
#######################################################
#                                                     #
#                        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_2-D1
# Molecule2: number of CA atoms  126 ( 1027),  selected  126 , name T0372_D1.pdb
# PARAMETERS: T0372TS393_2-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      -       -           -
LGA    I       7      -       -           -
LGA    T       8      -       -           -
LGA    L       9      -       -           -
LGA    A      10      -       -           -
LGA    D      11      -       -           -
LGA    R      12      -       -           -
LGA    D      13      -       -           -
LGA    T      14      -       -           -
LGA    I      15      -       -           -
LGA    T      16      -       -           -
LGA    A      17      -       -           -
LGA    F      18      -       -           -
LGA    T      19      -       -           -
LGA    M      20      -       -           -
LGA    K      21      -       -           -
LGA    S      22      -       -           -
LGA    D      23      -       -           -
LGA    R      24      -       -           -
LGA    R      25      D       6          4.154
LGA    N      26      I       7          1.990
LGA    C      27      T       8           #
LGA    -       -      L       9           -
LGA    -       -      A      10           -
LGA    D      28      D      11           #
LGA    L      29      R      12           -
LGA    S      30      D      13           -
LGA    F      31      -       -           -
LGA    S      32      -       -           -
LGA    N      33      -       -           -
LGA    L      34      -       -           -
LGA    C      35      -       -           -
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      -       -           -
LGA    V      47      T      14          0.866
LGA    I      48      I      15          1.163
LGA    D      49      T      16          1.873
LGA    D      50      A      17          2.612
LGA    F      51      F      18          3.077
LGA    -       -      T      19           -
LGA    -       -      M      20           -
LGA    -       -      K      21           -
LGA    -       -      S      22           -
LGA    -       -      D      23           -
LGA    -       -      R      24           -
LGA    -       -      R      25           -
LGA    -       -      N      26           -
LGA    -       -      C      27           -
LGA    -       -      D      28           -
LGA    -       -      L      29           -
LGA    -       -      S      30           -
LGA    -       -      F      31           -
LGA    -       -      S      32           -
LGA    -       -      N      33           -
LGA    -       -      L      34           -
LGA    -       -      C      35           -
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           -
LGA    -       -      V      47           -
LGA    -       -      I      48           -
LGA    -       -      D      49           -
LGA    L      52      D      50          3.198
LGA    V      53      F      51          0.834
LGA    F      54      L      52           #
LGA    K      55      -       -           -
LGA    F      56      -       -           -
LGA    W      57      -       -           -
LGA    A      58      -       -           -
LGA    G      59      -       -           -
LGA    E      60      -       -           -
LGA    Q      61      -       -           -
LGA    L      62      -       -           -
LGA    A      63      -       -           -
LGA    Y      64      -       -           -
LGA    M      65      -       -           -
LGA    M      66      V      53          2.314
LGA    P      67      F      54           #
LGA    V      68      K      55           -
LGA    G      69      -       -           -
LGA    N      70      -       -           -
LGA    G      71      -       -           -
LGA    D      72      -       -           -
LGA    L      73      -       -           -
LGA    K      74      -       -           -
LGA    A      75      -       -           -
LGA    V      76      -       -           -
LGA    L      77      -       -           -
LGA    R      78      -       -           -
LGA    K      79      -       -           -
LGA    L      80      -       -           -
LGA    I      81      -       -           -
LGA    E      82      -       -           -
LGA    D      83      -       -           -
LGA    A      84      F      56          2.412
LGA    D      85      W      57          1.054
LGA    K      86      A      58          2.497
LGA    -       -      G      59           -
LGA    -       -      E      60           -
LGA    -       -      Q      61           -
LGA    E      87      L      62          2.109
LGA    K      88      A      63           -
LGA    -       -      Y      64           -
LGA    -       -      M      65           -
LGA    -       -      M      66           -
LGA    -       -      P      67           -
LGA    -       -      V      68           -
LGA    -       -      G      69           -
LGA    -       -      N      70           -
LGA    -       -      G      71           -
LGA    -       -      D      72           -
LGA    -       -      L      73           -
LGA    -       -      K      74           -
LGA    -       -      A      75           -
LGA    -       -      V      76           -
LGA    -       -      L      77           -
LGA    -       -      R      78           -
LGA    -       -      K      79           -
LGA    -       -      L      80           -
LGA    -       -      I      81           -
LGA    -       -      E      82           -
LGA    -       -      D      83           -
LGA    -       -      A      84           -
LGA    -       -      D      85           -
LGA    -       -      K      86           -
LGA    -       -      E      87           -
LGA    -       -      K      88           -
LGA    H      89      H      89          1.630
LGA    N      90      N      90          1.885
LGA    F      91      F      91          2.687
LGA    C      92      C      92          1.976
LGA    M      93      M      93          2.277
LGA    L      94      L      94          1.853
LGA    G      95      G      95          3.133
LGA    V      96      V      96          0.978
LGA    C      97      C      97          2.713
LGA    -       -      S      98           -
LGA    -       -      N      99           -
LGA    S      98      M     100          2.719
LGA    N      99      R     101           #
LGA    M     100      A     102          3.010
LGA    R     101      D     103          3.842
LGA    A     102      L     104           #
LGA    D     103      E     105          4.568
LGA    L     104      A     106           #
LGA    -       -      I     107           -
LGA    -       -      L     108           -
LGA    -       -      P     109           -
LGA    -       -      E     110           -
LGA    -       -      R     111           -
LGA    -       -      F     112           -
LGA    -       -      I     113           -
LGA    E     105      F     114          4.339
LGA    A     106      T     115           -
LGA    I     107      -       -           -
LGA    L     108      -       -           -
LGA    P     109      -       -           -
LGA    E     110      -       -           -
LGA    R     111      -       -           -
LGA    F     112      -       -           -
LGA    I     113      -       -           -
LGA    F     114      -       -           -
LGA    T     115      E     116           #
LGA    -       -      D     117           -
LGA    -       -      K     290           -
LGA    E     116      Y     291          3.013
LGA    D     117      M     292          5.366
LGA    K     290      A     293           -
LGA    Y     291      C     294           -
LGA    M     292      L     295           -
LGA    A     293      K     296           -
LGA    C     294      D     297           -
LGA    L     295      H     298           -
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     30    2.77    36.67     16.078     1.046

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.689434 * X  +  -0.722335 * Y  +   0.053972 * Z  +  42.596573
  Y_new =   0.034574 * X  +   0.107242 * Y  +   0.993632 * Z  +  58.079563
  Z_new =  -0.723523 * X  +  -0.683177 * Y  +   0.098910 * Z  +  -3.617872 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.427016    1.714577  [ DEG:   -81.7620     98.2380 ]
  Theta =   0.808893    2.332700  [ DEG:    46.3461    133.6539 ]
  Phi   =   0.050106   -3.091486  [ DEG:     2.8709   -177.1291 ]
 
# 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_2-D1                               
REMARK     2: T0372_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0372TS393_2-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   30   2.77   36.67  16.078
REMARK  ---------------------------------------------------------- 
MOLECULE T0372TS393_2-D1
PFRMAT TS
TARGET T0372
MODEL 2
PARENT N/A
ATOM      1  CA  MET     1      18.757  36.198 -14.941  1.00 25.00           C
ATOM      2  CA  ILE     2      21.780  35.581 -12.607  1.00 25.00           C
ATOM      3  CA  PRO     3      19.387  34.105 -10.088  1.00 25.00           C
ATOM      4  CA  PHE     4      21.161  32.390  -7.147  1.00 25.00           C
ATOM      5  CA  LYS     5      22.739  28.869  -7.266  1.00 25.00           C
ATOM      6  CA  ASP     6      24.887  28.538 -10.436  1.00 25.00           C
ATOM      7  CA  ILE     7      28.217  30.340  -9.843  1.00 25.00           C
ATOM      8  CA  THR     8      30.762  28.130  -8.126  1.00 25.00           C
ATOM      9  CA  LEU     9      31.788  30.857  -5.672  1.00 25.00           C
ATOM     10  CA  ALA    10      33.191  32.649  -8.750  1.00 25.00           C
ATOM     11  CA  ASP    11      36.217  34.364 -10.281  1.00 25.00           C
ATOM     12  CA  ARG    12      37.792  32.016  -7.696  1.00 25.00           C
ATOM     13  CA  ASP    13      41.144  32.198  -9.539  1.00 25.00           C
ATOM     14  CA  THR    14      40.940  36.022  -9.587  1.00 25.00           C
ATOM     15  CA  ILE    15      40.194  36.053  -5.831  1.00 25.00           C
ATOM     16  CA  THR    16      43.192  33.757  -5.191  1.00 25.00           C
ATOM     17  CA  ALA    17      45.432  36.063  -7.272  1.00 25.00           C
ATOM     18  CA  PHE    18      44.192  39.097  -5.292  1.00 25.00           C
ATOM     19  CA  THR    19      44.918  37.277  -2.002  1.00 25.00           C
ATOM     20  CA  MET    20      48.443  36.416  -3.229  1.00 25.00           C
ATOM     21  CA  LYS    21      49.853  35.059   0.076  1.00 25.00           C
ATOM     22  CA  SER    22      51.874  36.316   3.062  1.00 25.00           C
ATOM     23  CA  ASP    23      51.376  39.466   5.128  1.00 25.00           C
ATOM     24  CA  ARG    24      51.488  43.118   6.005  1.00 25.00           C
ATOM     25  CA  ARG    25      50.225  46.557   5.130  1.00 25.00           C
ATOM     26  CA  ASN    26      49.361  50.133   4.154  1.00 25.00           C
ATOM     27  CA  CYS    27      45.799  51.384   3.674  1.00 25.00           C
ATOM     28  CA  ASP    28      44.557  54.344   5.622  1.00 25.00           C
ATOM     29  CA  LEU    29      43.835  58.025   4.770  1.00 25.00           C
ATOM     30  CA  SER    30      41.936  57.386   1.506  1.00 25.00           C
ATOM     31  CA  PHE    31      42.303  59.285  -1.819  1.00 25.00           C
ATOM     32  CA  SER    32      44.040  56.253  -3.387  1.00 25.00           C
ATOM     33  CA  ASN    33      47.395  58.097  -3.299  1.00 25.00           C
ATOM     34  CA  LEU    34      46.840  58.980   0.387  1.00 25.00           C
ATOM     35  CA  CYS    35      46.024  55.320   1.166  1.00 25.00           C
ATOM     36  CA  SER    36      49.209  54.200  -0.641  1.00 25.00           C
ATOM     37  CA  TRP    37      51.265  56.739   1.355  1.00 25.00           C
ATOM     38  CA  ARG    38      49.713  55.469   4.617  1.00 25.00           C
ATOM     39  CA  PHE    39      53.291  55.255   5.805  1.00 25.00           C
ATOM     40  CA  LEU    40      56.963  56.177   6.555  1.00 25.00           C
ATOM     41  CA  TYR    41      60.580  56.840   7.646  1.00 25.00           C
ATOM     42  CA  ASP    42      62.354  60.101   8.166  1.00 25.00           C
ATOM     43  CA  THR    43      59.394  61.655   6.262  1.00 25.00           C
ATOM     44  CA  GLN    44      55.956  62.805   7.411  1.00 25.00           C
ATOM     45  CA  PHE    45      52.184  63.189   7.730  1.00 25.00           C
ATOM     46  CA  ALA    46      49.455  61.266   9.431  1.00 25.00           C
ATOM     47  CA  VAL    47      46.507  58.891   9.461  1.00 25.00           C
ATOM     48  CA  ILE    48      42.803  57.954   9.734  1.00 25.00           C
ATOM     49  CA  ASP    49      41.896  59.900  12.896  1.00 25.00           C
ATOM     50  CA  ASP    50      40.490  62.892  10.902  1.00 25.00           C
ATOM     51  CA  PHE    51      38.179  62.603   7.884  1.00 25.00           C
ATOM     52  CA  LEU    52      37.931  64.146   4.414  1.00 25.00           C
ATOM     53  CA  VAL    53      38.799  61.232   2.163  1.00 25.00           C
ATOM     54  CA  PHE    54      37.454  63.352  -0.714  1.00 25.00           C
ATOM     55  CA  LYS    55      39.248  62.773  -4.001  1.00 25.00           C
ATOM     56  CA  PHE    56      35.969  64.105  -5.441  1.00 25.00           C
ATOM     57  CA  TRP    57      33.046  65.374  -7.603  1.00 25.00           C
ATOM     58  CA  ALA    58      30.331  67.123  -9.680  1.00 25.00           C
ATOM     59  CA  GLY    59      26.524  67.131  -9.445  1.00 25.00           C
ATOM     60  CA  GLU    60      26.010  63.536  -8.188  1.00 25.00           C
ATOM     61  CA  GLN    61      28.297  60.632  -7.291  1.00 25.00           C
ATOM     62  CA  LEU    62      31.136  58.089  -7.238  1.00 25.00           C
ATOM     63  CA  ALA    63      34.307  57.937  -5.196  1.00 25.00           C
ATOM     64  CA  TYR    64      36.118  58.596  -1.964  1.00 25.00           C
ATOM     65  CA  MET    65      35.962  57.213   1.561  1.00 25.00           C
ATOM     66  CA  MET    66      37.875  54.269   2.937  1.00 25.00           C
ATOM     67  CA  PRO    67      36.888  55.774   6.334  1.00 25.00           C
ATOM     68  CA  VAL    68      33.988  58.142   7.177  1.00 25.00           C
ATOM     69  CA  GLY    69      32.972  56.732  10.561  1.00 25.00           C
ATOM     70  CA  ASN    70      32.312  56.597  14.333  1.00 25.00           C
ATOM     71  CA  GLY    71      33.635  54.204  16.987  1.00 25.00           C
ATOM     72  CA  ASP    72      31.839  51.072  15.879  1.00 25.00           C
ATOM     73  CA  LEU    73      33.224  51.861  12.370  1.00 25.00           C
ATOM     74  CA  LYS    74      36.613  50.100  12.644  1.00 25.00           C
ATOM     75  CA  ALA    75      34.939  46.721  11.974  1.00 25.00           C
ATOM     76  CA  VAL    76      33.167  48.179   8.909  1.00 25.00           C
ATOM     77  CA  LEU    77      36.492  49.575   7.619  1.00 25.00           C
ATOM     78  CA  ARG    78      38.145  46.155   8.108  1.00 25.00           C
ATOM     79  CA  LYS    79      35.281  44.470   6.203  1.00 25.00           C
ATOM     80  CA  LEU    80      35.658  46.999   3.352  1.00 25.00           C
ATOM     81  CA  ILE    81      39.426  46.329   3.222  1.00 25.00           C
ATOM     82  CA  GLU    82      38.776  42.557   3.095  1.00 25.00           C
ATOM     83  CA  ASP    83      36.269  43.060   0.245  1.00 25.00           C
ATOM     84  CA  ALA    84      38.824  45.182  -1.662  1.00 25.00           C
ATOM     85  CA  ASP    85      41.479  42.465  -1.173  1.00 25.00           C
ATOM     86  CA  LYS    86      39.037  39.811  -2.460  1.00 25.00           C
ATOM     87  CA  GLU    87      36.690  41.708  -4.764  1.00 25.00           C
ATOM     88  CA  LYS    88      38.355  41.451  -8.179  1.00 25.00           C
ATOM     89  CA  HIS    89      37.102  44.528 -10.133  1.00 25.00           C
ATOM     90  CA  ASN    90      34.258  46.823 -11.214  1.00 25.00           C
ATOM     91  CA  PHE    91      35.252  48.940  -8.236  1.00 25.00           C
ATOM     92  CA  CYS    92      32.364  47.369  -6.350  1.00 25.00           C
ATOM     93  CA  MET    93      32.986  49.006  -2.987  1.00 25.00           C
ATOM     94  CA  LEU    94      31.960  47.758   0.432  1.00 25.00           C
ATOM     95  CA  GLY    95      29.098  48.914   2.672  1.00 25.00           C
ATOM     96  CA  VAL    96      26.826  51.678   3.878  1.00 25.00           C
ATOM     97  CA  CYS    97      26.051  54.083   6.786  1.00 25.00           C
ATOM     98  CA  SER    98      25.533  57.836   6.645  1.00 25.00           C
ATOM     99  CA  ASN    99      21.815  58.531   6.050  1.00 25.00           C
ATOM    100  CA  MET   100      22.481  59.026   2.311  1.00 25.00           C
ATOM    101  CA  ARG   101      24.415  55.723   2.193  1.00 25.00           C
ATOM    102  CA  ALA   102      21.524  53.939   3.961  1.00 25.00           C
ATOM    103  CA  ASP   103      19.040  55.426   1.453  1.00 25.00           C
ATOM    104  CA  LEU   104      21.240  54.257  -1.456  1.00 25.00           C
ATOM    105  CA  GLU   105      21.405  50.740   0.051  1.00 25.00           C
ATOM    106  CA  ALA   106      17.595  50.694   0.424  1.00 25.00           C
ATOM    107  CA  ILE   107      17.199  51.790  -3.224  1.00 25.00           C
ATOM    108  CA  LEU   108      16.293  55.498  -2.784  1.00 25.00           C
ATOM    109  CA  PRO   109      14.354  55.804   0.522  1.00 25.00           C
ATOM    110  CA  GLU   110      15.228  55.805   4.190  1.00 25.00           C
ATOM    111  CA  ARG   111      17.417  55.384   7.307  1.00 25.00           C
ATOM    112  CA  PHE   112      19.819  55.354  10.214  1.00 25.00           C
ATOM    113  CA  ILE   113      21.830  52.341   9.108  1.00 25.00           C
ATOM    114  CA  PHE   114      23.023  49.641   6.684  1.00 25.00           C
ATOM    115  CA  THR   115      26.060  47.327   6.316  1.00 25.00           C
ATOM    116  CA  GLU   116      26.074  44.021   4.384  1.00 25.00           C
ATOM    117  CA  ASP   117      22.759  43.773   2.526  1.00 25.00           C
ATOM    290  CA  LYS   290      46.524  72.936 -20.284  1.00 25.00           C
ATOM    291  CA  TYR   291      49.730  70.852 -20.057  1.00 25.00           C
ATOM    292  CA  MET   292      48.228  68.810 -17.187  1.00 25.00           C
ATOM    293  CA  ALA   293      45.049  68.217 -19.240  1.00 25.00           C
ATOM    294  CA  CYS   294      47.161  67.079 -22.226  1.00 25.00           C
ATOM    295  CA  LEU   295      49.111  64.681 -19.964  1.00 25.00           C
ATOM    296  CA  LYS   296      50.873  62.483 -22.509  1.00 25.00           C
ATOM    297  CA  ASP   297      51.868  60.233 -25.394  1.00 25.00           C
ATOM    298  CA  HIS   298      49.950  62.720 -27.562  1.00 25.00           C
TER
END
