA  ASN    26      31.579  59.093  12.895  1.00 25.00           C
ATOM     27  CA  CYS    27      33.383  55.768  13.383  1.00 25.00           C
ATOM     28  CA  ASP    28      32.830  52.959  10.905  1.00 25.00           C
ATOM     29  CA  LEU    29      33.064  49.534  12.542  1.00 25.00           C
ATOM     30  CA  SER    30      34.878  46.555  11.115  1.00 25.00           C
ATOM     31  CA  PHE    31      37.621  45.532   8.714  1.00 25.00           C
ATOM     32  CA  SER    32      35.687  46.831   5.674  1.00 25.00           C
ATOM     33  CA  ASN    33      35.288  50.248   7.359  1.00 25.00           C
ATOM     34  CA  LEU    34      39.043  50.343   8.109  1.00 25.00           C
ATOM     35  CA  CYS    35      39.820  49.476   4.461  1.00 25.00           C
ATOM     36  CA  SER    36      37.478  52.263   3.273  1.00 25.00           C
ATOM     37  CA  TRP    37      39.196  54.746   5.631  1.00 25.00           C
ATOM     38  CA  ARG    38      42.623  53.677   4.296  1.00 25.00           C
ATOM     39  CA  PHE    39      44.025  57.182   4.354  1.00 25.00           C
ATOM     40  CA  LEU    40      46.249  60.249   4.972  1.00 25.00           C
ATOM     41  CA  TYR    41      46.879  64.055   5.093  1.00 25.00           C
ATOM     42  CA  ASP    42      44.537  66.499   6.912  1.00 25.00           C
ATOM     43  CA  THR    43      43.926  66.775  10.686  1.00 25.00           C
ATOM     44  CA  GLN    44      43.891  63.033  11.236  1.00 25.00           C
ATOM     45  CA  PHE    45      43.848  59.253  10.759  1.00 25.00           C
ATOM     46  CA  ALA    46      43.672  55.695   9.359  1.00 25.00           C
ATOM     47  CA  VAL    47      46.887  53.714   8.942  1.00 25.00           C
ATOM     48  CA  ILE    48      48.220  50.632  10.806  1.00 25.00           C
ATOM     49  CA  ASP    49      49.931  47.704   9.053  1.00 25.00           C
ATOM     50  CA  ASP    50      50.804  50.312   6.430  1.00 25.00           C
ATOM     51  CA  PHE    51      47.539  51.192   4.791  1.00 25.00           C
ATOM     52  CA  LEU    52      44.701  49.230   3.281  1.00 25.00           C
ATOM     53  CA  VAL    53      42.950  45.865   2.971  1.00 25.00           C
ATOM     54  CA  PHE    54      41.283  47.127  -0.209  1.00 25.00           C
ATOM     55  CA  LYS    55      39.475  44.172  -1.660  1.00 25.00           C
ATOM     56  CA  PHE    56      40.138  40.413  -1.187  1.00 25.00           C
ATOM     57  CA  TRP    57      38.135  37.150  -1.279  1.00 25.00           C
ATOM     58  CA  ALA    58      35.659  34.334  -2.137  1.00 25.00           C
ATOM     59  CA  GLY    59      35.071  34.314  -5.866  1.00 25.00           C
ATOM     60  CA  GLU    60      34.901  37.526  -8.000  1.00 25.00           C
ATOM     61  CA  GLN    61      33.159  40.606  -6.518  1.00 25.00           C
ATOM     62  CA  LEU    62      35.048  41.757  -3.492  1.00 25.00           C
ATOM     63  CA  ALA    63      34.164  42.817   0.098  1.00 25.00           C
ATOM     64  CA  TYR    64      35.194  46.411   0.794  1.00 25.00           C
ATOM     65  CA  MET    65      33.737  49.644   2.174  1.00 25.00           C
ATOM     66  CA  MET    66      31.113  51.338   4.241  1.00 25.00           C
ATOM     67  CA  PRO    67      33.220  54.314   5.257  1.00 25.00           C
ATOM     68  CA  VAL    68      33.922  55.086   1.571  1.00 25.00           C
ATOM     69  CA  GLY    69      31.995  58.384   1.660  1.00 25.00           C
ATOM     70  CA  ASN    70      28.389  59.471   2.513  1.00 25.00           C
ATOM     71  CA  GLY    71      26.716  61.261  -0.407  1.00 25.00           C
ATOM     72  CA  ASP    72      27.731  64.281   1.675  1.00 25.00           C
ATOM     73  CA  LEU    73      28.806  67.003  -0.722  1.00 25.00           C
ATOM     74  CA  LYS    74      29.851  67.229  -4.399  1.00 25.00           C
ATOM     75  CA  ALA    75      33.473  66.429  -3.445  1.00 25.00           C
ATOM     76  CA  VAL    76      32.294  63.410  -1.404  1.00 25.00           C
ATOM     77  CA  LEU    77      30.205  62.188  -4.372  1.00 25.00           C
ATOM     78  CA  ARG    78      33.233  62.561  -6.688  1.00 25.00           C
ATOM     79  CA  LYS    79      35.394  60.583  -4.220  1.00 25.00           C
ATOM     80  CA  LEU    80      32.740  57.826  -4.067  1.00 25.00           C
ATOM     81  CA  ILE    81      32.625  57.690  -7.893  1.00 25.00           C
ATOM     82  CA  GLU    82      36.444  57.424  -8.022  1.00 25.00           C
ATOM     83  CA  ASP    83      36.356  54.582  -5.457  1.00 25.00           C
ATOM     84  CA  ALA    84      33.692  52.764  -7.524  1.00 25.00           C
ATOM     85  CA  ASP    85      35.829  53.167 -10.677  1.00 25.00           C
ATOM     86  CA  LYS    86      38.875  51.774  -8.821  1.00 25.00           C
ATOM     87  CA  GLU    87      37.553  49.075  -6.463  1.00 25.00           C
ATOM     88  CA  LYS    88      35.521  49.382  -3.280  1.00 25.00           C
ATOM     89  CA  HIS    89      33.011  52.189  -2.629  1.00 25.00           C
ATOM     90  CA  ASN    90      29.563  53.847  -2.186  1.00 25.00           C
ATOM     91  CA  PHE    91      28.847  54.726   1.481  1.00 25.00           C
ATOM     92  CA  CYS    92      26.119  52.071   1.719  1.00 25.00           C
ATOM     93  CA  MET    93      23.116  50.106   0.346  1.00 25.00           C
ATOM     94  CA  LEU    94      21.241  47.547   2.445  1.00 25.00           C
ATOM     95  CA  GLY    95      18.229  45.391   1.548  1.00 25.00           C
ATOM     96  CA  VAL    96      19.292  46.248  -1.973  1.00 25.00           C
ATOM     97  CA  CYS    97      19.743  43.539  -4.545  1.00 25.00           C
ATOM     98  CA  SER    98      16.195  43.690  -5.870  1.00 25.00           C
ATOM     99  CA  ASN    99      13.566  46.388  -6.557  1.00 25.00           C
ATOM    100  CA  MET   100      16.032  49.106  -5.464  1.00 25.00           C
ATOM    101  CA  ARG   101      18.711  47.639  -7.775  1.00 25.00           C
ATOM    102  CA  ALA   102      16.219  47.604 -10.683  1.00 25.00           C
ATOM    103  CA  ASP   103      15.311  51.257  -9.980  1.00 25.00           C
ATOM    104  CA  LEU   104      19.024  52.197  -9.933  1.00 25.00           C
ATOM    105  CA  GLU   105      19.547  50.392 -13.269  1.00 25.00           C
ATOM    106  CA  ALA   106      16.558  52.254 -14.775  1.00 25.00           C
ATOM    107  CA  ILE   107      17.978  55.586 -13.533  1.00 25.00           C
ATOM    108  CA  LEU   108      17.767  57.665 -10.394  1.00 25.00           C
ATOM    109  CA  PRO   109      15.961  59.203  -7.369  1.00 25.00           C
ATOM    110  CA  GLU   110      16.199  62.867  -6.246  1.00 25.00           C
ATOM    111  CA  ARG   111      18.834  62.950  -8.989  1.00 25.00           C
ATOM    112  CA  PHE   112      21.704  61.203  -7.147  1.00 25.00           C
ATOM    113  CA  ILE   113      23.617  58.015  -7.980  1.00 25.00           C
ATOM    114  CA  PHE   114      25.600  55.273  -6.305  1.00 25.00           C
ATOM    115  CA  THR   115      26.436  51.973  -8.111  1.00 25.00           C
ATOM    116  CA  GLU   116      27.953  51.466 -11.556  1.00 25.00           C
ATOM    117  CA  ASP   117      28.335  48.161 -13.409  1.00 25.00           C
ATOM    290  CA  LYS   290      36.158  27.851  21.715  1.00 25.00           C
ATOM    291  CA  TYR   291      34.430  31.086  22.819  1.00 25.00           C
ATOM    292  CA  MET   292      33.179  31.666  19.245  1.00 25.00           C
ATOM    293  CA  ALA   293      31.834  28.083  19.110  1.00 25.00           C
ATOM    294  CA  CYS   294      30.046  28.601  22.456  1.00 25.00           C
ATOM    295  CA  LEU   295      28.504  31.857  21.156  1.00 25.00           C
ATOM    296  CA  LYS   296      24.911  33.092  21.747  1.00 25.00           C
ATOM    297  CA  ASP   297      23.372  30.080  23.488  1.00 25.00           C
ATOM    298  CA  HIS   298      25.940  29.839  26.286  1.00 25.00           C
TER
END
