
#######################################################
#                                                     #
#                        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   23 (  114),  selected   23 , name T0321TS102_3-D1
# Molecule2: number of CA atoms   96 (  710),  selected   96 , name T0321_D1.pdb
# PARAMETERS: T0321TS102_3-D1.T0321_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    S      69      -       -           -
LGA    W      70      M       1          4.208
LGA    N      71      W       2          3.813
LGA    Y      72      E       3          1.084
LGA    -       -      I       4           -
LGA    V      73      Y       5          2.667
LGA    E      74      D       6          2.679
LGA    -       -      A       7           -
LGA    A      75      M       8          5.195
LGA    S      76      I       9           -
LGA    -       -      N      10           -
LGA    -       -      G      11           -
LGA    -       -      I      12           -
LGA    -       -      P      13           -
LGA    -       -      E      14           -
LGA    -       -      D      15           -
LGA    -       -      F      16           -
LGA    -       -      L      17           -
LGA    -       -      V      18           -
LGA    -       -      D      19           -
LGA    -       -      E      20           -
LGA    -       -      L      21           -
LGA    -       -      V      22           -
LGA    -       -      C      23           -
LGA    -       -      G      24           -
LGA    -       -      T      25           -
LGA    -       -      T      26           -
LGA    -       -      H      27           -
LGA    -       -      S      28           -
LGA    -       -      V      29           -
LGA    -       -      I      30           -
LGA    -       -      R      31           -
LGA    -       -      S      32           -
LGA    -       -      G      33           -
LGA    -       -      N      34           -
LGA    -       -      G      35           -
LGA    -       -      V      36           -
LGA    -       -      G      37           -
LGA    -       -      L      38           -
LGA    -       -      G      39           -
LGA    -       -      P      40           -
LGA    -       -      N      41           -
LGA    -       -      R      42           -
LGA    -       -      P      43           -
LGA    -       -      F      44           -
LGA    -       -      E      45           -
LGA    -       -      T      46           -
LGA    -       -      R      47           -
LGA    -       -      M      48           -
LGA    -       -      P      49           -
LGA    -       -      M      50           -
LGA    -       -      L      51           -
LGA    -       -      T      52           -
LGA    -       -      Q      53           -
LGA    -       -      N      54           -
LGA    -       -      L      55           -
LGA    -       -      L      56           -
LGA    -       -      G      57           -
LGA    -       -      L      58           -
LGA    -       -      P      59           -
LGA    -       -      L      60           -
LGA    -       -      R      61           -
LGA    -       -      V      62           -
LGA    -       -      A      63           -
LGA    -       -      A      64           -
LGA    -       -      G      65           -
LGA    -       -      C      66           -
LGA    -       -      V      67           -
LGA    -       -      K      68           -
LGA    -       -      S      69           -
LGA    -       -      W      70           -
LGA    -       -      N      71           -
LGA    -       -      Y      72           -
LGA    -       -      V      73           -
LGA    -       -      E      74           -
LGA    -       -      A      75           -
LGA    I      77      S      76           #
LGA    -       -      I      77           -
LGA    G      78      G      78          3.246
LGA    L      79      L      79          2.198
LGA    -       -      A      80           -
LGA    A      80      A      81          0.647
LGA    A      81      I      82          1.290
LGA    I      82      N      83          0.414
LGA    N      83      A      84          1.678
LGA    A      84      Y      85          2.691
LGA    Y      85      Y      86          2.608
LGA    Y      86      N      87          2.108
LGA    N      87      N      88          2.160
LGA    -       -      P      89           -
LGA    -       -      Q      90           -
LGA    N      88      V      91          1.105
LGA    P      89      A      92          2.907
LGA    -       -      R      93           -
LGA    -       -      E      94           -
LGA    Q      90      H      95          1.073
LGA    V      91      G      96           #

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   23   96    5.0     19    2.61    26.32     14.467     0.702

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.006703 * X  +   0.185407 * Y  +   0.982639 * Z  +  -9.697199
  Y_new =  -0.072436 * X  +   0.979990 * Y  +  -0.185401 * Z  +  41.069210
  Z_new =  -0.997351 * X  +  -0.072421 * Y  +   0.006861 * Z  +  84.971519 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.476334    1.665259  [ DEG:   -84.5877     95.4123 ]
  Theta =   1.497987    1.643606  [ DEG:    85.8283     94.1717 ]
  Phi   =  -1.663067    1.478525  [ DEG:   -95.2867     84.7133 ]
 
# 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: T0321TS102_3-D1                               
REMARK     2: T0321_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0321TS102_3-D1.T0321_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   23   96   5.0   19   2.61   26.32  14.467
REMARK  ---------------------------------------------------------- 
MOLECULE T0321TS102_3-D1
PFRMAT TS
TARGET T0321
MODEL 3
PARENT 1uar_A
ATOM      1  N   SER    69      -9.180  37.940  49.620  1.00  1.00
ATOM      2  CA  SER    69      -8.470  38.739  50.660  1.00  1.00
ATOM      3  C   SER    69      -7.354  37.943  51.306  1.00  1.00
ATOM      4  O   SER    69      -6.958  36.890  50.799  1.00  1.00
ATOM      5  CB  SER    69      -9.488  39.116  51.754  1.00  1.00
ATOM      6  N   TRP    70      -6.840  38.443  52.425  1.00  1.00
ATOM      7  CA  TRP    70      -5.765  37.754  53.133  1.00  1.00
ATOM      8  C   TRP    70      -6.266  36.416  53.665  1.00  1.00
ATOM      9  O   TRP    70      -7.471  36.218  53.842  1.00  1.00
ATOM     10  CB  TRP    70      -5.260  38.592  54.315  1.00  1.00
ATOM     11  N   ASN    71      -5.338  35.502  53.920  1.00  1.00
ATOM     12  CA  ASN    71      -5.688  34.189  54.456  1.00  1.00
ATOM     13  C   ASN    71      -6.056  34.321  55.931  1.00  1.00
ATOM     14  O   ASN    71      -6.963  33.640  56.424  1.00  1.00
ATOM     15  CB  ASN    71      -4.519  33.226  54.296  1.00  1.00
ATOM     16  N   TYR    72      -5.350  35.210  56.625  1.00  1.00
ATOM     17  CA  TYR    72      -5.573  35.435  58.046  1.00  1.00
ATOM     18  C   TYR    72      -5.766  36.898  58.397  1.00  1.00
ATOM     19  O   TYR    72      -4.946  37.494  59.103  1.00  1.00
ATOM     20  CB  TYR    72      -4.407  34.854  58.848  1.00  1.00
ATOM     21  N   VAL    73      -6.862  37.504  57.920  1.00  1.00
ATOM     22  CA  VAL    73      -7.095  38.915  58.236  1.00  1.00
ATOM     23  C   VAL    73      -7.319  39.114  59.732  1.00  1.00
ATOM     24  O   VAL    73      -7.164  40.222  60.248  1.00  1.00
ATOM     25  CB  VAL    73      -8.340  39.247  57.422  1.00  1.00
ATOM     26  N   GLU    74      -7.667  38.040  60.440  1.00  1.00
ATOM     27  CA  GLU    74      -7.922  38.162  61.869  1.00  1.00
ATOM     28  C   GLU    74      -6.686  38.477  62.706  1.00  1.00
ATOM     29  O   GLU    74      -6.816  38.897  63.860  1.00  1.00
ATOM     30  CB  GLU    74      -8.627  36.905  62.419  1.00  1.00
ATOM     31  N   ALA    75      -5.490  38.290  62.144  1.00  1.00
ATOM     32  CA  ALA    75      -4.280  38.606  62.900  1.00  1.00
ATOM     33  C   ALA    75      -3.763  40.004  62.561  1.00  1.00
ATOM     34  O   ALA    75      -2.703  40.407  63.031  1.00  1.00
ATOM     35  CB  ALA    75      -3.136  37.568  62.673  1.00  1.00
ATOM     36  N   SER    76      -4.515  40.733  61.742  1.00  1.00
ATOM     37  CA  SER    76      -4.141  42.094  61.365  1.00  1.00
ATOM     38  C   SER    76      -5.235  43.049  61.850  1.00  1.00
ATOM     39  O   SER    76      -6.395  42.917  61.456  1.00  1.00
ATOM     40  CB  SER    76      -3.988  42.184  59.839  1.00  1.00
ATOM     41  N   ILE    77      -4.882  44.001  62.712  1.00  1.00
ATOM     42  CA  ILE    77      -5.871  44.954  63.208  1.00  1.00
ATOM     43  C   ILE    77      -5.581  46.368  62.713  1.00  1.00
ATOM     44  O   ILE    77      -4.428  46.734  62.469  1.00  1.00
ATOM     45  CB  ILE    77      -5.940  44.967  64.755  1.00  1.00
ATOM     46  N   GLY    78      -6.636  47.159  62.570  1.00  1.00
ATOM     47  CA  GLY    78      -6.502  48.529  62.092  1.00  1.00
ATOM     48  C   GLY    78      -6.209  49.482  63.242  1.00  1.00
ATOM     49  O   GLY    78      -6.353  49.134  64.413  1.00  1.00
ATOM     50  N   LEU    79      -5.792  50.697  62.910  1.00  1.00
ATOM     51  CA  LEU    79      -5.520  51.666  63.960  1.00  1.00
ATOM     52  C   LEU    79      -6.822  51.980  64.689  1.00  1.00
ATOM     53  O   LEU    79      -6.816  52.266  65.887  1.00  1.00
ATOM     54  CB  LEU    79      -4.908  52.954  63.389  1.00  1.00
ATOM     55  N   ALA    80      -7.939  51.916  63.963  1.00  1.00
ATOM     56  CA  ALA    80      -9.247  52.172  64.556  1.00  1.00
ATOM     57  C   ALA    80      -9.539  51.097  65.602  1.00  1.00
ATOM     58  O   ALA    80      -9.966  51.404  66.716  1.00  1.00
ATOM     59  CB  ALA    80     -10.339  52.146  63.482  1.00  1.00
ATOM     60  N   ALA    81      -9.312  49.841  65.226  1.00  1.00
ATOM     61  CA  ALA    81      -9.543  48.707  66.122  1.00  1.00
ATOM     62  C   ALA    81      -8.750  48.884  67.411  1.00  1.00
ATOM     63  O   ALA    81      -9.283  48.734  68.510  1.00  1.00
ATOM     64  CB  ALA    81      -9.130  47.396  65.437  1.00  1.00
ATOM     65  N   ILE    82      -7.475  49.228  67.277  1.00  1.00
ATOM     66  CA  ILE    82      -6.633  49.402  68.444  1.00  1.00
ATOM     67  C   ILE    82      -7.141  50.525  69.346  1.00  1.00
ATOM     68  O   ILE    82      -7.243  50.342  70.557  1.00  1.00
ATOM     69  CB  ILE    82      -5.171  49.650  68.018  1.00  1.00
ATOM     70  N   ASN    83      -7.489  51.674  68.771  1.00  1.00
ATOM     71  CA  ASN    83      -7.966  52.774  69.595  1.00  1.00
ATOM     72  C   ASN    83      -9.248  52.417  70.343  1.00  1.00
ATOM     73  O   ASN    83      -9.476  52.900  71.449  1.00  1.00
ATOM     74  CB  ASN    83      -8.186  54.046  68.762  1.00  1.00
ATOM     75  N   ALA    84     -10.076  51.560  69.753  1.00  1.00
ATOM     76  CA  ALA    84     -11.323  51.159  70.396  1.00  1.00
ATOM     77  C   ALA    84     -11.161  49.978  71.361  1.00  1.00
ATOM     78  O   ALA    84     -12.134  49.515  71.964  1.00  1.00
ATOM     79  CB  ALA    84     -12.384  50.850  69.337  1.00  1.00
ATOM     80  N   TYR    85      -9.932  49.505  71.524  1.00  1.00
ATOM     81  CA  TYR    85      -9.674  48.396  72.443  1.00  1.00
ATOM     82  C   TYR    85      -8.623  48.776  73.481  1.00  1.00
ATOM     83  O   TYR    85      -8.066  47.911  74.153  1.00  1.00
ATOM     84  CB  TYR    85      -9.223  47.158  71.663  1.00  1.00
ATOM     85  N   TYR    86      -8.362  50.074  73.615  1.00  1.00
ATOM     86  CA  TYR    86      -7.363  50.564  74.562  1.00  1.00
ATOM     87  C   TYR    86      -7.684  50.243  76.016  1.00  1.00
ATOM     88  O   TYR    86      -6.801  50.292  76.872  1.00  1.00
ATOM     89  CB  TYR    86      -7.178  52.073  74.413  1.00  1.00
ATOM     90  N   ASN    87      -8.943  49.919  76.294  1.00  1.00
ATOM     91  CA  ASN    87      -9.356  49.591  77.654  1.00  1.00
ATOM     92  C   ASN    87      -9.891  48.164  77.763  1.00  1.00
ATOM     93  O   ASN    87     -10.479  47.791  78.780  1.00  1.00
ATOM     94  CB  ASN    87     -10.425  50.580  78.132  1.00  1.00
ATOM     95  N   ASN    88      -9.696  47.370  76.713  1.00  1.00
ATOM     96  CA  ASN    88     -10.153  45.984  76.722  1.00  1.00
ATOM     97  C   ASN    88      -9.271  45.255  77.729  1.00  1.00
ATOM     98  O   ASN    88      -8.045  45.241  77.595  1.00  1.00
ATOM     99  CB  ASN    88      -9.993  45.355  75.333  1.00  1.00
ATOM    100  N   PRO    89      -9.876  44.656  78.765  1.00  1.00
ATOM    101  CA  PRO    89      -9.077  43.944  79.769  1.00  1.00
ATOM    102  C   PRO    89      -8.282  42.756  79.231  1.00  1.00
ATOM    103  O   PRO    89      -7.307  42.320  79.846  1.00  1.00
ATOM    104  CB  PRO    89     -10.120  43.535  80.812  1.00  1.00
ATOM    105  N   GLN    90      -8.691  42.239  78.078  1.00  1.00
ATOM    106  CA  GLN    90      -8.013  41.097  77.478  1.00  1.00
ATOM    107  C   GLN    90      -6.989  41.503  76.425  1.00  1.00
ATOM    108  O   GLN    90      -6.398  40.644  75.790  1.00  1.00
ATOM    109  CB  GLN    90      -9.039  40.154  76.843  1.00  1.00
ATOM    110  N   VAL    91      -6.777  42.804  76.252  1.00  1.00
ATOM    111  CA  VAL    91      -5.825  43.298  75.250  1.00  1.00
ATOM    112  C   VAL    91      -4.582  43.953  75.860  1.00  1.00
ATOM    113  O   VAL    91      -4.680  44.760  76.783  1.00  1.00
ATOM    114  CB  VAL    91      -6.494  44.335  74.308  1.00  1.00
TER
END
