
#######################################################
#                                                     #
#                        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   92 (   92),  selected   92 , name T0329TS168_3-D2
# Molecule2: number of CA atoms   92 (  716),  selected   92 , name T0329_D2.pdb
# PARAMETERS: T0329TS168_3-D2.T0329_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    T      17      T      17           -
LGA    -       -      S      18           -
LGA    S      18      A      19           #
LGA    A      19      -       -           -
LGA    D      20      -       -           -
LGA    L      21      D      20          3.243
LGA    T      22      L      21           #
LGA    S      23      -       -           -
LGA    A      24      -       -           -
LGA    L      25      T      22          4.009
LGA    N      26      S      23          3.148
LGA    -       -      A      24           -
LGA    -       -      L      25           -
LGA    -       -      N      26           -
LGA    Y      27      Y      27          1.532
LGA    A      28      A      28          2.383
LGA    F      29      F      29          3.900
LGA    E      30      E      30          1.938
LGA    Q      31      Q      31          2.633
LGA    T      32      T      32          2.015
LGA    G      33      G      33          2.305
LGA    H      34      H      34          1.085
LGA    R      35      R      35          2.729
LGA    H      36      H      36          3.940
LGA    D      37      -       -           -
LGA    F      38      D      37           #
LGA    T      39      F      38          3.668
LGA    V      40      T      39          5.001
LGA    -       -      V      40           -
LGA    E      41      E      41          3.570
LGA    D      42      D      42          3.111
LGA    I      43      I      43           #
LGA    K      44      K      44          4.334
LGA    N      45      N      45          0.738
LGA    F      46      F      46          3.771
LGA    F      47      -       -           -
LGA    G      48      -       -           -
LGA    S      49      -       -           -
LGA    G      50      F      47          5.766
LGA    -       -      G      48           -
LGA    V      51      S      49          4.992
LGA    V      52      G      50          1.040
LGA    -       -      V      51           -
LGA    -       -      V      52           -
LGA    V      53      V      53          3.761
LGA    A      54      A      54          4.935
LGA    V      55      V      55           -
LGA    T      56      -       -           -
LGA    R      57      T      56           #
LGA    A      58      R      57           -
LGA    L      59      A      58           -
LGA    A      60      L      59           -
LGA    Y      61      A      60           -
LGA    E      62      Y      61           -
LGA    A      63      E      62           -
LGA    G      64      A      63           -
LGA    S      65      G      64           -
LGA    S      66      S      65           -
LGA    R      67      S      66           -
LGA    E      68      R      67           -
LGA    S      69      E      68           -
LGA    L      70      S      69           -
LGA    V      71      L      70           -
LGA    -       -      V      71           -
LGA    -       -      A      72           -
LGA    A      72      F      73           #
LGA    F      73      G      74          1.378
LGA    G      74      T      75          4.411
LGA    T      75      K      76           -
LGA    K      76      D      77          4.368
LGA    D      77      E      78          3.884
LGA    E      78      Q      79          2.192
LGA    Q      79      I      80          2.252
LGA    I      80      P      81          5.366
LGA    P      81      -       -           -
LGA    E      82      -       -           -
LGA    A      83      -       -           -
LGA    V      84      -       -           -
LGA    T      85      E      82          4.066
LGA    Q      86      -       -           -
LGA    T      87      -       -           -
LGA    E      88      A      83          4.675
LGA    -       -      V      84           -
LGA    V      89      T      85          1.404
LGA    -       -      Q      86           -
LGA    N      90      T      87          2.275
LGA    R      91      E      88          2.116
LGA    V      92      V      89          2.459
LGA    L      93      N      90          2.505
LGA    E      94      R      91          1.798
LGA    V      95      V      92          1.753
LGA    F      96      L      93          2.643
LGA    K      97      E      94          3.100
LGA    P      98      V      95          2.036
LGA    Y      99      F      96          1.816
LGA    Y     100      K      97          1.361
LGA    A     101      P      98          1.360
LGA    D     102      Y      99          1.589
LGA    H     103      Y     100          2.779
LGA    C     104      A     101          2.751
LGA    Q     105      D     102          2.421
LGA    I     106      H     103           -
LGA    K     107      C     104           -
LGA    T     108      Q     105           -
LGA    -       -      I     106           -
LGA    -       -      K     107           -
LGA    -       -      T     108           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   92   92    5.0     51    3.16    37.25     32.871     1.563

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.353407 * X  +  -0.544492 * Y  +   0.760679 * Z  +  -1.195493
  Y_new =   0.835109 * X  +  -0.182789 * Y  +  -0.518827 * Z  +  12.554077
  Z_new =   0.421540 * X  +   0.818607 * Y  +   0.390111 * Z  +  44.598743 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.126080   -2.015512  [ DEG:    64.5197   -115.4803 ]
  Theta =  -0.435143   -2.706449  [ DEG:   -24.9319   -155.0681 ]
  Phi   =   1.170462   -1.971130  [ DEG:    67.0626   -112.9374 ]
 
# 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: T0329TS168_3-D2                               
REMARK     2: T0329_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0329TS168_3-D2.T0329_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   92   92   5.0   51   3.16   37.25  32.871
REMARK  ---------------------------------------------------------- 
MOLECULE T0329TS168_3-D2
PFRMAT TS
TARGET T0329
MODEL 3
PARENT N/A
ATOM     17  CA  THR    17      -3.322  17.094  54.153  1.00 25.00           C
ATOM     18  CA  SER    18      -5.272  14.019  52.909  1.00 25.00           C
ATOM     19  CA  ALA    19      -8.114  15.715  54.836  1.00 25.00           C
ATOM     20  CA  ASP    20      -7.256  19.069  53.199  1.00 25.00           C
ATOM     21  CA  LEU    21      -7.271  17.415  49.745  1.00 25.00           C
ATOM     22  CA  THR    22     -10.683  15.842  50.486  1.00 25.00           C
ATOM     23  CA  SER    23     -12.042  19.248  51.587  1.00 25.00           C
ATOM     24  CA  ALA    24     -10.717  20.846  48.367  1.00 25.00           C
ATOM     25  CA  LEU    25     -12.378  18.090  46.289  1.00 25.00           C
ATOM     26  CA  ASN    26     -15.685  18.657  48.134  1.00 25.00           C
ATOM     27  CA  TYR    27     -15.436  22.422  47.477  1.00 25.00           C
ATOM     28  CA  ALA    28     -14.774  21.754  43.763  1.00 25.00           C
ATOM     29  CA  PHE    29     -17.812  19.428  43.615  1.00 25.00           C
ATOM     30  CA  GLU    30     -19.978  22.109  45.283  1.00 25.00           C
ATOM     31  CA  GLN    31     -18.747  24.711  42.757  1.00 25.00           C
ATOM     32  CA  THR    32     -21.391  27.222  41.681  1.00 25.00           C
ATOM     33  CA  GLY    33     -24.335  24.972  42.546  1.00 25.00           C
ATOM     34  CA  HIS    34     -23.052  22.032  40.609  1.00 25.00           C
ATOM     35  CA  ARG    35     -26.410  20.325  40.982  1.00 25.00           C
ATOM     36  CA  HIS    36     -24.877  17.195  42.572  1.00 25.00           C
ATOM     37  CA  ASP    37     -24.759  13.853  40.723  1.00 25.00           C
ATOM     38  CA  PHE    38     -22.289  12.099  38.329  1.00 25.00           C
ATOM     39  CA  THR    39     -20.849  10.218  41.316  1.00 25.00           C
ATOM     40  CA  VAL    40     -17.983  12.441  40.164  1.00 25.00           C
ATOM     41  CA  GLU    41     -15.980   9.177  40.257  1.00 25.00           C
ATOM     42  CA  ASP    42     -17.028   8.402  36.655  1.00 25.00           C
ATOM     43  CA  ILE    43     -15.958  11.913  35.564  1.00 25.00           C
ATOM     44  CA  LYS    44     -12.574  11.448  37.294  1.00 25.00           C
ATOM     45  CA  ASN    45     -12.110   8.078  35.535  1.00 25.00           C
ATOM     46  CA  PHE    46     -12.947   9.692  32.166  1.00 25.00           C
ATOM     47  CA  PHE    47     -10.411  12.481  32.844  1.00 25.00           C
ATOM     48  CA  GLY    48     -13.089  14.747  31.428  1.00 25.00           C
ATOM     49  CA  SER    49     -13.325  16.440  34.843  1.00 25.00           C
ATOM     50  CA  GLY    50     -10.172  17.730  36.503  1.00 25.00           C
ATOM     51  CA  VAL    51      -7.259  16.152  34.600  1.00 25.00           C
ATOM     52  CA  VAL    52      -4.291  17.140  32.390  1.00 25.00           C
ATOM     53  CA  VAL    53      -6.630  17.531  29.383  1.00 25.00           C
ATOM     54  CA  ALA    54      -8.981  19.722  31.465  1.00 25.00           C
ATOM     55  CA  VAL    55      -6.022  21.884  32.577  1.00 25.00           C
ATOM     56  CA  THR    56      -4.895  22.257  28.936  1.00 25.00           C
ATOM     57  CA  ARG    57      -8.442  23.280  27.917  1.00 25.00           C
ATOM     58  CA  ALA    58      -8.533  25.866  30.740  1.00 25.00           C
ATOM     59  CA  LEU    59      -5.151  27.259  29.607  1.00 25.00           C
ATOM     60  CA  ALA    60      -6.430  27.504  26.006  1.00 25.00           C
ATOM     61  CA  TYR    61      -4.972  31.053  26.347  1.00 25.00           C
ATOM     62  CA  GLU    62      -2.666  30.055  23.445  1.00 25.00           C
ATOM     63  CA  ALA    63      -3.944  27.292  21.147  1.00 25.00           C
ATOM     64  CA  GLY    64      -2.018  24.453  19.443  1.00 25.00           C
ATOM     65  CA  SER    65      -1.144  22.962  22.860  1.00 25.00           C
ATOM     66  CA  SER    66      -4.821  23.153  23.913  1.00 25.00           C
ATOM     67  CA  ARG    67      -5.867  21.414  20.664  1.00 25.00           C
ATOM     68  CA  GLU    68      -3.273  18.661  21.275  1.00 25.00           C
ATOM     69  CA  SER    69      -4.577  18.192  24.846  1.00 25.00           C
ATOM     70  CA  LEU    70      -8.165  17.943  23.530  1.00 25.00           C
ATOM     71  CA  VAL    71      -7.063  15.334  20.952  1.00 25.00           C
ATOM     72  CA  ALA    72      -5.305  13.325  23.698  1.00 25.00           C
ATOM     73  CA  PHE    73      -8.466  13.467  25.858  1.00 25.00           C
ATOM     74  CA  GLY    74      -9.244   9.728  25.435  1.00 25.00           C
ATOM     75  CA  THR    75     -12.747  10.732  26.528  1.00 25.00           C
ATOM     76  CA  LYS    76     -13.851  10.218  22.917  1.00 25.00           C
ATOM     77  CA  ASP    77     -17.539  10.567  22.191  1.00 25.00           C
ATOM     78  CA  GLU    78     -17.356  13.326  19.540  1.00 25.00           C
ATOM     79  CA  GLN    79     -19.374  15.667  21.803  1.00 25.00           C
ATOM     80  CA  ILE    80     -17.021  14.907  24.728  1.00 25.00           C
ATOM     81  CA  PRO    81     -13.986  15.641  22.511  1.00 25.00           C
ATOM     82  CA  GLU    82     -15.559  18.958  21.417  1.00 25.00           C
ATOM     83  CA  ALA    83     -16.212  19.884  25.076  1.00 25.00           C
ATOM     84  CA  VAL    84     -19.866  20.586  24.513  1.00 25.00           C
ATOM     85  CA  THR    85     -21.559  23.232  22.392  1.00 25.00           C
ATOM     86  CA  GLN    86     -21.091  26.118  24.775  1.00 25.00           C
ATOM     87  CA  THR    87     -22.345  27.161  28.239  1.00 25.00           C
ATOM     88  CA  GLU    88     -21.689  23.629  29.567  1.00 25.00           C
ATOM     89  CA  VAL    89     -18.150  23.711  28.106  1.00 25.00           C
ATOM     90  CA  ASN    90     -17.523  27.112  29.750  1.00 25.00           C
ATOM     91  CA  ARG    91     -18.767  25.747  33.105  1.00 25.00           C
ATOM     92  CA  VAL    92     -16.449  22.718  32.761  1.00 25.00           C
ATOM     93  CA  LEU    93     -13.498  25.033  31.989  1.00 25.00           C
ATOM     94  CA  GLU    94     -14.328  27.156  35.067  1.00 25.00           C
ATOM     95  CA  VAL    95     -14.479  24.002  37.234  1.00 25.00           C
ATOM     96  CA  PHE    96     -11.084  22.872  35.868  1.00 25.00           C
ATOM     97  CA  LYS    97      -9.599  26.317  36.640  1.00 25.00           C
ATOM     98  CA  PRO    98     -10.998  26.148  40.202  1.00 25.00           C
ATOM     99  CA  TYR    99      -9.484  22.660  40.657  1.00 25.00           C
ATOM    100  CA  TYR   100      -6.099  23.939  39.402  1.00 25.00           C
ATOM    101  CA  ALA   101      -6.276  26.881  41.847  1.00 25.00           C
ATOM    102  CA  ASP   102      -7.087  24.478  44.717  1.00 25.00           C
ATOM    103  CA  HIS   103      -4.116  22.269  43.740  1.00 25.00           C
ATOM    104  CA  CYS   104      -1.824  25.337  43.673  1.00 25.00           C
ATOM    105  CA  GLN   105      -3.078  26.379  47.139  1.00 25.00           C
ATOM    106  CA  ILE   106      -3.581  30.153  46.610  1.00 25.00           C
ATOM    107  CA  LYS   107       0.236  30.282  47.000  1.00 25.00           C
ATOM    108  CA  THR   108       1.937  26.884  47.161  1.00 25.00           C
TER
END
