
#######################################################
#                                                     #
#                        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_3-D1
# Molecule2: number of CA atoms  123 (  939),  selected  123 , name T0307_D1.pdb
# PARAMETERS: T0307TS599_3-D1.T0307_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      I      10           -
LGA    -       -      M      11           -
LGA    -       -      T      12           -
LGA    -       -      F      13           -
LGA    -       -      S      14           -
LGA    -       -      G      15           -
LGA    -       -      Q      16           -
LGA    -       -      E      17           -
LGA    I      10      L      18          2.070
LGA    M      11      T      19          1.194
LGA    T      12      A      20          3.571
LGA    F      13      I      21           -
LGA    S      14      I      22           -
LGA    G      15      -       -           -
LGA    Q      16      -       -           -
LGA    E      17      K      23           #
LGA    L      18      M      24           #
LGA    T      19      A      25           -
LGA    A      20      K      26           #
LGA    I      21      S      27          0.755
LGA    I      22      -       -           -
LGA    K      23      M      28           #
LGA    M      24      V      29          3.477
LGA    A      25      M      30          3.010
LGA    K      26      A      31          5.133
LGA    S      27      D      32          2.856
LGA    M      28      G      33           -
LGA    V      29      K      34           #
LGA    -       -      I      35           -
LGA    M      30      K      36          3.905
LGA    A      31      P      37          2.919
LGA    D      32      A      38          3.080
LGA    -       -      E      39           -
LGA    -       -      I      40           -
LGA    G      33      A      41          0.855
LGA    K      34      V      42          1.242
LGA    I      35      M      43          2.375
LGA    K      36      T      44           #
LGA    P      37      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           -
LGA    -       -      D      58           -
LGA    -       -      L      59           -
LGA    -       -      L      60           -
LGA    A      38      L      61          3.934
LGA    E      39      K      62           -
LGA    -       -      A      63           -
LGA    I      40      S      64          4.685
LGA    -       -      D      65           -
LGA    -       -      S      66           -
LGA    -       -      I      67           -
LGA    -       -      E      68           -
LGA    A      41      A      69          5.686
LGA    -       -      S      70           -
LGA    V      42      Q      71          3.088
LGA    M      43      A      72          3.837
LGA    T      44      V      73           #
LGA    R      45      A      74           #
LGA    E      46      L      75          2.222
LGA    F      47      I      76           #
LGA    M      48      A      77           -
LGA    R      49      -       -           -
LGA    F      50      -       -           -
LGA    G      51      -       -           -
LGA    I      52      -       -           -
LGA    L      53      R      78          4.894
LGA    Q      54      -       -           -
LGA    D      55      -       -           -
LGA    Q      56      -       -           -
LGA    V      57      M      79          3.838
LGA    D      58      D      80          2.541
LGA    L      59      E      81          1.828
LGA    L      60      E      82          2.918
LGA    L      61      R      83          2.889
LGA    K      62      K      84          1.293
LGA    A      63      K      85          1.015
LGA    S      64      Y      86          1.707
LGA    D      65      V      87          1.822
LGA    S      66      A      88          1.099
LGA    I      67      S      89          1.032
LGA    E      68      Y      90          1.152
LGA    A      69      L      91          1.300
LGA    S      70      G      92          1.506
LGA    Q      71      V      93          1.037
LGA    A      72      I      94          0.827
LGA    V      73      M      95          0.647
LGA    A      74      A      96          1.329
LGA    L      75      S      97          3.018
LGA    I      76      -       -           -
LGA    A      77      -       -           -
LGA    R      78      D      98          5.359
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     41    2.87     9.76     22.323     1.379

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.659437 * X  +   0.697034 * Y  +  -0.281579 * Z  +  20.572773
  Y_new =  -0.725860 * X  +  -0.492897 * Y  +   0.479770 * Z  +  14.232539
  Z_new =   0.195627 * X  +   0.520765 * Y  +   0.830984 * Z  +  13.267506 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.559810   -2.581782  [ DEG:    32.0748   -147.9252 ]
  Theta =  -0.196897   -2.944696  [ DEG:   -11.2813   -168.7187 ]
  Phi   =  -2.308283    0.833310  [ DEG:  -132.2549     47.7452 ]
 
# 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_3-D1                               
REMARK     2: T0307_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0307TS599_3-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   41   2.87    9.76  22.323
REMARK  ---------------------------------------------------------- 
MOLECULE T0307TS599_3-D1
PFRMAT TS                                                                       
TARGET T0307                                                                    
MODEL  3                                                                        
PARENT N/A                                                                      
ATOM     10  CA  ILE    10      21.516  12.354  34.892  1.00  0.00              
ATOM     11  CA  MET    11      25.031  12.950  33.796  1.00  0.00              
ATOM     12  CA  THR    12      27.650  11.059  35.838  1.00  0.00              
ATOM     13  CA  PHE    13      31.010  10.140  34.317  1.00  0.00              
ATOM     14  CA  SER    14      32.645   7.094  35.884  1.00  0.00              
ATOM     15  CA  GLY    15      35.280   5.783  33.424  1.00  0.00              
ATOM     16  CA  GLN    16      33.295   2.820  32.136  1.00  0.00              
ATOM     17  CA  GLU    17      29.906   4.570  31.746  1.00  0.00              
ATOM     18  CA  LEU    18      30.739   7.764  29.775  1.00  0.00              
ATOM     19  CA  THR    19      32.895   5.722  27.335  1.00  0.00              
ATOM     20  CA  ALA    20      30.030   3.266  26.711  1.00  0.00              
ATOM     21  CA  ILE    21      27.660   6.195  26.110  1.00  0.00              
ATOM     22  CA  ILE    22      30.063   7.827  23.616  1.00  0.00              
ATOM     23  CA  LYS    23      30.351   4.538  21.628  1.00  0.00              
ATOM     24  CA  MET    24      26.528   4.329  21.617  1.00  0.00              
ATOM     25  CA  ALA    25      26.287   7.970  20.411  1.00  0.00              
ATOM     26  CA  LYS    26      28.448   7.228  17.416  1.00  0.00              
ATOM     27  CA  SER    27      26.323   4.165  16.477  1.00  0.00              
ATOM     28  CA  MET    28      23.083   6.266  16.757  1.00  0.00              
ATOM     29  CA  VAL    29      24.083   9.517  15.016  1.00  0.00              
ATOM     30  CA  MET    30      22.296  12.748  15.999  1.00  0.00              
ATOM     31  CA  ALA    31      22.022  15.399  13.219  1.00  0.00              
ATOM     32  CA  ASP    32      19.580  17.930  14.736  1.00  0.00              
ATOM     33  CA  GLY    33      21.352  17.936  18.080  1.00  0.00              
ATOM     34  CA  LYS    34      19.029  15.635  19.922  1.00  0.00              
ATOM     35  CA  ILE    35      21.658  13.358  21.582  1.00  0.00              
ATOM     36  CA  LYS    36      24.544  15.078  23.201  1.00  0.00              
ATOM     37  CA  PRO    37      28.134  14.353  23.426  1.00  0.00              
ATOM     38  CA  ALA    38      28.225  14.809  27.236  1.00  0.00              
ATOM     39  CA  GLU    39      25.638  12.240  28.186  1.00  0.00              
ATOM     40  CA  ILE    40      27.216  10.121  30.989  1.00  0.00              
ATOM     41  CA  ALA    41      25.425   8.174  33.663  1.00  0.00              
ATOM     42  CA  VAL    42      26.766   6.850  36.913  1.00  0.00              
ATOM     43  CA  MET    43      24.917   3.889  38.315  1.00  0.00              
ATOM     44  CA  THR    44      26.279   3.757  41.889  1.00  0.00              
ATOM     45  CA  ARG    45      25.904   7.539  42.257  1.00  0.00              
ATOM     46  CA  GLU    46      22.247   7.359  41.191  1.00  0.00              
ATOM     47  CA  PHE    47      21.318   4.599  43.566  1.00  0.00              
ATOM     48  CA  MET    48      22.881   6.292  46.589  1.00  0.00              
ATOM     49  CA  ARG    49      21.035   9.499  45.665  1.00  0.00              
ATOM     50  CA  PHE    50      17.655   7.768  45.660  1.00  0.00              
ATOM     51  CA  GLY    51      18.372   6.218  49.064  1.00  0.00              
ATOM     52  CA  ILE    52      18.750   2.534  48.445  1.00  0.00              
ATOM     53  CA  LEU    53      16.097   2.092  45.768  1.00  0.00              
ATOM     54  CA  GLN    54      13.208   3.924  47.319  1.00  0.00              
ATOM     55  CA  ASP    55      10.414   2.958  44.867  1.00  0.00              
ATOM     56  CA  GLN    56      10.125   6.546  43.582  1.00  0.00              
ATOM     57  CA  VAL    57      13.843   7.329  42.987  1.00  0.00              
ATOM     58  CA  ASP    58      14.700   4.223  41.005  1.00  0.00              
ATOM     59  CA  LEU    59      11.430   4.351  38.983  1.00  0.00              
ATOM     60  CA  LEU    60      11.171   7.916  37.593  1.00  0.00              
ATOM     61  CA  LEU    61      14.890   7.677  36.652  1.00  0.00              
ATOM     62  CA  LYS    62      14.522   4.331  34.863  1.00  0.00              
ATOM     63  CA  ALA    63      11.453   5.320  32.840  1.00  0.00              
ATOM     64  CA  SER    64      13.009   8.612  31.680  1.00  0.00              
ATOM     65  CA  ASP    65      15.939   6.811  30.140  1.00  0.00              
ATOM     66  CA  SER    66      14.037   4.259  28.146  1.00  0.00              
ATOM     67  CA  ILE    67      11.600   6.486  26.220  1.00  0.00              
ATOM     68  CA  GLU    68      14.347   9.069  25.616  1.00  0.00              
ATOM     69  CA  ALA    69      16.934   6.720  24.106  1.00  0.00              
ATOM     70  CA  SER    70      14.650   5.148  21.576  1.00  0.00              
ATOM     71  CA  GLN    71      13.357   8.546  20.401  1.00  0.00              
ATOM     72  CA  ALA    72      16.837  10.005  19.964  1.00  0.00              
ATOM     73  CA  VAL    73      18.457   7.490  17.654  1.00  0.00              
ATOM     74  CA  ALA    74      15.290   7.521  15.518  1.00  0.00              
ATOM     75  CA  LEU    75      15.109  11.302  15.247  1.00  0.00              
ATOM     76  CA  ILE    76      18.780  11.565  14.159  1.00  0.00              
ATOM     77  CA  ALA    77      18.219   8.862  11.496  1.00  0.00              
ATOM     78  CA  ARG    78      15.264  10.829  10.064  1.00  0.00              
ATOM     79  CA  MET    79      17.247  14.094   9.951  1.00  0.00              
ATOM     80  CA  ASP    80      20.233  12.593   8.058  1.00  0.00              
ATOM     81  CA  GLU    81      18.127  10.928   5.384  1.00  0.00              
ATOM     82  CA  GLU    82      16.206  14.161   4.749  1.00  0.00              
ATOM     83  CA  ARG    83      19.444  16.126   4.404  1.00  0.00              
ATOM     84  CA  LYS    84      20.832  13.595   1.951  1.00  0.00              
ATOM     85  CA  LYS    85      17.643  13.737  -0.120  1.00  0.00              
ATOM     86  CA  TYR    86      17.607  17.552  -0.262  1.00  0.00              
ATOM     87  CA  VAL    87      21.274  17.540  -1.147  1.00  0.00              
ATOM     88  CA  ALA    88      20.818  14.974  -3.973  1.00  0.00              
ATOM     89  CA  SER    89      18.002  17.063  -5.416  1.00  0.00              
ATOM     90  CA  TYR    90      20.108  20.251  -5.279  1.00  0.00              
ATOM     91  CA  LEU    91      23.088  18.680  -6.956  1.00  0.00              
ATOM     92  CA  GLY    92      20.810  17.338  -9.690  1.00  0.00              
ATOM     93  CA  VAL    93      19.412  20.855 -10.303  1.00  0.00              
ATOM     94  CA  ILE    94      22.473  23.201 -10.280  1.00  0.00              
ATOM     95  CA  MET    95      21.473  26.755 -10.999  1.00  0.00              
ATOM     96  CA  ALA    96      23.387  29.948 -10.442  1.00  0.00              
ATOM     97  CA  SER    97      23.042  32.839 -12.906  1.00  0.00              
ATOM     98  CA  ASP    98      26.712  33.073 -13.856  1.00  0.00              
ATOM     99  CA  GLY    99      27.184  29.305 -13.732  1.00  0.00              
ATOM    100  CA  ASP   100      29.181  29.089 -10.537  1.00  0.00              
ATOM    101  CA  ILE   101      27.049  26.867  -8.386  1.00  0.00              
ATOM    102  CA  ASP   102      26.697  27.752  -4.762  1.00  0.00              
ATOM    103  CA  ASP   103      26.407  24.350  -3.095  1.00  0.00              
ATOM    104  CA  ASN   104      22.835  25.003  -1.858  1.00  0.00              
ATOM    105  CA  GLU   105      21.462  26.169  -5.206  1.00  0.00              
ATOM    106  CA  LEU   106      18.614  24.135  -6.643  1.00  0.00              
ATOM    107  CA  ALA   107      17.828  24.697 -10.290  1.00  0.00              
ATOM    108  CA  LEU   108      14.794  24.017 -12.370  1.00  0.00              
ATOM    109  CA  TRP   109      15.689  23.455 -16.043  1.00  0.00              
ATOM    110  CA  THR   110      13.616  26.273 -17.599  1.00  0.00              
ATOM    111  CA  LEU   111      14.965  28.633 -14.912  1.00  0.00              
ATOM    112  CA  ILE   112      18.551  27.501 -15.053  1.00  0.00              
ATOM    113  CA  SER   113      18.761  27.529 -18.813  1.00  0.00              
ATOM    114  CA  THR   114      17.293  31.031 -18.882  1.00  0.00              
ATOM    115  CA  LEU   115      19.677  32.458 -16.238  1.00  0.00              
ATOM    116  CA  CYS   116      22.763  30.990 -17.887  1.00  0.00              
ATOM    117  CA  GLY   117      21.807  31.692 -21.484  1.00  0.00              
ATOM    118  CA  LEU   118      21.687  27.958 -22.310  1.00  0.00              
ATOM    119  CA  PRO   119      19.065  26.820 -24.734  1.00  0.00              
ATOM    120  CA  THR   120      16.122  25.330 -22.753  1.00  0.00              
ATOM    121  CA  MET   121      16.491  21.832 -24.169  1.00  0.00              
ATOM    122  CA  THR   122      20.240  21.507 -23.629  1.00  0.00              
ATOM    123  CA  VAL   123      20.402  22.327 -19.937  1.00  0.00              
ATOM    124  CA  MET   124      17.238  20.270 -19.268  1.00  0.00              
ATOM    125  CA  GLU   125      18.748  17.230 -21.041  1.00  0.00              
ATOM    126  CA  ALA   126      21.888  17.607 -18.886  1.00  0.00              
ATOM    127  CA  ILE   127      19.677  17.776 -15.759  1.00  0.00              
ATOM    128  CA  ASN   128      17.844  14.570 -16.830  1.00  0.00              
ATOM    129  CA  ASN   129      21.179  12.836 -17.257  1.00  0.00              
ATOM    130  CA  MET   130      22.443  13.921 -13.785  1.00  0.00              
ATOM    131  CA  LYS   131      18.903  12.085 -12.389  1.00  0.00              
ATOM    132  CA  ASN   132      22.255  13.541 -12.132  1.00  0.00              
TER                                                                             
END
