
#######################################################
#                                                     #
#                        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_3-D1
# Molecule2: number of CA atoms  122 (  967),  selected  122 , name T0342_D1.pdb
# PARAMETERS: T0342TS168_3-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      -       -           -
LGA    L      18      F      17           #
LGA    Y      19      L      18           #
LGA    F      20      -       -           -
LGA    A      21      Y      19           #
LGA    Y      22      F      20          3.025
LGA    G      23      A      21           #
LGA    S      24      Y      22          2.242
LGA    N      25      G      23          2.025
LGA    L      26      S      24          4.663
LGA    L      27      N      25          4.272
LGA    T      28      L      26          3.341
LGA    E      29      L      27          3.892
LGA    R      30      -       -           -
LGA    I      31      -       -           -
LGA    H      32      T      28          1.299
LGA    L      33      E      29          2.496
LGA    R      34      R      30           -
LGA    N      35      -       -           -
LGA    P      36      I      31           #
LGA    S      37      H      32          2.050
LGA    -       -      L      33           -
LGA    A      38      R      34          2.610
LGA    A      39      N      35          4.625
LGA    F      40      P      36           -
LGA    F      41      S      37           -
LGA    C      42      -       -           -
LGA    V      43      -       -           -
LGA    A      44      -       -           -
LGA    R      45      A      38          3.661
LGA    L      46      A      39          1.519
LGA    Q      47      F      40          4.134
LGA    D      48      F      41          2.307
LGA    F      49      C      42          3.442
LGA    K      50      -       -           -
LGA    L      51      -       -           -
LGA    D      52      -       -           -
LGA    F      53      -       -           -
LGA    G      54      -       -           -
LGA    N      55      -       -           -
LGA    S      56      -       -           -
LGA    Q      57      -       -           -
LGA    G      58      -       -           -
LGA    K      59      -       -           -
LGA    T      60      -       -           -
LGA    S      61      -       -           -
LGA    Q      62      -       -           -
LGA    T      63      -       -           -
LGA    W      64      -       -           -
LGA    H      65      -       -           -
LGA    G      66      V      43          2.228
LGA    G      67      A      44          2.238
LGA    I      68      -       -           -
LGA    A      69      -       -           -
LGA    T      70      -       -           -
LGA    I      71      -       -           -
LGA    F      72      -       -           -
LGA    Q      73      -       -           -
LGA    S      74      -       -           -
LGA    P      75      -       -           -
LGA    G      76      -       -           -
LGA    D      77      -       -           -
LGA    E      78      -       -           -
LGA    V      79      -       -           -
LGA    W      80      -       -           -
LGA    G      81      -       -           -
LGA    V      82      -       -           -
LGA    V      83      -       -           -
LGA    W      84      -       -           -
LGA    K      85      R      45          3.645
LGA    M      86      L      46          2.402
LGA    N      87      Q      47          4.500
LGA    K      88      D      48           #
LGA    S      89      F      49          3.054
LGA    N      90      K      50          3.415
LGA    L      91      L      51          2.549
LGA    N      92      D      52          3.592
LGA    S      93      F      53           #
LGA    -       -      G      54           -
LGA    -       -      N      55           -
LGA    -       -      S      56           -
LGA    -       -      Q      57           -
LGA    -       -      G      58           -
LGA    -       -      K      59           -
LGA    -       -      T      60           -
LGA    -       -      S      61           -
LGA    -       -      Q      62           -
LGA    -       -      T      63           -
LGA    -       -      W      64           -
LGA    -       -      H      65           -
LGA    -       -      G      66           -
LGA    -       -      G      67           -
LGA    -       -      I      68           -
LGA    L      94      A      69          3.493
LGA    D      95      T      70          5.508
LGA    E      96      -       -           -
LGA    Q      97      -       -           -
LGA    E      98      -       -           -
LGA    G      99      -       -           -
LGA    V     100      I      71          4.507
LGA    K     101      F      72          2.762
LGA    S     102      Q      73          2.262
LGA    G     103      S      74           -
LGA    -       -      P      75           -
LGA    -       -      G      76           -
LGA    -       -      D      77           -
LGA    -       -      E      78           -
LGA    -       -      V      79           -
LGA    -       -      W      80           -
LGA    -       -      G      81           -
LGA    -       -      V      82           -
LGA    -       -      V      83           -
LGA    -       -      W      84           -
LGA    -       -      K      85           -
LGA    -       -      M      86           -
LGA    -       -      N      87           -
LGA    -       -      K      88           -
LGA    -       -      S      89           -
LGA    -       -      N      90           -
LGA    -       -      L      91           -
LGA    -       -      N      92           -
LGA    -       -      S      93           -
LGA    -       -      L      94           -
LGA    -       -      D      95           -
LGA    -       -      E      96           -
LGA    -       -      Q      97           -
LGA    -       -      E      98           -
LGA    -       -      G      99           -
LGA    -       -      V     100           -
LGA    -       -      K     101           -
LGA    -       -      S     102           -
LGA    -       -      G     103           -
LGA    -       -      M     104           -
LGA    -       -      Y     105           -
LGA    M     104      V     106           #
LGA    Y     105      V     107           -
LGA    V     106      I     108          4.546
LGA    V     107      E     109          3.320
LGA    I     108      V     110           -
LGA    E     109      K     111           -
LGA    V     110      V     112           -
LGA    K     111      A     113           -
LGA    V     112      T     114           -
LGA    A     113      Q     115           -
LGA    T     114      E     116           -
LGA    Q     115      G     117           -
LGA    E     116      K     118           -
LGA    G     117      E     119           -
LGA    K     118      I     120           -
LGA    E     119      -       -           -
LGA    I     120      -       -           -
LGA    T     121      T     121           #
LGA    C     122      -       -           -
LGA    R     123      C     122          4.493
LGA    S     124      R     123          1.958
LGA    Y     125      S     124          2.839
LGA    L     126      Y     125          2.832
LGA    M     127      L     126          4.361
LGA    T     128      M     127          3.777
LGA    N     129      T     128          3.186
LGA    Y     130      N     129          3.961
LGA    E     131      Y     130          1.204
LGA    S     132      E     131          1.312
LGA    A     133      S     132          3.864
LGA    P     134      A     133          1.709
LGA    P     135      P     134          2.269
LGA    -       -      P     135           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  122  122    5.0     46    3.29     4.35     19.651     1.358

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.250879 * X  +   0.599700 * Y  +  -0.759881 * Z  +  -2.473033
  Y_new =   0.647916 * X  +   0.687251 * Y  +   0.328467 * Z  +  90.112495
  Z_new =   0.719211 * X  +  -0.409933 * Y  +  -0.560972 * Z  +   0.314414 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.510522    0.631070  [ DEG:  -143.8423     36.1577 ]
  Theta =  -0.802667   -2.338926  [ DEG:   -45.9894   -134.0106 ]
  Phi   =   1.940228   -1.201365  [ DEG:   111.1669    -68.8331 ]
 
# 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_3-D1                               
REMARK     2: T0342_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0342TS168_3-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   46   3.29    4.35  19.651
REMARK  ---------------------------------------------------------- 
MOLECULE T0342TS168_3-D1
PFRMAT TS
TARGET T0342
MODEL 3
PARENT N/A
ATOM     14  CA  GLU    14     -18.788  82.757  -0.800  1.00 25.00           C
ATOM     15  CA  GLU    15     -15.391  84.059  -1.913  1.00 25.00           C
ATOM     16  CA  SER    16     -11.842  85.271  -2.139  1.00 25.00           C
ATOM     17  CA  PHE    17      -8.363  86.835  -1.655  1.00 25.00           C
ATOM     18  CA  LEU    18      -4.800  85.519  -2.153  1.00 25.00           C
ATOM     19  CA  TYR    19      -1.916  83.582  -0.501  1.00 25.00           C
ATOM     20  CA  PHE    20      -0.711  84.471   2.965  1.00 25.00           C
ATOM     21  CA  ALA    21       1.179  87.703   3.904  1.00 25.00           C
ATOM     22  CA  TYR    22       3.943  89.592   2.032  1.00 25.00           C
ATOM     23  CA  GLY    23       5.500  92.984   2.375  1.00 25.00           C
ATOM     24  CA  SER    24       6.934  91.289   5.517  1.00 25.00           C
ATOM     25  CA  ASN    25       3.946  90.011   7.494  1.00 25.00           C
ATOM     26  CA  LEU    26       5.482  87.329   9.714  1.00 25.00           C
ATOM     27  CA  LEU    27       1.910  86.660  10.625  1.00 25.00           C
ATOM     28  CA  THR    28       1.647  84.049   7.897  1.00 25.00           C
ATOM     29  CA  GLU    29      -0.317  81.176   9.495  1.00 25.00           C
ATOM     30  CA  ARG    30      -1.143  79.778   6.027  1.00 25.00           C
ATOM     31  CA  ILE    31       2.552  79.981   5.038  1.00 25.00           C
ATOM     32  CA  HIS    32       3.538  78.152   8.255  1.00 25.00           C
ATOM     33  CA  LEU    33       0.945  75.429   7.532  1.00 25.00           C
ATOM     34  CA  ARG    34       2.303  75.047   3.972  1.00 25.00           C
ATOM     35  CA  ASN    35       0.467  74.331   0.686  1.00 25.00           C
ATOM     36  CA  PRO    36      -2.859  74.426   2.567  1.00 25.00           C
ATOM     37  CA  SER    37      -4.781  76.435   5.246  1.00 25.00           C
ATOM     38  CA  ALA    38      -5.325  79.297   2.787  1.00 25.00           C
ATOM     39  CA  ALA    39      -5.370  82.907   3.992  1.00 25.00           C
ATOM     40  CA  PHE    40      -5.304  86.590   3.133  1.00 25.00           C
ATOM     41  CA  PHE    41      -3.077  89.447   1.927  1.00 25.00           C
ATOM     42  CA  CYS    42      -1.742  89.440  -1.619  1.00 25.00           C
ATOM     43  CA  VAL    43       1.396  87.315  -1.131  1.00 25.00           C
ATOM     44  CA  ALA    44       3.430  84.358   0.266  1.00 25.00           C
ATOM     45  CA  ARG    45       2.522  80.726  -0.584  1.00 25.00           C
ATOM     46  CA  LEU    46       4.676  77.665  -1.320  1.00 25.00           C
ATOM     47  CA  GLN    47       7.460  75.658  -3.047  1.00 25.00           C
ATOM     48  CA  ASP    48      10.429  77.987  -3.522  1.00 25.00           C
ATOM     49  CA  PHE    49      11.977  81.459  -3.808  1.00 25.00           C
ATOM     50  CA  LYS    50       8.805  82.911  -5.251  1.00 25.00           C
ATOM     51  CA  LEU    51       7.976  84.204  -1.815  1.00 25.00           C
ATOM     52  CA  ASP    52       7.644  85.034   1.867  1.00 25.00           C
ATOM     53  CA  PHE    53       5.840  86.035   5.024  1.00 25.00           C
ATOM     54  CA  GLY    54       6.405  82.758   6.951  1.00 25.00           C
ATOM     55  CA  ASN    55       8.689  80.758   4.604  1.00 25.00           C
ATOM     56  CA  SER    56       9.527  78.605   7.626  1.00 25.00           C
ATOM     57  CA  GLN    57      13.096  79.663   6.719  1.00 25.00           C
ATOM     58  CA  GLY    58      13.342  78.933   2.987  1.00 25.00           C
ATOM     59  CA  LYS    59      16.786  77.458   2.517  1.00 25.00           C
ATOM     60  CA  THR    60      18.541  80.602   3.889  1.00 25.00           C
ATOM     61  CA  SER    61      17.833  83.165   6.601  1.00 25.00           C
ATOM     62  CA  GLN    62      20.677  85.690   6.408  1.00 25.00           C
ATOM     63  CA  THR    63      18.528  88.483   4.845  1.00 25.00           C
ATOM     64  CA  TRP    64      16.275  88.613   7.916  1.00 25.00           C
ATOM     65  CA  HIS    65      13.688  85.885   7.459  1.00 25.00           C
ATOM     66  CA  GLY    66      12.583  84.910   3.967  1.00 25.00           C
ATOM     67  CA  GLY    67      12.485  85.335   0.201  1.00 25.00           C
ATOM     68  CA  ILE    68      13.709  88.573  -1.322  1.00 25.00           C
ATOM     69  CA  ALA    69      12.823  89.885  -4.791  1.00 25.00           C
ATOM     70  CA  THR    70      10.493  92.446  -6.298  1.00 25.00           C
ATOM     71  CA  ILE    71       6.887  92.335  -7.649  1.00 25.00           C
ATOM     72  CA  PHE    72       3.496  93.256  -9.071  1.00 25.00           C
ATOM     73  CA  GLN    73       2.209  96.275 -11.068  1.00 25.00           C
ATOM     74  CA  SER    74       3.218  99.046 -13.536  1.00 25.00           C
ATOM     75  CA  PRO    75       3.795  99.775 -17.191  1.00 25.00           C
ATOM     76  CA  GLY    76       5.161  96.195 -17.250  1.00 25.00           C
ATOM     77  CA  ASP    77       1.843  94.454 -16.835  1.00 25.00           C
ATOM     78  CA  GLU    78       1.871  91.667 -14.271  1.00 25.00           C
ATOM     79  CA  VAL    79       2.798  88.279 -12.771  1.00 25.00           C
ATOM     80  CA  TRP    80       5.305  88.088  -9.874  1.00 25.00           C
ATOM     81  CA  GLY    81       8.616  87.588  -8.017  1.00 25.00           C
ATOM     82  CA  VAL    82       7.972  88.521  -4.383  1.00 25.00           C
ATOM     83  CA  VAL    83       8.889  91.095  -1.713  1.00 25.00           C
ATOM     84  CA  TRP    84       9.814  89.655   1.748  1.00 25.00           C
ATOM     85  CA  LYS    85      12.099  89.831   4.804  1.00 25.00           C
ATOM     86  CA  MET    86      14.162  92.077   2.500  1.00 25.00           C
ATOM     87  CA  ASN    87      11.522  94.739   3.142  1.00 25.00           C
ATOM     88  CA  LYS    88      12.595  96.126   6.517  1.00 25.00           C
ATOM     89  CA  SER    89      11.231  99.614   7.321  1.00 25.00           C
ATOM     90  CA  ASN    90       7.905  98.726   5.643  1.00 25.00           C
ATOM     91  CA  LEU    91       7.718  95.483   7.674  1.00 25.00           C
ATOM     92  CA  ASN    92       8.403  97.434  10.897  1.00 25.00           C
ATOM     93  CA  SER    93       5.646  99.936   9.999  1.00 25.00           C
ATOM     94  CA  LEU    94       3.212  97.053   9.338  1.00 25.00           C
ATOM     95  CA  ASP    95       4.109  95.489  12.717  1.00 25.00           C
ATOM     96  CA  GLU    96       3.524  98.852  14.457  1.00 25.00           C
ATOM     97  CA  GLN    97       0.125  99.184  12.725  1.00 25.00           C
ATOM     98  CA  GLU    98       1.557 102.450  11.490  1.00 25.00           C
ATOM     99  CA  GLY    99       3.503 104.440   8.962  1.00 25.00           C
ATOM    100  CA  VAL   100       4.425 102.533   5.744  1.00 25.00           C
ATOM    101  CA  LYS   101       7.795 103.969   4.887  1.00 25.00           C
ATOM    102  CA  SER   102       7.965 102.478   1.396  1.00 25.00           C
ATOM    103  CA  GLY   103       4.422 101.528   0.336  1.00 25.00           C
ATOM    104  CA  MET   104       4.089  98.189   1.980  1.00 25.00           C
ATOM    105  CA  TYR   105       7.543  97.287   0.743  1.00 25.00           C
ATOM    106  CA  VAL   106       5.905  95.773  -2.310  1.00 25.00           C
ATOM    107  CA  VAL   107       2.533  96.618  -3.930  1.00 25.00           C
ATOM    108  CA  ILE   108      -0.042  94.012  -4.908  1.00 25.00           C
ATOM    109  CA  GLU   109      -2.815  91.669  -6.046  1.00 25.00           C
ATOM    110  CA  VAL   110      -3.210  87.947  -6.257  1.00 25.00           C
ATOM    111  CA  LYS   111      -1.146  86.767  -9.164  1.00 25.00           C
ATOM    112  CA  VAL   112      -0.378  83.112  -8.449  1.00 25.00           C
ATOM    113  CA  ALA   113      -1.030  81.114 -11.616  1.00 25.00           C
ATOM    114  CA  THR   114       0.892  77.950 -12.536  1.00 25.00           C
ATOM    115  CA  GLN   115      -0.665  77.088 -15.834  1.00 25.00           C
ATOM    116  CA  GLU   116       0.749  76.863 -19.348  1.00 25.00           C
ATOM    117  CA  GLY   117       4.163  77.983 -20.707  1.00 25.00           C
ATOM    118  CA  LYS   118       4.578  79.317 -17.122  1.00 25.00           C
ATOM    119  CA  GLU   119       3.685  81.809 -14.392  1.00 25.00           C
ATOM    120  CA  ILE   120       6.141  83.521 -12.051  1.00 25.00           C
ATOM    121  CA  THR   121       4.675  81.918  -8.965  1.00 25.00           C
ATOM    122  CA  CYS   122       3.469  82.222  -5.379  1.00 25.00           C
ATOM    123  CA  ARG   123       3.429  86.013  -5.663  1.00 25.00           C
ATOM    124  CA  SER   124       1.656  89.362  -5.781  1.00 25.00           C
ATOM    125  CA  TYR   125       4.015  91.112  -3.379  1.00 25.00           C
ATOM    126  CA  LEU   126       2.109  92.870  -0.535  1.00 25.00           C
ATOM    127  CA  MET   127      -1.244  94.246   0.614  1.00 25.00           C
ATOM    128  CA  THR   128      -1.452  97.918   1.624  1.00 25.00           C
ATOM    129  CA  ASN   129      -2.192 100.380   4.401  1.00 25.00           C
ATOM    130  CA  TYR   130      -2.452 101.782   7.957  1.00 25.00           C
ATOM    131  CA  GLU   131      -3.027 104.403  10.654  1.00 25.00           C
ATOM    132  CA  SER   132      -2.523 105.572  14.227  1.00 25.00           C
ATOM    133  CA  ALA   133      -1.300 105.129  17.735  1.00 25.00           C
ATOM    134  CA  PRO   134      -1.901 101.411  18.161  1.00 25.00           C
ATOM    135  CA  PRO   135      -0.821  97.807  18.362  1.00 25.00           C
TER
END
