
#######################################################
#                                                     #
#                        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  101 (  101),  selected  101 , name T0304TS599_2-D1
# Molecule2: number of CA atoms  101 (  799),  selected  101 , name T0304_D1.pdb
# PARAMETERS: T0304TS599_2-D1.T0304_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    R      17      R      17           -
LGA    P      18      P      18           -
LGA    W      19      W      19           -
LGA    -       -      W      20           -
LGA    -       -      G      21           -
LGA    W      20      L      22           #
LGA    G      21      P      23          2.019
LGA    L      22      C      24          2.887
LGA    P      23      T      25          3.570
LGA    C      24      V      26          2.953
LGA    T      25      T      27          1.944
LGA    V      26      P      28          1.848
LGA    T      27      C      29          4.285
LGA    P      28      -       -           -
LGA    C      29      -       -           -
LGA    F      30      F      30          2.447
LGA    G      31      -       -           -
LGA    A      32      -       -           -
LGA    R      33      -       -           -
LGA    L      34      G      31          2.473
LGA    V      35      A      32          3.556
LGA    Q      36      R      33          1.401
LGA    E      37      L      34          5.188
LGA    G      38      V      35           -
LGA    N      39      Q      36           -
LGA    R      40      E      37           -
LGA    L      41      G      38           -
LGA    H      42      N      39           -
LGA    Y      43      R      40           -
LGA    L      44      L      41           -
LGA    -       -      H      42           -
LGA    -       -      Y      43           -
LGA    -       -      L      44           -
LGA    -       -      A      45           -
LGA    -       -      D      46           -
LGA    -       -      R      47           -
LGA    -       -      A      48           -
LGA    A      45      G      49           #
LGA    D      46      -       -           -
LGA    R      47      -       -           -
LGA    A      48      -       -           -
LGA    G      49      -       -           -
LGA    I      50      I      50          3.532
LGA    R      51      R      51           #
LGA    G      52      G      52           #
LGA    L      53      L      53          0.903
LGA    F      54      F      54          0.967
LGA    S      55      S      55          1.049
LGA    D      56      D      56          1.237
LGA    A      57      A      57          0.944
LGA    D      58      D      58          0.525
LGA    A      59      A      59          0.825
LGA    Y      60      Y      60          1.303
LGA    H      61      H      61          1.104
LGA    L      62      L      62          1.936
LGA    D      63      D      63          2.596
LGA    Q      64      Q      64          2.612
LGA    A      65      A      65          2.753
LGA    F      66      F      66          3.262
LGA    P      67      P      67          2.261
LGA    L      68      L      68          0.575
LGA    L      69      L      69          2.099
LGA    M      70      M      70          1.597
LGA    K      71      K      71          0.814
LGA    Q      72      Q      72          2.690
LGA    L      73      L      73          3.110
LGA    E      74      E      74          2.183
LGA    L      75      L      75          4.057
LGA    M      76      M      76           #
LGA    L      77      L      77          3.749
LGA    T      78      T      78          4.442
LGA    S      79      -       -           -
LGA    G      80      -       -           -
LGA    E      81      S      79          2.141
LGA    L      82      G      80          1.717
LGA    N      83      E      81           #
LGA    P      84      -       -           -
LGA    R      85      -       -           -
LGA    H      86      L      82          4.171
LGA    Q      87      N      83          2.553
LGA    H      88      P      84           #
LGA    -       -      R      85           -
LGA    T      89      H      86          4.452
LGA    V      90      Q      87          3.319
LGA    -       -      H      88           -
LGA    T      91      T      89          4.877
LGA    L      92      -       -           -
LGA    Y      93      -       -           -
LGA    A      94      -       -           -
LGA    K      95      -       -           -
LGA    G      96      -       -           -
LGA    L      97      -       -           -
LGA    T      98      -       -           -
LGA    C      99      V      90          5.173
LGA    K     100      T      91          2.784
LGA    A     101      L      92          2.181
LGA    D     102      Y      93          4.239
LGA    T     103      A      94           -
LGA    L     104      K      95           -
LGA    S     105      G      96           -
LGA    S     106      L      97           -
LGA    C     107      T      98           -
LGA    D     108      C      99           -
LGA    -       -      K     100           -
LGA    Y     109      A     101           #
LGA    V     110      D     102          3.824
LGA    Y     111      T     103           -
LGA    -       -      L     104           -
LGA    -       -      S     105           -
LGA    -       -      S     106           -
LGA    -       -      C     107           -
LGA    -       -      D     108           -
LGA    -       -      Y     109           -
LGA    -       -      V     110           -
LGA    -       -      Y     111           -
LGA    -       -      L     112           -
LGA    L     112      A     113           #
LGA    A     113      V     114           -
LGA    V     114      Y     115           -
LGA    Y     115      P     116           -
LGA    P     116      T     117           -
LGA    T     117      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  101  101    5.0     50    2.87    58.00     31.811     1.681

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.303989 * X  +   0.168630 * Y  +   0.937633 * Z  +  42.799732
  Y_new =  -0.878776 * X  +   0.330433 * Y  +  -0.344334 * Z  +  29.175949
  Z_new =  -0.367890 * X  +  -0.928643 * Y  +   0.047740 * Z  +  41.505131 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.519433    1.622160  [ DEG:   -87.0571     92.9429 ]
  Theta =   0.376739    2.764854  [ DEG:    21.5855    158.4144 ]
  Phi   =  -1.903834    1.237758  [ DEG:  -109.0817     70.9183 ]
 
# 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: T0304TS599_2-D1                               
REMARK     2: T0304_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0304TS599_2-D1.T0304_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  101  101   5.0   50   2.87   58.00  31.811
REMARK  ---------------------------------------------------------- 
MOLECULE T0304TS599_2-D1
PFRMAT TS                                                                       
TARGET T0304                                                                    
MODEL  2                                                                        
PARENT N/A                                                                      
ATOM     17  CA  ARG    17      27.846  31.777  46.180  1.00  0.00              
ATOM     18  CA  PRO    18      30.735  34.076  46.744  1.00  0.00              
ATOM     19  CA  TRP    19      33.595  31.674  45.901  1.00  0.00              
ATOM     20  CA  TRP    20      32.474  30.357  42.549  1.00  0.00              
ATOM     21  CA  GLY    21      35.709  29.800  40.703  1.00  0.00              
ATOM     22  CA  LEU    22      35.389  26.989  38.184  1.00  0.00              
ATOM     23  CA  PRO    23      36.944  27.271  34.865  1.00  0.00              
ATOM     24  CA  CYS    24      34.481  25.833  32.402  1.00  0.00              
ATOM     25  CA  THR    25      36.940  23.548  30.577  1.00  0.00              
ATOM     26  CA  VAL    26      38.457  21.721  33.528  1.00  0.00              
ATOM     27  CA  THR    27      41.719  19.775  33.437  1.00  0.00              
ATOM     28  CA  PRO    28      42.051  17.218  36.280  1.00  0.00              
ATOM     29  CA  CYS    29      45.521  18.309  37.369  1.00  0.00              
ATOM     30  CA  PHE    30      44.193  21.906  37.746  1.00  0.00              
ATOM     31  CA  GLY    31      40.947  20.894  39.461  1.00  0.00              
ATOM     32  CA  ALA    32      42.859  19.201  42.306  1.00  0.00              
ATOM     33  CA  ARG    33      44.796  22.439  42.815  1.00  0.00              
ATOM     34  CA  LEU    34      41.582  24.509  42.934  1.00  0.00              
ATOM     35  CA  VAL    35      39.963  22.151  45.505  1.00  0.00              
ATOM     36  CA  GLN    36      43.101  22.279  47.561  1.00  0.00              
ATOM     37  CA  GLU    37      43.215  26.106  47.630  1.00  0.00              
ATOM     38  CA  GLY    38      39.675  26.446  48.861  1.00  0.00              
ATOM     39  CA  ASN    39      38.038  27.987  45.831  1.00  0.00              
ATOM     40  CA  ARG    40      34.655  26.367  45.344  1.00  0.00              
ATOM     41  CA  LEU    41      33.624  25.698  41.765  1.00  0.00              
ATOM     42  CA  HIS    42      30.933  23.082  42.018  1.00  0.00              
ATOM     43  CA  TYR    43      28.119  23.447  39.466  1.00  0.00              
ATOM     44  CA  LEU    44      30.273  23.812  36.324  1.00  0.00              
ATOM     45  CA  ALA    45      32.739  21.146  37.403  1.00  0.00              
ATOM     46  CA  ASP    46      29.987  18.557  38.008  1.00  0.00              
ATOM     47  CA  ARG    47      28.167  18.931  34.743  1.00  0.00              
ATOM     48  CA  ALA    48      31.274  18.263  32.713  1.00  0.00              
ATOM     49  CA  GLY    49      32.597  15.436  34.939  1.00  0.00              
ATOM     50  CA  ILE    50      35.819  17.064  36.190  1.00  0.00              
ATOM     51  CA  ARG    51      38.115  14.162  35.228  1.00  0.00              
ATOM     52  CA  GLY    52      36.499  13.474  31.846  1.00  0.00              
ATOM     53  CA  LEU    53      36.345  17.026  30.479  1.00  0.00              
ATOM     54  CA  PHE    54      39.878  17.545  29.358  1.00  0.00              
ATOM     55  CA  SER    55      41.479  16.113  26.240  1.00  0.00              
ATOM     56  CA  ASP    56      44.495  13.966  27.294  1.00  0.00              
ATOM     57  CA  ALA    57      47.027  16.440  25.896  1.00  0.00              
ATOM     58  CA  ASP    58      45.604  19.271  27.960  1.00  0.00              
ATOM     59  CA  ALA    59      45.713  17.195  31.143  1.00  0.00              
ATOM     60  CA  TYR    60      49.367  16.441  30.722  1.00  0.00              
ATOM     61  CA  HIS    61      50.259  20.103  29.948  1.00  0.00              
ATOM     62  CA  LEU    62      48.340  21.557  32.902  1.00  0.00              
ATOM     63  CA  ASP    63      49.846  19.074  35.401  1.00  0.00              
ATOM     64  CA  GLN    64      53.346  19.805  34.209  1.00  0.00              
ATOM     65  CA  ALA    65      52.934  23.580  34.417  1.00  0.00              
ATOM     66  CA  PHE    66      51.486  23.623  37.943  1.00  0.00              
ATOM     67  CA  PRO    67      54.109  21.457  39.511  1.00  0.00              
ATOM     68  CA  LEU    68      56.873  23.621  37.975  1.00  0.00              
ATOM     69  CA  LEU    69      55.186  26.808  39.196  1.00  0.00              
ATOM     70  CA  MET    70      54.686  25.479  42.689  1.00  0.00              
ATOM     71  CA  LYS    71      58.314  24.381  42.967  1.00  0.00              
ATOM     72  CA  GLN    72      59.620  27.725  41.812  1.00  0.00              
ATOM     73  CA  LEU    73      57.399  29.426  44.316  1.00  0.00              
ATOM     74  CA  GLU    74      58.624  27.140  47.142  1.00  0.00              
ATOM     75  CA  LEU    75      62.239  28.008  46.371  1.00  0.00              
ATOM     76  CA  MET    76      61.355  31.738  46.426  1.00  0.00              
ATOM     77  CA  LEU    77      59.492  31.372  49.771  1.00  0.00              
ATOM     78  CA  THR    78      62.373  29.497  51.415  1.00  0.00              
ATOM     79  CA  SER    79      64.864  32.173  50.194  1.00  0.00              
ATOM     80  CA  GLY    80      62.919  35.071  51.559  1.00  0.00              
ATOM     81  CA  GLU    81      61.867  36.734  48.371  1.00  0.00              
ATOM     82  CA  LEU    82      58.204  36.373  49.159  1.00  0.00              
ATOM     83  CA  ASN    83      57.292  37.779  52.588  1.00  0.00              
ATOM     84  CA  PRO    84      55.001  36.297  55.191  1.00  0.00              
ATOM     85  CA  ARG    85      52.020  38.597  54.454  1.00  0.00              
ATOM     86  CA  HIS    86      52.271  37.869  50.749  1.00  0.00              
ATOM     87  CA  GLN    87      52.477  34.043  50.985  1.00  0.00              
ATOM     88  CA  HIS    88      50.072  33.391  48.321  1.00  0.00              
ATOM     89  CA  THR    89      47.640  36.282  48.325  1.00  0.00              
ATOM     90  CA  VAL    90      44.296  35.602  46.818  1.00  0.00              
ATOM     91  CA  THR    91      42.252  38.342  45.253  1.00  0.00              
ATOM     92  CA  LEU    92      38.720  37.710  44.170  1.00  0.00              
ATOM     93  CA  TYR    93      37.259  39.931  41.480  1.00  0.00              
ATOM     94  CA  ALA    94      33.623  39.880  40.698  1.00  0.00              
ATOM     95  CA  LYS    95      33.526  40.741  37.058  1.00  0.00              
ATOM     96  CA  GLY    96      36.388  39.045  35.497  1.00  0.00              
ATOM     97  CA  LEU    97      40.055  39.120  36.529  1.00  0.00              
ATOM     98  CA  THR    98      41.903  35.923  35.825  1.00  0.00              
ATOM     99  CA  CYS    99      45.307  35.265  37.276  1.00  0.00              
ATOM    100  CA  LYS   100      47.626  33.226  35.130  1.00  0.00              
ATOM    101  CA  ALA   101      49.701  30.549  36.760  1.00  0.00              
ATOM    102  CA  ASP   102      53.022  32.146  35.731  1.00  0.00              
ATOM    103  CA  THR   103      52.441  35.848  36.514  1.00  0.00              
ATOM    104  CA  LEU   104      50.566  35.330  39.804  1.00  0.00              
ATOM    105  CA  SER   105      53.061  32.719  40.897  1.00  0.00              
ATOM    106  CA  SER   106      56.145  34.913  40.264  1.00  0.00              
ATOM    107  CA  CYS   107      54.817  37.879  42.268  1.00  0.00              
ATOM    108  CA  ASP   108      52.773  36.052  44.911  1.00  0.00              
ATOM    109  CA  TYR   109      49.252  37.131  43.904  1.00  0.00              
ATOM    110  CA  VAL   110      46.474  34.958  42.638  1.00  0.00              
ATOM    111  CA  TYR   111      43.606  36.627  40.897  1.00  0.00              
ATOM    112  CA  LEU   112      40.401  34.811  40.469  1.00  0.00              
ATOM    113  CA  ALA   113      37.703  36.165  38.245  1.00  0.00              
ATOM    114  CA  VAL   114      34.081  35.292  38.818  1.00  0.00              
ATOM    115  CA  TYR   115      31.596  35.582  35.917  1.00  0.00              
ATOM    116  CA  PRO   116      27.844  35.297  36.239  1.00  0.00              
ATOM    117  CA  THR   117      26.752  32.057  34.485  1.00  0.00              
TER                                                                             
END
