
#######################################################
#                                                     #
#                        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  122 (  122),  selected  122 , name T0342TS168_4-D1
# Molecule2: number of CA atoms  122 (  967),  selected  122 , name T0342_D1.pdb
# PARAMETERS: T0342TS168_4-D1.T0342_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    E      14      E      14           -
LGA    E      15      E      15           -
LGA    S      16      S      16           -
LGA    F      17      F      17           -
LGA    L      18      L      18           -
LGA    Y      19      Y      19           -
LGA    F      20      -       -           -
LGA    A      21      -       -           -
LGA    Y      22      -       -           -
LGA    G      23      F      20           #
LGA    S      24      -       -           -
LGA    N      25      -       -           -
LGA    L      26      A      21          4.583
LGA    L      27      Y      22          2.888
LGA    T      28      G      23          4.944
LGA    E      29      S      24           -
LGA    R      30      N      25           -
LGA    I      31      -       -           -
LGA    H      32      L      26          4.738
LGA    -       -      L      27           -
LGA    -       -      T      28           -
LGA    -       -      E      29           -
LGA    -       -      R      30           -
LGA    -       -      I      31           -
LGA    -       -      H      32           -
LGA    -       -      L      33           -
LGA    -       -      R      34           -
LGA    -       -      N      35           -
LGA    -       -      P      36           -
LGA    -       -      S      37           -
LGA    -       -      A      38           -
LGA    -       -      A      39           -
LGA    -       -      F      40           -
LGA    L      33      F      41          5.410
LGA    R      34      C      42          5.443
LGA    N      35      V      43          2.990
LGA    P      36      A      44          2.821
LGA    S      37      R      45          1.838
LGA    A      38      L      46          2.904
LGA    A      39      Q      47          3.582
LGA    F      40      D      48          3.332
LGA    F      41      F      49          1.103
LGA    C      42      K      50          4.041
LGA    V      43      L      51           #
LGA    A      44      D      52           #
LGA    R      45      F      53           #
LGA    L      46      G      54          4.629
LGA    Q      47      N      55          1.275
LGA    -       -      S      56           -
LGA    -       -      Q      57           -
LGA    -       -      G      58           -
LGA    -       -      K      59           -
LGA    D      48      T      60          4.457
LGA    F      49      S      61          4.279
LGA    -       -      Q      62           -
LGA    -       -      T      63           -
LGA    -       -      W      64           -
LGA    -       -      H      65           -
LGA    -       -      G      66           -
LGA    K      50      G      67          2.192
LGA    -       -      I      68           -
LGA    -       -      A      69           -
LGA    L      51      T      70          4.254
LGA    D      52      I      71          4.041
LGA    F      53      F      72           #
LGA    G      54      -       -           -
LGA    N      55      -       -           -
LGA    S      56      Q      73           #
LGA    Q      57      S      74          5.145
LGA    G      58      -       -           -
LGA    K      59      -       -           -
LGA    T      60      -       -           -
LGA    S      61      -       -           -
LGA    Q      62      -       -           -
LGA    T      63      P      75           #
LGA    W      64      G      76          2.145
LGA    H      65      D      77          1.433
LGA    G      66      E      78          2.360
LGA    G      67      -       -           -
LGA    I      68      V      79          1.244
LGA    A      69      W      80          4.563
LGA    T      70      G      81           #
LGA    I      71      V      82           -
LGA    F      72      V      83           -
LGA    Q      73      W      84           -
LGA    S      74      K      85           -
LGA    P      75      M      86           -
LGA    G      76      N      87           -
LGA    D      77      K      88           -
LGA    E      78      S      89           -
LGA    V      79      N      90           -
LGA    W      80      L      91           -
LGA    G      81      N      92           -
LGA    V      82      S      93           -
LGA    V      83      L      94           -
LGA    W      84      D      95           -
LGA    K      85      E      96           -
LGA    M      86      Q      97          4.563
LGA    N      87      E      98          1.835
LGA    K      88      G      99          1.507
LGA    S      89      V     100          3.514
LGA    -       -      K     101           -
LGA    -       -      S     102           -
LGA    N      90      G     103          3.163
LGA    L      91      M     104           #
LGA    N      92      Y     105           #
LGA    S      93      -       -           -
LGA    L      94      V     106          2.915
LGA    D      95      V     107          2.889
LGA    E      96      -       -           -
LGA    Q      97      I     108           #
LGA    E      98      -       -           -
LGA    G      99      -       -           -
LGA    V     100      -       -           -
LGA    K     101      E     109           #
LGA    S     102      V     110           #
LGA    G     103      K     111           #
LGA    M     104      V     112           #
LGA    -       -      A     113           -
LGA    -       -      T     114           -
LGA    -       -      Q     115           -
LGA    -       -      E     116           -
LGA    -       -      G     117           -
LGA    -       -      K     118           -
LGA    -       -      E     119           -
LGA    -       -      I     120           -
LGA    -       -      T     121           -
LGA    -       -      C     122           -
LGA    -       -      R     123           -
LGA    Y     105      S     124          1.763
LGA    V     106      Y     125          1.040
LGA    V     107      L     126          2.579
LGA    I     108      M     127          0.391
LGA    -       -      T     128           -
LGA    E     109      N     129           #
LGA    V     110      Y     130          2.833
LGA    K     111      E     131          4.108
LGA    V     112      S     132          2.251
LGA    A     113      A     133          3.077
LGA    T     114      -       -           -
LGA    Q     115      -       -           -
LGA    E     116      -       -           -
LGA    G     117      -       -           -
LGA    K     118      -       -           -
LGA    E     119      P     134          3.621
LGA    I     120      P     135          3.813
LGA    T     121      -       -           -
LGA    C     122      -       -           -
LGA    R     123      -       -           -
LGA    S     124      -       -           -
LGA    Y     125      -       -           -
LGA    L     126      -       -           -
LGA    M     127      -       -           -
LGA    T     128      -       -           -
LGA    N     129      -       -           -
LGA    Y     130      -       -           -
LGA    E     131      -       -           -
LGA    S     132      -       -           -
LGA    A     133      -       -           -
LGA    P     134      -       -           -
LGA    P     135      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  122  122    5.0     44    3.41     4.55     20.105     1.255

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.288434 * X  +  -0.857187 * Y  +  -0.426656 * Z  +   8.556043
  Y_new =  -0.931229 * X  +   0.354794 * Y  +  -0.083268 * Z  +  98.572296
  Z_new =   0.222751 * X  +   0.373297 * Y  +  -0.900573 * Z  +   0.486884 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.748640   -0.392953  [ DEG:   157.4854    -22.5146 ]
  Theta =  -0.224636   -2.916957  [ DEG:   -12.8707   -167.1293 ]
  Phi   =  -1.871160    1.270433  [ DEG:  -107.2096     72.7904 ]
 
# 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: T0342TS168_4-D1                               
REMARK     2: T0342_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0342TS168_4-D1.T0342_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  122  122   5.0   44   3.41    4.55  20.105
REMARK  ---------------------------------------------------------- 
MOLECULE T0342TS168_4-D1
PFRMAT TS
TARGET T0342
MODEL 4
PARENT N/A
ATOM     14  CA  GLU    14      15.966 113.967  -6.648  1.00 25.00           C
ATOM     15  CA  GLU    15      17.614 111.691  -4.000  1.00 25.00           C
ATOM     16  CA  SER    16      15.157 108.834  -3.286  1.00 25.00           C
ATOM     17  CA  PHE    17      12.412 106.378  -2.594  1.00 25.00           C
ATOM     18  CA  LEU    18      10.751 103.053  -1.603  1.00 25.00           C
ATOM     19  CA  TYR    19       9.606  99.451  -1.181  1.00 25.00           C
ATOM     20  CA  PHE    20       6.843  99.322   1.432  1.00 25.00           C
ATOM     21  CA  ALA    21       7.432  95.763   0.423  1.00 25.00           C
ATOM     22  CA  TYR    22       6.808  93.279   3.211  1.00 25.00           C
ATOM     23  CA  GLY    23       3.180  94.506   3.269  1.00 25.00           C
ATOM     24  CA  SER    24       3.440  93.105   6.815  1.00 25.00           C
ATOM     25  CA  ASN    25       6.821  92.568   8.601  1.00 25.00           C
ATOM     26  CA  LEU    26       7.141  89.224   6.798  1.00 25.00           C
ATOM     27  CA  LEU    27       3.548  88.361   7.708  1.00 25.00           C
ATOM     28  CA  THR    28       1.790  88.732   4.379  1.00 25.00           C
ATOM     29  CA  GLU    29       2.187  85.143   3.104  1.00 25.00           C
ATOM     30  CA  ARG    30       3.784  86.441  -0.126  1.00 25.00           C
ATOM     31  CA  ILE    31       6.197  88.608   1.909  1.00 25.00           C
ATOM     32  CA  HIS    32       7.126  85.587   4.070  1.00 25.00           C
ATOM     33  CA  LEU    33       7.755  83.498   0.923  1.00 25.00           C
ATOM     34  CA  ARG    34       9.972  86.274  -0.506  1.00 25.00           C
ATOM     35  CA  ASN    35      11.998  86.195   2.730  1.00 25.00           C
ATOM     36  CA  PRO    36      15.721  85.536   2.499  1.00 25.00           C
ATOM     37  CA  SER    37      16.062  89.326   2.150  1.00 25.00           C
ATOM     38  CA  ALA    38      13.516  91.210  -0.042  1.00 25.00           C
ATOM     39  CA  ALA    39      12.746  94.936  -0.547  1.00 25.00           C
ATOM     40  CA  PHE    40      12.265  97.634   2.106  1.00 25.00           C
ATOM     41  CA  PHE    41      10.930  99.130   5.384  1.00 25.00           C
ATOM     42  CA  CYS    42       7.610  97.298   5.681  1.00 25.00           C
ATOM     43  CA  VAL    43       3.937  98.313   5.568  1.00 25.00           C
ATOM     44  CA  ALA    44       0.647  96.924   6.790  1.00 25.00           C
ATOM     45  CA  ARG    45      -2.297  95.283   8.464  1.00 25.00           C
ATOM     46  CA  LEU    46      -3.418  98.795   9.343  1.00 25.00           C
ATOM     47  CA  GLN    47      -5.413 100.288  12.173  1.00 25.00           C
ATOM     48  CA  ASP    48      -7.587  97.123  12.002  1.00 25.00           C
ATOM     49  CA  PHE    49      -4.707  95.233  13.695  1.00 25.00           C
ATOM     50  CA  LYS    50      -1.580  97.394  13.851  1.00 25.00           C
ATOM     51  CA  LEU    51       1.520  98.038  11.693  1.00 25.00           C
ATOM     52  CA  ASP    52       4.793  97.211   9.925  1.00 25.00           C
ATOM     53  CA  PHE    53       8.160  96.679  11.547  1.00 25.00           C
ATOM     54  CA  GLY    54      10.431  99.592  10.447  1.00 25.00           C
ATOM     55  CA  ASN    55      11.685 103.123   9.831  1.00 25.00           C
ATOM     56  CA  SER    56      10.700 105.980   7.515  1.00 25.00           C
ATOM     57  CA  GLN    57      13.992 107.944   7.922  1.00 25.00           C
ATOM     58  CA  GLY    58      14.245 108.007  11.723  1.00 25.00           C
ATOM     59  CA  LYS    59      16.223 107.280  14.869  1.00 25.00           C
ATOM     60  CA  THR    60      17.543 103.795  15.562  1.00 25.00           C
ATOM     61  CA  SER    61      17.354 103.492  11.788  1.00 25.00           C
ATOM     62  CA  GLN    62      20.112 101.820   9.816  1.00 25.00           C
ATOM     63  CA  THR    63      20.213  99.645   6.684  1.00 25.00           C
ATOM     64  CA  TRP    64      16.815 100.557   5.312  1.00 25.00           C
ATOM     65  CA  HIS    65      15.559  98.765   8.483  1.00 25.00           C
ATOM     66  CA  GLY    66      16.271  95.106   7.793  1.00 25.00           C
ATOM     67  CA  GLY    67      14.456  94.440   4.474  1.00 25.00           C
ATOM     68  CA  ILE    68      11.177  92.866   5.724  1.00 25.00           C
ATOM     69  CA  ALA    69      11.786  92.816   9.445  1.00 25.00           C
ATOM     70  CA  THR    70      10.779  89.461  10.997  1.00 25.00           C
ATOM     71  CA  ILE    71       7.458  88.383  12.420  1.00 25.00           C
ATOM     72  CA  PHE    72       4.967  86.940  14.880  1.00 25.00           C
ATOM     73  CA  GLN    73       2.070  85.348  16.795  1.00 25.00           C
ATOM     74  CA  SER    74       3.720  83.320  19.602  1.00 25.00           C
ATOM     75  CA  PRO    75       5.444  79.942  20.129  1.00 25.00           C
ATOM     76  CA  GLY    76       8.229  80.968  17.743  1.00 25.00           C
ATOM     77  CA  ASP    77      10.314  83.855  19.123  1.00 25.00           C
ATOM     78  CA  GLU    78      11.484  87.523  18.822  1.00 25.00           C
ATOM     79  CA  VAL    79      11.547  90.025  15.937  1.00 25.00           C
ATOM     80  CA  TRP    80      11.407  93.746  15.074  1.00 25.00           C
ATOM     81  CA  GLY    81       7.709  92.981  14.622  1.00 25.00           C
ATOM     82  CA  VAL    82       4.272  93.245  13.014  1.00 25.00           C
ATOM     83  CA  VAL    83       1.433  91.492  11.252  1.00 25.00           C
ATOM     84  CA  TRP    84      -0.968  90.428   8.562  1.00 25.00           C
ATOM     85  CA  LYS    85      -4.688  90.002   7.657  1.00 25.00           C
ATOM     86  CA  MET    86      -4.390  90.234   3.914  1.00 25.00           C
ATOM     87  CA  ASN    87      -7.714  92.062   4.126  1.00 25.00           C
ATOM     88  CA  LYS    88     -10.838  93.601   2.559  1.00 25.00           C
ATOM     89  CA  SER    89     -11.827  95.615  -0.544  1.00 25.00           C
ATOM     90  CA  ASN    90      -8.851  97.963   0.001  1.00 25.00           C
ATOM     91  CA  LEU    91      -6.506  94.954   0.334  1.00 25.00           C
ATOM     92  CA  ASN    92      -7.908  93.471  -2.907  1.00 25.00           C
ATOM     93  CA  SER    93      -7.377  96.816  -4.695  1.00 25.00           C
ATOM     94  CA  LEU    94      -3.771  96.957  -3.413  1.00 25.00           C
ATOM     95  CA  ASP    95      -3.166  93.384  -4.651  1.00 25.00           C
ATOM     96  CA  GLU    96      -4.593  94.305  -8.083  1.00 25.00           C
ATOM     97  CA  GLN    97      -2.314  97.379  -8.234  1.00 25.00           C
ATOM     98  CA  GLU    98      -0.039  96.964 -11.168  1.00 25.00           C
ATOM     99  CA  GLY    99       1.786  93.680 -10.753  1.00 25.00           C
ATOM    100  CA  VAL   100       0.495  91.666  -7.824  1.00 25.00           C
ATOM    101  CA  LYS   101       0.170  89.068  -5.022  1.00 25.00           C
ATOM    102  CA  SER   102       3.730  88.219  -6.013  1.00 25.00           C
ATOM    103  CA  GLY   103       6.489  90.339  -4.475  1.00 25.00           C
ATOM    104  CA  MET   104       4.427  92.252  -1.995  1.00 25.00           C
ATOM    105  CA  TYR   105       1.366  90.893  -0.296  1.00 25.00           C
ATOM    106  CA  VAL   106      -0.771  93.970   0.349  1.00 25.00           C
ATOM    107  CA  VAL   107      -1.922  96.997   2.340  1.00 25.00           C
ATOM    108  CA  ILE   108      -1.645 100.074   4.577  1.00 25.00           C
ATOM    109  CA  GLU   109       0.134 102.127   7.158  1.00 25.00           C
ATOM    110  CA  VAL   110      -0.870 103.557  10.526  1.00 25.00           C
ATOM    111  CA  LYS   111       1.256 103.670  13.723  1.00 25.00           C
ATOM    112  CA  VAL   112       0.127 101.235  16.480  1.00 25.00           C
ATOM    113  CA  ALA   113       1.518 100.597  19.961  1.00 25.00           C
ATOM    114  CA  THR   114       4.808 100.961  21.828  1.00 25.00           C
ATOM    115  CA  GLN   115       3.228  99.443  24.901  1.00 25.00           C
ATOM    116  CA  GLU   116       1.943  98.492  28.344  1.00 25.00           C
ATOM    117  CA  GLY   117      -1.543  97.151  27.631  1.00 25.00           C
ATOM    118  CA  LYS   118      -1.079  94.572  24.890  1.00 25.00           C
ATOM    119  CA  GLU   119       0.783  94.689  21.588  1.00 25.00           C
ATOM    120  CA  ILE   120       3.608  95.519  19.111  1.00 25.00           C
ATOM    121  CA  THR   121       4.630  97.344  15.935  1.00 25.00           C
ATOM    122  CA  CYS   122       5.443 101.048  15.526  1.00 25.00           C
ATOM    123  CA  ARG   123       7.763 102.972  13.237  1.00 25.00           C
ATOM    124  CA  SER   124       5.319 102.304  10.364  1.00 25.00           C
ATOM    125  CA  TYR   125       7.199 101.810   7.094  1.00 25.00           C
ATOM    126  CA  LEU   126       5.242 103.259   4.184  1.00 25.00           C
ATOM    127  CA  MET   127       8.242 104.970   2.747  1.00 25.00           C
ATOM    128  CA  THR   128       7.849 107.120  -0.350  1.00 25.00           C
ATOM    129  CA  ASN   129       7.109 107.143  -4.043  1.00 25.00           C
ATOM    130  CA  TYR   130       8.964 104.682  -6.377  1.00 25.00           C
ATOM    131  CA  GLU   131      12.343 105.617  -7.770  1.00 25.00           C
ATOM    132  CA  SER   132      11.058 106.828 -11.076  1.00 25.00           C
ATOM    133  CA  ALA   133       8.495 106.843 -13.947  1.00 25.00           C
ATOM    134  CA  PRO   134       8.691 103.038 -14.203  1.00 25.00           C
ATOM    135  CA  PRO   135       7.444 102.314 -10.638  1.00 25.00           C
TER
END
