
#######################################################
#                                                     #
#                        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  117 (  117),  selected  117 , name T0352TS599_2
# Molecule2: number of CA atoms  109 ( 1766),  selected  109 , name T0352.pdb
# PARAMETERS: T0352TS599_2.T0352.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      -       -           -
LGA    T       2      M       1          1.494
LGA    T       3      -       -           -
LGA    H       4      -       -           -
LGA    D       5      T       2          1.876
LGA    R       6      T       3          1.512
LGA    V       7      H       4          1.586
LGA    R       8      D       5          1.451
LGA    L       9      R       6          1.491
LGA    Q      10      V       7          1.468
LGA    L      11      R       8          1.236
LGA    Q      12      L       9          1.446
LGA    A      13      Q      10          1.113
LGA    L      14      L      11          1.140
LGA    E      15      Q      12          1.530
LGA    A      16      A      13          0.821
LGA    L      17      L      14          1.153
LGA    L      18      E      15          1.441
LGA    R      19      A      16          0.850
LGA    E      20      L      17          1.024
LGA    H      21      L      18          1.410
LGA    Q      22      R      19          0.737
LGA    H      23      E      20           -
LGA    W      24      H      21           -
LGA    -       -      Q      22           -
LGA    -       -      H      23           -
LGA    R      25      W      24           #
LGA    N      26      R      25          1.879
LGA    D      27      N      26           #
LGA    -       -      D      27           -
LGA    -       -      E      28           -
LGA    E      28      P      29          5.037
LGA    P      29      Q      30          4.211
LGA    Q      30      -       -           -
LGA    P      31      -       -           -
LGA    H      32      -       -           -
LGA    Q      33      -       -           -
LGA    F      34      -       -           -
LGA    N      35      -       -           -
LGA    S      36      -       -           -
LGA    T      37      -       -           -
LGA    Q      38      P      31           #
LGA    P      39      H      32          3.973
LGA    F      40      Q      33          2.204
LGA    F      41      F      34          1.538
LGA    M      42      N      35          4.041
LGA    D      43      S      36          4.028
LGA    T      44      T      37          3.741
LGA    M      45      Q      38          2.974
LGA    E      46      P      39          5.183
LGA    -       -      F      40           -
LGA    -       -      F      41           -
LGA    -       -      M      42           -
LGA    -       -      D      43           -
LGA    -       -      T      44           -
LGA    P      47      M      45           #
LGA    -       -      E      46           -
LGA    -       -      P      47           -
LGA    -       -      L      48           -
LGA    -       -      E      49           -
LGA    -       -      W      50           -
LGA    -       -      L      51           -
LGA    -       -      Q      52           -
LGA    -       -      W      53           -
LGA    -       -      V      54           -
LGA    L      48      L      55          4.964
LGA    E      49      I      56          3.153
LGA    W      50      P      57          3.623
LGA    L      51      -       -           -
LGA    Q      52      R      58          2.827
LGA    W      53      M      59          4.313
LGA    V      54      H      60          2.773
LGA    L      55      D      61          2.182
LGA    I      56      L      62          2.784
LGA    P      57      -       -           -
LGA    R      58      L      63           #
LGA    M      59      D      64           #
LGA    H      60      N      65          4.078
LGA    D      61      K      66          3.256
LGA    L      62      Q      67          0.665
LGA    L      63      P      68           #
LGA    D      64      L      69           -
LGA    N      65      P      70           -
LGA    K      66      G      71           -
LGA    Q      67      A      72           -
LGA    P      68      F      73           -
LGA    L      69      A      74           -
LGA    P      70      V      75           -
LGA    G      71      A      76           -
LGA    A      72      P      77           -
LGA    F      73      Y      78           -
LGA    A      74      Y      79           -
LGA    V      75      E      80           -
LGA    A      76      M      81           -
LGA    P      77      A      82           -
LGA    Y      78      L      83           -
LGA    Y      79      A      84           -
LGA    E      80      T      85           -
LGA    M      81      D      86           -
LGA    A      82      H      87           -
LGA    L      83      P      88           -
LGA    A      84      Q      89           -
LGA    T      85      R      90           -
LGA    D      86      A      91           -
LGA    H      87      L      92           -
LGA    P      88      I      93           -
LGA    Q      89      L      94           -
LGA    R      90      A      95           -
LGA    A      91      E      96           -
LGA    L      92      L      97           -
LGA    I      93      E      98           -
LGA    L      94      K      99           -
LGA    A      95      L     100           -
LGA    E      96      D     101           -
LGA    L      97      A     102           -
LGA    E      98      L     103           -
LGA    K      99      F     104           -
LGA    L     100      A     105           -
LGA    D     101      D     106           -
LGA    A     102      D     107           -
LGA    L     103      A     108           -
LGA    F     104      S     109           -
LGA    A     105      -       -           -
LGA    D     106      -       -           -
LGA    D     107      -       -           -
LGA    A     108      -       -           -
LGA    S     109      -       -           -
LGA    L     110      -       -           -
LGA    E     111      -       -           -
LGA    H     112      -       -           -
LGA    H     113      -       -           -
LGA    H     114      -       -           -
LGA    H     115      -       -           -
LGA    H     116      -       -           -
LGA    H     117      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  117  109    5.0     41    2.74    14.63     25.947     1.443

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.074698 * X  +   0.617602 * Y  +   0.782935 * Z  +  -0.208093
  Y_new =   0.092352 * X  +  -0.786039 * Y  +   0.611240 * Z  +  12.884425
  Z_new =   0.992921 * X  +   0.026648 * Y  +  -0.115752 * Z  + -10.842237 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.915323   -0.226270  [ DEG:   167.0357    -12.9643 ]
  Theta =  -1.451736   -1.689857  [ DEG:   -83.1783    -96.8217 ]
  Phi   =   0.890691   -2.250902  [ DEG:    51.0328   -128.9672 ]
 
# 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: T0352TS599_2                                  
REMARK     2: T0352.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0352TS599_2.T0352.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  117  109   5.0   41   2.74   14.63  25.947
REMARK  ---------------------------------------------------------- 
MOLECULE T0352TS599_2
PFRMAT TS                                                                       
TARGET T0352                                                                    
MODEL  2                                                                        
PARENT N/A                                                                      
ATOM      1  CA  MET     1       4.066  -4.979 -11.319  1.00  0.00              
ATOM      2  CA  THR     2       3.688  -7.378  -7.890  1.00  0.00              
ATOM      3  CA  THR     3       2.237  -8.803  -4.716  1.00  0.00              
ATOM      4  CA  HIS     4       2.483  -6.697  -8.344  1.00  0.00              
ATOM      5  CA  ASP     5      -0.938  -8.041  -9.205  1.00  0.00              
ATOM      6  CA  ARG     6      -2.345  -6.986  -5.865  1.00  0.00              
ATOM      7  CA  VAL     7      -0.906  -3.526  -6.233  1.00  0.00              
ATOM      8  CA  ARG     8      -2.345  -3.160  -9.703  1.00  0.00              
ATOM      9  CA  LEU     9      -5.745  -4.287  -8.520  1.00  0.00              
ATOM     10  CA  GLN    10      -5.700  -1.770  -5.686  1.00  0.00              
ATOM     11  CA  LEU    11      -4.663   1.021  -8.094  1.00  0.00              
ATOM     12  CA  GLN    12      -7.520   0.098 -10.449  1.00  0.00              
ATOM     13  CA  ALA    13      -9.924   0.246  -7.486  1.00  0.00              
ATOM     14  CA  LEU    14      -8.587   3.696  -6.537  1.00  0.00              
ATOM     15  CA  GLU    15      -8.973   4.922 -10.113  1.00  0.00              
ATOM     16  CA  ALA    16     -12.571   3.655 -10.284  1.00  0.00              
ATOM     17  CA  LEU    17     -13.476   5.342  -7.064  1.00  0.00              
ATOM     18  CA  LEU    18     -12.036   8.643  -8.122  1.00  0.00              
ATOM     19  CA  ARG    19     -13.943   8.485 -11.412  1.00  0.00              
ATOM     20  CA  GLU    20     -17.262   7.630  -9.709  1.00  0.00              
ATOM     21  CA  HIS    21     -16.990  10.829  -7.697  1.00  0.00              
ATOM     22  CA  GLN    22     -16.642  12.918 -10.882  1.00  0.00              
ATOM     23  CA  HIS    23     -13.413  14.471  -9.770  1.00  0.00              
ATOM     24  CA  TRP    24     -10.885  12.810 -12.062  1.00  0.00              
ATOM     25  CA  ARG    25     -12.687  13.523 -15.342  1.00  0.00              
ATOM     26  CA  ASN    26     -12.945  17.239 -14.440  1.00  0.00              
ATOM     27  CA  ASP    27      -9.519  18.138 -13.017  1.00  0.00              
ATOM     28  CA  GLU    28      -8.169  20.924 -15.143  1.00  0.00              
ATOM     29  CA  PRO    29      -6.115  23.485 -13.374  1.00  0.00              
ATOM     30  CA  GLN    30      -7.827  26.786 -13.796  1.00  0.00              
ATOM     31  CA  PRO    31      -6.568  29.262 -16.404  1.00  0.00              
ATOM     32  CA  HIS    32      -5.760  31.824 -13.720  1.00  0.00              
ATOM     33  CA  GLN    33      -3.543  29.299 -11.825  1.00  0.00              
ATOM     34  CA  PHE    34      -1.694  28.363 -14.985  1.00  0.00              
ATOM     35  CA  ASN    35      -1.072  32.063 -15.831  1.00  0.00              
ATOM     36  CA  SER    36       0.685  32.722 -12.505  1.00  0.00              
ATOM     37  CA  THR    37       3.055  29.715 -12.767  1.00  0.00              
ATOM     38  CA  GLN    38       2.235  27.604  -9.760  1.00  0.00              
ATOM     39  CA  PRO    39       0.486  24.413 -10.940  1.00  0.00              
ATOM     40  CA  PHE    40      -3.021  23.859  -9.714  1.00  0.00              
ATOM     41  CA  PHE    41      -5.029  20.753 -10.330  1.00  0.00              
ATOM     42  CA  MET    42      -7.544  19.591  -7.746  1.00  0.00              
ATOM     43  CA  ASP    43     -10.953  18.608  -9.086  1.00  0.00              
ATOM     44  CA  THR    44     -12.343  16.903  -5.942  1.00  0.00              
ATOM     45  CA  MET    45      -9.316  14.783  -5.103  1.00  0.00              
ATOM     46  CA  GLU    46      -8.909  15.044  -1.303  1.00  0.00              
ATOM     47  CA  PRO    47      -5.282  15.076  -0.092  1.00  0.00              
ATOM     48  CA  LEU    48      -5.443  11.764   1.690  1.00  0.00              
ATOM     49  CA  GLU    49      -6.979   9.971  -1.304  1.00  0.00              
ATOM     50  CA  TRP    50      -4.387  11.408  -3.583  1.00  0.00              
ATOM     51  CA  LEU    51      -1.458  10.395  -1.315  1.00  0.00              
ATOM     52  CA  GLN    52      -2.766   6.881  -0.938  1.00  0.00              
ATOM     53  CA  TRP    53      -3.208   6.491  -4.661  1.00  0.00              
ATOM     54  CA  VAL    54       0.252   7.858  -5.454  1.00  0.00              
ATOM     55  CA  LEU    55       2.126   5.738  -2.879  1.00  0.00              
ATOM     56  CA  ILE    56       0.513   2.370  -3.141  1.00  0.00              
ATOM     57  CA  PRO    57      -0.259   1.515   0.506  1.00  0.00              
ATOM     58  CA  ARG    58       1.402  -1.911   0.830  1.00  0.00              
ATOM     59  CA  MET    59       4.602  -0.562  -0.803  1.00  0.00              
ATOM     60  CA  HIS    60       4.723   2.447   1.442  1.00  0.00              
ATOM     61  CA  ASP    61       4.398   0.307   4.538  1.00  0.00              
ATOM     62  CA  LEU    62       7.194  -2.010   3.340  1.00  0.00              
ATOM     63  CA  LEU    63       9.531   0.884   2.576  1.00  0.00              
ATOM     64  CA  ASP    64       8.853   2.601   5.930  1.00  0.00              
ATOM     65  CA  ASN    65       9.366  -0.566   7.897  1.00  0.00              
ATOM     66  CA  LYS    66      12.705  -1.516   6.260  1.00  0.00              
ATOM     67  CA  GLN    67      11.400  -4.798   4.993  1.00  0.00              
ATOM     68  CA  PRO    68      13.036  -6.066   1.861  1.00  0.00              
ATOM     69  CA  LEU    69      10.827  -6.302  -1.051  1.00  0.00              
ATOM     70  CA  PRO    70       8.895  -9.415  -1.889  1.00  0.00              
ATOM     71  CA  GLY    71      10.623 -11.517  -4.580  1.00  0.00              
ATOM     72  CA  ALA    72       8.288 -10.572  -7.417  1.00  0.00              
ATOM     73  CA  PHE    73       8.322  -6.799  -6.860  1.00  0.00              
ATOM     74  CA  ALA    74      11.106  -4.304  -6.509  1.00  0.00              
ATOM     75  CA  VAL    75       9.345  -1.678  -4.430  1.00  0.00              
ATOM     76  CA  ALA    76      10.982   1.585  -5.307  1.00  0.00              
ATOM     77  CA  PRO    77      10.561   1.184  -9.113  1.00  0.00              
ATOM     78  CA  TYR    78       6.983   0.017  -8.967  1.00  0.00              
ATOM     79  CA  TYR    79       5.675   2.774  -6.728  1.00  0.00              
ATOM     80  CA  GLU    80       7.408   5.455  -8.823  1.00  0.00              
ATOM     81  CA  MET    81       6.015   4.104 -12.117  1.00  0.00              
ATOM     82  CA  ALA    82       2.496   3.876 -10.855  1.00  0.00              
ATOM     83  CA  LEU    83       2.454   7.411  -9.489  1.00  0.00              
ATOM     84  CA  ALA    84       3.819   8.825 -12.753  1.00  0.00              
ATOM     85  CA  THR    85       1.307   7.041 -14.985  1.00  0.00              
ATOM     86  CA  ASP    86      -1.692   8.131 -12.907  1.00  0.00              
ATOM     87  CA  HIS    87      -0.796  11.839 -12.874  1.00  0.00              
ATOM     88  CA  PRO    88      -0.255  12.190 -16.640  1.00  0.00              
ATOM     89  CA  GLN    89      -2.628  15.040 -17.688  1.00  0.00              
ATOM     90  CA  ARG    90      -1.234  17.153 -14.794  1.00  0.00              
ATOM     91  CA  ALA    91       2.352  16.451 -15.883  1.00  0.00              
ATOM     92  CA  LEU    92       1.580  17.448 -19.504  1.00  0.00              
ATOM     93  CA  ILE    93      -0.053  20.656 -18.202  1.00  0.00              
ATOM     94  CA  LEU    94       3.006  21.433 -16.034  1.00  0.00              
ATOM     95  CA  ALA    95       5.263  20.842 -19.092  1.00  0.00              
ATOM     96  CA  GLU    96       3.101  23.166 -21.200  1.00  0.00              
ATOM     97  CA  LEU    97       3.247  25.878 -18.486  1.00  0.00              
ATOM     98  CA  GLU    98       7.046  25.638 -18.478  1.00  0.00              
ATOM     99  CA  LYS    99       7.024  26.058 -22.270  1.00  0.00              
ATOM    100  CA  LEU   100       4.792  29.108 -22.001  1.00  0.00              
ATOM    101  CA  ASP   101       7.222  30.598 -19.480  1.00  0.00              
ATOM    102  CA  ALA   102       9.988  30.247 -22.072  1.00  0.00              
ATOM    103  CA  LEU   103       7.788  31.991 -24.672  1.00  0.00              
ATOM    104  CA  PHE   104       7.038  34.844 -22.217  1.00  0.00              
ATOM    105  CA  ALA   105      10.743  35.338 -21.559  1.00  0.00              
ATOM    106  CA  ASP   106      11.656  35.441 -25.275  1.00  0.00              
ATOM    107  CA  ASP   107       8.932  37.930 -26.232  1.00  0.00              
ATOM    108  CA  ALA   108       6.913  35.599 -28.394  1.00  0.00              
ATOM    109  CA  SER   109       3.214  35.736 -27.374  1.00  0.00              
ATOM    110  CA  LEU   110       1.938  32.335 -26.278  1.00  0.00              
ATOM    111  CA  GLU   111      -1.131  33.476 -24.291  1.00  0.00              
ATOM    112  CA  HIS   112      -4.095  31.568 -25.575  1.00  0.00              
ATOM    113  CA  HIS   113      -6.824  34.128 -24.867  1.00  0.00              
ATOM    114  CA  HIS   114      -4.723  34.977 -27.938  1.00  0.00              
ATOM    115  CA  HIS   115      -3.167  38.500 -26.227  1.00  0.00              
ATOM    116  CA  HIS   116      -0.243  39.899 -28.894  1.00  0.00              
ATOM    117  CA  HIS   117       3.166  39.838 -26.727  1.00  0.00              
TER                                                                             
END
