
#######################################################
#                                                     #
#                        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  125 (  125),  selected  125 , name T0285TS168_2
# Molecule2: number of CA atoms   99 (  800),  selected   99 , name T0285.pdb
# PARAMETERS: T0285TS168_2.T0285.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    A       1      -       -           -
LGA    Y       2      -       -           -
LGA    L       3      -       -           -
LGA    P       4      -       -           -
LGA    D       5      -       -           -
LGA    D       6      -       -           -
LGA    S       7      -       -           -
LGA    P       8      -       -           -
LGA    A       9      -       -           -
LGA    K      10      S       7           #
LGA    R      11      P       8          4.796
LGA    L      12      A       9          2.942
LGA    L      13      K      10          1.445
LGA    F      14      R      11          1.934
LGA    Q      15      L      12          2.889
LGA    M      16      -       -           -
LGA    V      17      -       -           -
LGA    G      18      L      13           #
LGA    N      19      F      14           -
LGA    A      20      Q      15           -
LGA    I      21      -       -           -
LGA    N      22      -       -           -
LGA    R      23      -       -           -
LGA    N      24      -       -           -
LGA    T      25      -       -           -
LGA    Q      26      -       -           -
LGA    Q      27      -       -           -
LGA    L      28      -       -           -
LGA    T      29      -       -           -
LGA    Q      30      -       -           -
LGA    D      31      -       -           -
LGA    L      32      -       -           -
LGA    R      33      -       -           -
LGA    A      34      -       -           -
LGA    M      35      -       -           -
LGA    P      36      -       -           -
LGA    N      37      -       -           -
LGA    W      38      -       -           -
LGA    S      39      -       -           -
LGA    L      40      -       -           -
LGA    R      41      -       -           -
LGA    F      42      -       -           -
LGA    V      43      -       -           -
LGA    Y      44      -       -           -
LGA    I      45      M      16           #
LGA    V      46      V      17          4.307
LGA    D      47      G      18          3.473
LGA    R      48      N      19          4.839
LGA    N      49      A      20           -
LGA    N      50      I      21           -
LGA    Q      51      N      22           -
LGA    D      52      R      23           -
LGA    L      53      N      24           -
LGA    L      54      T      25           -
LGA    K      55      -       -           -
LGA    R      56      -       -           -
LGA    P      57      Q      26          4.569
LGA    L      58      Q      27          3.301
LGA    P      59      -       -           -
LGA    P      60      -       -           -
LGA    G      61      L      28          1.920
LGA    I      62      T      29          1.789
LGA    M      63      Q      30           -
LGA    -       -      D      31           -
LGA    -       -      L      32           -
LGA    -       -      R      33           -
LGA    -       -      A      34           -
LGA    -       -      M      35           -
LGA    -       -      P      36           -
LGA    -       -      N      37           -
LGA    -       -      W      38           -
LGA    -       -      S      39           -
LGA    -       -      L      40           -
LGA    -       -      R      41           -
LGA    -       -      F      42           -
LGA    -       -      V      43           -
LGA    -       -      Y      44           -
LGA    V      64      I      45          0.975
LGA    L      65      V      46          3.226
LGA    -       -      D      47           -
LGA    -       -      R      48           -
LGA    -       -      N      49           -
LGA    -       -      N      50           -
LGA    -       -      Q      51           -
LGA    -       -      D      52           -
LGA    -       -      L      53           -
LGA    -       -      L      54           -
LGA    -       -      K      55           -
LGA    -       -      R      56           -
LGA    -       -      P      57           -
LGA    -       -      L      58           -
LGA    -       -      P      59           -
LGA    -       -      P      60           -
LGA    -       -      G      61           -
LGA    A      66      I      62          4.708
LGA    -       -      M      63           -
LGA    -       -      V      64           -
LGA    -       -      L      65           -
LGA    P      67      A      66          1.330
LGA    R      68      P      67          3.476
LGA    -       -      R      68           -
LGA    -       -      L      69           -
LGA    L      69      T      70          1.866
LGA    -       -      A      71           -
LGA    T      70      K      72          4.178
LGA    A      71      H      73          4.319
LGA    K      72      P      74           -
LGA    H      73      Y      75           -
LGA    P      74      D      76          4.870
LGA    Y      75      K      77           -
LGA    D      76      -       -           -
LGA    K      77      -       -           -
LGA    V      78      V      78          3.683
LGA    Q      79      Q      79           #
LGA    D      80      -       -           -
LGA    R      81      D      80          3.025
LGA    N      82      -       -           -
LGA    R      83      -       -           -
LGA    K      84      -       -           -
LGA    L      85      -       -           -
LGA    Y      86      R      81          4.731
LGA    G      87      N      82          1.370
LGA    R      88      R      83          1.402
LGA    H      89      K      84          2.509
LGA    I      90      L      85          2.275
LGA    T      91      Y      86          0.611
LGA    L      92      G      87          0.664
LGA    N      93      R      88          1.913
LGA    D      94      H      89          1.954
LGA    G      95      I      90          2.007
LGA    N      96      T      91          3.321
LGA    -       -      L      92           -
LGA    -       -      N      93           -
LGA    -       -      D      94           -
LGA    -       -      G      95           -
LGA    -       -      N      96           -
LGA    S      97      S      97          2.639
LGA    V      98      V      98          1.723
LGA    K      99      K      99           #
LGA    V     100      V     100          2.514
LGA    V     101      V     101          3.422
LGA    T     102      T     102          2.914
LGA    I     103      I     103          4.676
LGA    S     104      S     104           -
LGA    A     105      -       -           -
LGA    G     106      A     105           #
LGA    R     107      -       -           -
LGA    D     108      -       -           -
LGA    E     109      -       -           -
LGA    G     110      -       -           -
LGA    P     111      -       -           -
LGA    D     112      -       -           -
LGA    R     113      -       -           -
LGA    D     114      -       -           -
LGA    I     115      -       -           -
LGA    I     116      -       -           -
LGA    W     117      -       -           -
LGA    E     118      -       -           -
LGA    M     119      -       -           -
LGA    F     120      -       -           -
LGA    L     121      -       -           -
LGA    E     122      -       -           -
LGA    N     123      -       -           -
LGA    L     124      -       -           -
LGA    E     125      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  125   99    5.0     40    3.13    22.50     23.705     1.239

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.988511 * X  +   0.042171 * Y  +  -0.145146 * Z  +  20.355816
  Y_new =  -0.151125 * X  +   0.258675 * Y  +  -0.954070 * Z  +   6.265951
  Z_new =  -0.002689 * X  +   0.965044 * Y  +   0.262076 * Z  +  82.674019 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.305623   -1.835970  [ DEG:    74.8067   -105.1933 ]
  Theta =   0.002689    3.138904  [ DEG:     0.1541    179.8459 ]
  Phi   =  -0.151706    2.989886  [ DEG:    -8.6921    171.3079 ]
 
# 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: T0285TS168_2                                  
REMARK     2: T0285.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0285TS168_2.T0285.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  125   99   5.0   40   3.13   22.50  23.705
REMARK  ---------------------------------------------------------- 
MOLECULE T0285TS168_2
PFRMAT TS
TARGET T0285
MODEL 2
PARENT N/A
ATOM      1  CA  ALA     1      11.884  40.618  86.484  1.00 25.00           C
ATOM      2  CA  TYR     2       9.350  38.386  84.759  1.00 25.00           C
ATOM      3  CA  LEU     3       8.241  36.041  81.906  1.00 25.00           C
ATOM      4  CA  PRO     4       9.451  32.448  82.474  1.00 25.00           C
ATOM      5  CA  ASP     5      10.338  28.852  81.780  1.00 25.00           C
ATOM      6  CA  ASP     6      10.646  27.823  85.440  1.00 25.00           C
ATOM      7  CA  SER     7      12.195  24.969  87.406  1.00 25.00           C
ATOM      8  CA  PRO     8      15.129  22.938  86.026  1.00 25.00           C
ATOM      9  CA  ALA     9      13.913  19.307  85.940  1.00 25.00           C
ATOM     10  CA  LYS    10      14.735  19.094  82.205  1.00 25.00           C
ATOM     11  CA  ARG    11      18.234  20.500  82.870  1.00 25.00           C
ATOM     12  CA  LEU    12      18.766  17.927  85.655  1.00 25.00           C
ATOM     13  CA  LEU    13      17.650  15.117  83.305  1.00 25.00           C
ATOM     14  CA  PHE    14      20.075  16.368  80.617  1.00 25.00           C
ATOM     15  CA  GLN    15      22.917  16.445  83.183  1.00 25.00           C
ATOM     16  CA  MET    16      22.074  12.867  84.260  1.00 25.00           C
ATOM     17  CA  VAL    17      22.093  11.735  80.602  1.00 25.00           C
ATOM     18  CA  GLY    18      25.498  13.407  80.076  1.00 25.00           C
ATOM     19  CA  ASN    19      26.865  11.660  83.198  1.00 25.00           C
ATOM     20  CA  ALA    20      25.554   8.296  81.921  1.00 25.00           C
ATOM     21  CA  ILE    21      27.210   8.913  78.524  1.00 25.00           C
ATOM     22  CA  ASN    22      30.516   9.764  80.262  1.00 25.00           C
ATOM     23  CA  ARG    23      30.280   6.555  82.337  1.00 25.00           C
ATOM     24  CA  ASN    24      29.626   4.519  79.160  1.00 25.00           C
ATOM     25  CA  THR    25      32.657   6.138  77.470  1.00 25.00           C
ATOM     26  CA  GLN    26      34.827   5.312  80.516  1.00 25.00           C
ATOM     27  CA  GLN    27      33.610   1.681  80.430  1.00 25.00           C
ATOM     28  CA  LEU    28      34.432   1.470  76.695  1.00 25.00           C
ATOM     29  CA  THR    29      37.932   2.875  77.359  1.00 25.00           C
ATOM     30  CA  GLN    30      38.464   0.301  80.145  1.00 25.00           C
ATOM     31  CA  ASP    31      37.348  -2.509  77.794  1.00 25.00           C
ATOM     32  CA  LEU    32      39.772  -1.257  75.107  1.00 25.00           C
ATOM     33  CA  ARG    33      42.615  -1.181  77.672  1.00 25.00           C
ATOM     34  CA  ALA    34      42.582  -3.121  80.870  1.00 25.00           C
ATOM     35  CA  MET    35      39.851  -5.697  80.927  1.00 25.00           C
ATOM     36  CA  PRO    36      39.583  -5.453  84.697  1.00 25.00           C
ATOM     37  CA  ASN    37      35.912  -4.816  83.939  1.00 25.00           C
ATOM     38  CA  TRP    38      32.893  -4.473  81.633  1.00 25.00           C
ATOM     39  CA  SER    39      30.271  -7.078  82.458  1.00 25.00           C
ATOM     40  CA  LEU    40      27.742  -4.240  82.337  1.00 25.00           C
ATOM     41  CA  ARG    41      27.267  -1.014  84.226  1.00 25.00           C
ATOM     42  CA  PHE    42      26.406   2.674  84.256  1.00 25.00           C
ATOM     43  CA  VAL    43      25.338   3.185  80.672  1.00 25.00           C
ATOM     44  CA  TYR    44      23.244   5.872  78.902  1.00 25.00           C
ATOM     45  CA  ILE    45      23.603   6.470  75.106  1.00 25.00           C
ATOM     46  CA  VAL    46      22.044   9.954  75.551  1.00 25.00           C
ATOM     47  CA  ASP    47      21.215  13.489  74.321  1.00 25.00           C
ATOM     48  CA  ARG    48      24.884  14.089  73.623  1.00 25.00           C
ATOM     49  CA  ASN    49      26.216  13.876  70.060  1.00 25.00           C
ATOM     50  CA  ASN    50      29.250  11.809  71.149  1.00 25.00           C
ATOM     51  CA  GLN    51      32.640  10.352  70.249  1.00 25.00           C
ATOM     52  CA  ASP    52      32.046   8.059  67.239  1.00 25.00           C
ATOM     53  CA  LEU    53      28.324   7.837  68.112  1.00 25.00           C
ATOM     54  CA  LEU    54      28.239   4.118  69.068  1.00 25.00           C
ATOM     55  CA  LYS    55      29.210   3.171  65.499  1.00 25.00           C
ATOM     56  CA  ARG    56      30.738  -0.233  66.224  1.00 25.00           C
ATOM     57  CA  PRO    57      27.260  -1.559  65.714  1.00 25.00           C
ATOM     58  CA  LEU    58      25.546  -1.512  69.069  1.00 25.00           C
ATOM     59  CA  PRO    59      21.828  -1.439  68.261  1.00 25.00           C
ATOM     60  CA  PRO    60      20.794  -1.207  71.916  1.00 25.00           C
ATOM     61  CA  GLY    61      23.386   1.440  72.532  1.00 25.00           C
ATOM     62  CA  ILE    62      25.108   0.549  75.853  1.00 25.00           C
ATOM     63  CA  MET    63      21.784   1.099  77.675  1.00 25.00           C
ATOM     64  CA  VAL    64      19.718   2.261  80.705  1.00 25.00           C
ATOM     65  CA  LEU    65      16.026   2.691  81.371  1.00 25.00           C
ATOM     66  CA  ALA    66      13.806   3.455  84.435  1.00 25.00           C
ATOM     67  CA  PRO    67      10.132   2.991  85.433  1.00 25.00           C
ATOM     68  CA  ARG    68       7.417   3.420  82.885  1.00 25.00           C
ATOM     69  CA  LEU    69       5.877   2.231  79.567  1.00 25.00           C
ATOM     70  CA  THR    70       2.670   4.251  79.265  1.00 25.00           C
ATOM     71  CA  ALA    71       0.365   6.573  81.205  1.00 25.00           C
ATOM     72  CA  LYS    72      -0.759   5.081  84.453  1.00 25.00           C
ATOM     73  CA  HIS    73       2.917   4.486  85.133  1.00 25.00           C
ATOM     74  CA  PRO    74       4.655   7.889  85.405  1.00 25.00           C
ATOM     75  CA  TYR    75       3.905   7.378  89.117  1.00 25.00           C
ATOM     76  CA  ASP    76       4.607   4.234  91.244  1.00 25.00           C
ATOM     77  CA  LYS    77       8.284   3.807  92.224  1.00 25.00           C
ATOM     78  CA  VAL    78       8.867   7.565  91.767  1.00 25.00           C
ATOM     79  CA  GLN    79       5.814   8.328  93.949  1.00 25.00           C
ATOM     80  CA  ASP    80       7.118   5.948  96.651  1.00 25.00           C
ATOM     81  CA  ARG    81      10.545   7.654  96.533  1.00 25.00           C
ATOM     82  CA  ASN    82       8.877  11.084  96.875  1.00 25.00           C
ATOM     83  CA  ARG    83       6.857   9.829  99.877  1.00 25.00           C
ATOM     84  CA  LYS    84      10.053   8.478 101.495  1.00 25.00           C
ATOM     85  CA  LEU    85      13.459  10.189 101.534  1.00 25.00           C
ATOM     86  CA  TYR    86      13.722  12.858  98.834  1.00 25.00           C
ATOM     87  CA  GLY    87      17.002  11.787  97.282  1.00 25.00           C
ATOM     88  CA  ARG    88      16.575  11.593  93.493  1.00 25.00           C
ATOM     89  CA  HIS    89      17.316  13.076  90.085  1.00 25.00           C
ATOM     90  CA  ILE    90      16.839  10.482  87.321  1.00 25.00           C
ATOM     91  CA  THR    91      14.229  11.654  84.742  1.00 25.00           C
ATOM     92  CA  LEU    92      13.517   8.340  82.939  1.00 25.00           C
ATOM     93  CA  ASN    93      13.237   6.917  79.412  1.00 25.00           C
ATOM     94  CA  ASP    94      10.495   7.422  76.765  1.00 25.00           C
ATOM     95  CA  GLY    95      11.295   7.344  73.048  1.00 25.00           C
ATOM     96  CA  ASN    96      10.031   3.798  72.450  1.00 25.00           C
ATOM     97  CA  SER    97      13.385   2.556  73.659  1.00 25.00           C
ATOM     98  CA  VAL    98      16.301   2.508  76.035  1.00 25.00           C
ATOM     99  CA  LYS    99      17.312   5.821  74.496  1.00 25.00           C
ATOM    100  CA  VAL   100      18.969   6.304  77.848  1.00 25.00           C
ATOM    101  CA  VAL   101      18.582   8.869  80.685  1.00 25.00           C
ATOM    102  CA  THR   102      20.504   7.454  83.691  1.00 25.00           C
ATOM    103  CA  ILE   103      22.759   7.299  86.752  1.00 25.00           C
ATOM    104  CA  SER   104      26.100   6.005  88.109  1.00 25.00           C
ATOM    105  CA  ALA   105      28.972   6.732  90.505  1.00 25.00           C
ATOM    106  CA  GLY   106      27.154   6.768  93.813  1.00 25.00           C
ATOM    107  CA  ARG   107      27.642   4.131  96.581  1.00 25.00           C
ATOM    108  CA  ASP   108      24.831   1.587  96.806  1.00 25.00           C
ATOM    109  CA  GLU   109      21.889   0.309  98.856  1.00 25.00           C
ATOM    110  CA  GLY   110      22.794  -3.175  97.475  1.00 25.00           C
ATOM    111  CA  PRO   111      23.381  -3.624  93.736  1.00 25.00           C
ATOM    112  CA  ASP   112      24.511  -2.627  90.262  1.00 25.00           C
ATOM    113  CA  ARG   113      23.998   0.565  88.285  1.00 25.00           C
ATOM    114  CA  ASP   114      20.283   0.656  89.211  1.00 25.00           C
ATOM    115  CA  ILE   115      19.409   1.865  85.683  1.00 25.00           C
ATOM    116  CA  ILE   116      21.498  -0.966  84.169  1.00 25.00           C
ATOM    117  CA  TRP   117      19.717  -3.512  86.408  1.00 25.00           C
ATOM    118  CA  GLU   118      16.316  -2.116  85.331  1.00 25.00           C
ATOM    119  CA  MET   119      17.349  -2.375  81.651  1.00 25.00           C
ATOM    120  CA  PHE   120      18.460  -6.000  82.193  1.00 25.00           C
ATOM    121  CA  LEU   121      15.112  -6.803  83.870  1.00 25.00           C
ATOM    122  CA  GLU   122      13.233  -5.219  80.932  1.00 25.00           C
ATOM    123  CA  ASN   123      15.303  -7.286  78.461  1.00 25.00           C
ATOM    124  CA  LEU   124      15.558 -10.771  79.936  1.00 25.00           C
ATOM    125  CA  GLU   125      14.164 -13.873  81.499  1.00 25.00           C
TER
END
