
#######################################################
#                                                     #
#                        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   96 (   96),  selected   96 , name T0321TS393_5-D1
# Molecule2: number of CA atoms   96 (  710),  selected   96 , name T0321_D1.pdb
# PARAMETERS: T0321TS393_5-D1.T0321_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    -       -      W       2           -
LGA    -       -      E       3           -
LGA    -       -      I       4           -
LGA    -       -      Y       5           -
LGA    -       -      D       6           -
LGA    -       -      A       7           -
LGA    -       -      M       8           -
LGA    -       -      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    W       2      G      24          2.544
LGA    E       3      T      25          3.900
LGA    I       4      T      26          2.370
LGA    Y       5      H      27          2.665
LGA    D       6      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    A       7      P      40           #
LGA    M       8      N      41          1.918
LGA    I       9      R      42          3.880
LGA    N      10      P      43          3.121
LGA    G      11      F      44          3.704
LGA    I      12      E      45           #
LGA    P      13      -       -           -
LGA    E      14      T      46           #
LGA    D      15      R      47          4.120
LGA    F      16      M      48          2.697
LGA    L      17      P      49          2.332
LGA    V      18      M      50          4.876
LGA    -       -      L      51           -
LGA    D      19      T      52          2.773
LGA    -       -      Q      53           -
LGA    E      20      N      54           #
LGA    L      21      L      55          3.357
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      L      56          3.957
LGA    V      36      G      57          2.722
LGA    G      37      -       -           -
LGA    L      38      L      58          2.486
LGA    G      39      P      59          2.956
LGA    P      40      L      60          3.766
LGA    N      41      R      61          2.675
LGA    R      42      V      62           -
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    S      76      A      63          3.483
LGA    I      77      A      64          2.947
LGA    G      78      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    -       -      S      76           -
LGA    -       -      I      77           -
LGA    -       -      G      78           -
LGA    -       -      L      79           -
LGA    L      79      A      80          2.899
LGA    A      80      A      81          3.174
LGA    A      81      I      82          4.417
LGA    I      82      N      83          2.777
LGA    N      83      A      84          3.565
LGA    A      84      -       -           -
LGA    Y      85      Y      85          3.864
LGA    Y      86      Y      86          2.029
LGA    N      87      N      87          1.100
LGA    N      88      N      88           #
LGA    -       -      P      89           -
LGA    -       -      Q      90           -
LGA    P      89      V      91          4.399
LGA    Q      90      A      92          3.168
LGA    V      91      R      93          1.302
LGA    A      92      E      94          1.214
LGA    R      93      H      95          1.954
LGA    E      94      G      96          2.790
LGA    H      95      -       -           -
LGA    G      96      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   96   96    5.0     36    3.13    16.67     21.429     1.116

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.447905 * X  +  -0.701219 * Y  +  -0.554683 * Z  + -19.905952
  Y_new =  -0.745174 * X  +  -0.050044 * Y  +   0.664990 * Z  +  51.367203
  Z_new =  -0.494062 * X  +   0.711187 * Y  +  -0.500116 * Z  +  60.075302 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.183675   -0.957918  [ DEG:   125.1154    -54.8846 ]
  Theta =   0.516756    2.624837  [ DEG:    29.6079    150.3921 ]
  Phi   =  -2.112005    1.029587  [ DEG:  -121.0090     58.9910 ]
 
# 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: T0321TS393_5-D1                               
REMARK     2: T0321_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0321TS393_5-D1.T0321_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   96   96   5.0   36   3.13   16.67  21.429
REMARK  ---------------------------------------------------------- 
MOLECULE T0321TS393_5-D1
PFRMAT TS
TARGET T0321
MODEL 5
PARENT N/A
ATOM      1  CA  MET     1      -0.520  65.816  65.739  1.00 25.00           C
ATOM      2  CA  TRP     2      -0.693  62.435  64.131  1.00 25.00           C
ATOM      3  CA  GLU     3       3.111  62.331  63.706  1.00 25.00           C
ATOM      4  CA  ILE     4       2.999  58.514  63.413  1.00 25.00           C
ATOM      5  CA  TYR     5       0.236  58.773  60.775  1.00 25.00           C
ATOM      6  CA  ASP     6       2.310  61.330  58.818  1.00 25.00           C
ATOM      7  CA  ALA     7       5.355  59.013  58.970  1.00 25.00           C
ATOM      8  CA  MET     8       3.226  56.091  57.707  1.00 25.00           C
ATOM      9  CA  ILE     9       1.922  58.253  54.827  1.00 25.00           C
ATOM     10  CA  ASN    10       5.507  59.254  53.925  1.00 25.00           C
ATOM     11  CA  GLY    11       4.885  63.042  54.100  1.00 25.00           C
ATOM     12  CA  ILE    12       3.135  66.406  54.666  1.00 25.00           C
ATOM     13  CA  PRO    13       4.360  67.280  51.196  1.00 25.00           C
ATOM     14  CA  GLU    14       0.918  67.702  49.619  1.00 25.00           C
ATOM     15  CA  ASP    15      -1.944  65.392  50.683  1.00 25.00           C
ATOM     16  CA  PHE    16      -4.934  63.539  52.118  1.00 25.00           C
ATOM     17  CA  LEU    17      -8.547  62.614  53.032  1.00 25.00           C
ATOM     18  CA  VAL    18      -9.570  60.859  56.265  1.00 25.00           C
ATOM     19  CA  ASP    19     -11.025  58.347  58.718  1.00 25.00           C
ATOM     20  CA  GLU    20     -13.773  56.368  60.343  1.00 25.00           C
ATOM     21  CA  LEU    21     -15.470  54.196  57.775  1.00 25.00           C
ATOM     22  CA  VAL    22     -16.329  50.509  57.396  1.00 25.00           C
ATOM     23  CA  CYS    23     -16.989  46.933  56.276  1.00 25.00           C
ATOM     24  CA  GLY    24     -15.195  45.400  59.199  1.00 25.00           C
ATOM     25  CA  THR    25     -17.569  43.917  61.837  1.00 25.00           C
ATOM     26  CA  THR    26     -21.259  44.147  62.834  1.00 25.00           C
ATOM     27  CA  HIS    27     -21.857  47.917  63.309  1.00 25.00           C
ATOM     28  CA  SER    28     -20.599  50.509  65.751  1.00 25.00           C
ATOM     29  CA  VAL    29     -17.411  52.544  64.983  1.00 25.00           C
ATOM     30  CA  ILE    30     -16.415  56.118  65.955  1.00 25.00           C
ATOM     31  CA  ARG    31     -14.968  59.027  67.823  1.00 25.00           C
ATOM     32  CA  SER    32     -13.150  59.339  64.447  1.00 25.00           C
ATOM     33  CA  GLY    33     -11.933  62.914  64.007  1.00 25.00           C
ATOM     34  CA  ASN    34     -15.137  63.694  65.905  1.00 25.00           C
ATOM     35  CA  GLY    35     -17.913  61.272  65.221  1.00 25.00           C
ATOM     36  CA  VAL    36     -17.939  59.283  62.001  1.00 25.00           C
ATOM     37  CA  GLY    37     -19.504  55.986  60.839  1.00 25.00           C
ATOM     38  CA  LEU    38     -19.270  52.181  60.585  1.00 25.00           C
ATOM     39  CA  GLY    39     -17.451  49.091  62.020  1.00 25.00           C
ATOM     40  CA  PRO    40     -16.865  47.456  65.412  1.00 25.00           C
ATOM     41  CA  ASN    41     -13.321  46.283  64.669  1.00 25.00           C
ATOM     42  CA  ARG    42     -10.411  44.447  66.241  1.00 25.00           C
ATOM     43  CA  PRO    43      -8.315  43.843  63.106  1.00 25.00           C
ATOM     44  CA  PHE    44      -8.493  41.812  59.912  1.00 25.00           C
ATOM     45  CA  GLU    45      -5.237  41.837  57.911  1.00 25.00           C
ATOM     46  CA  THR    46      -4.883  45.111  55.915  1.00 25.00           C
ATOM     47  CA  ARG    47      -5.627  43.054  52.760  1.00 25.00           C
ATOM     48  CA  MET    48      -9.324  43.507  53.578  1.00 25.00           C
ATOM     49  CA  PRO    49      -9.825  40.563  51.158  1.00 25.00           C
ATOM     50  CA  MET    50      -9.775  37.379  53.286  1.00 25.00           C
ATOM     51  CA  LEU    51     -11.440  39.258  56.179  1.00 25.00           C
ATOM     52  CA  THR    52     -14.133  40.583  53.800  1.00 25.00           C
ATOM     53  CA  GLN    53     -14.754  37.039  52.488  1.00 25.00           C
ATOM     54  CA  ASN    54     -15.067  35.739  56.077  1.00 25.00           C
ATOM     55  CA  LEU    55     -17.559  38.529  56.896  1.00 25.00           C
ATOM     56  CA  LEU    56     -19.601  37.656  53.777  1.00 25.00           C
ATOM     57  CA  GLY    57     -19.165  33.939  53.093  1.00 25.00           C
ATOM     58  CA  LEU    58     -21.975  34.408  50.561  1.00 25.00           C
ATOM     59  CA  PRO    59     -24.711  36.117  52.521  1.00 25.00           C
ATOM     60  CA  LEU    60     -26.832  38.396  50.407  1.00 25.00           C
ATOM     61  CA  ARG    61     -24.554  37.689  47.411  1.00 25.00           C
ATOM     62  CA  VAL    62     -24.850  41.340  46.294  1.00 25.00           C
ATOM     63  CA  ALA    63     -23.968  42.519  49.829  1.00 25.00           C
ATOM     64  CA  ALA    64     -20.921  40.198  49.869  1.00 25.00           C
ATOM     65  CA  GLY    65     -19.803  41.565  46.470  1.00 25.00           C
ATOM     66  CA  CYS    66     -20.180  45.151  47.761  1.00 25.00           C
ATOM     67  CA  VAL    67     -18.109  44.279  50.863  1.00 25.00           C
ATOM     68  CA  LYS    68     -15.395  42.736  48.646  1.00 25.00           C
ATOM     69  CA  SER    69     -13.495  45.942  47.957  1.00 25.00           C
ATOM     70  CA  TRP    70     -13.474  46.283  51.713  1.00 25.00           C
ATOM     71  CA  ASN    71     -10.135  48.074  51.062  1.00 25.00           C
ATOM     72  CA  TYR    72      -9.403  51.279  53.042  1.00 25.00           C
ATOM     73  CA  VAL    73     -12.798  51.080  54.802  1.00 25.00           C
ATOM     74  CA  GLU    74     -11.555  48.144  56.923  1.00 25.00           C
ATOM     75  CA  ALA    75      -8.411  50.121  57.860  1.00 25.00           C
ATOM     76  CA  SER    76     -10.567  53.128  58.847  1.00 25.00           C
ATOM     77  CA  ILE    77     -12.782  50.865  61.001  1.00 25.00           C
ATOM     78  CA  GLY    78      -9.677  49.401  62.700  1.00 25.00           C
ATOM     79  CA  LEU    79      -8.361  52.930  63.389  1.00 25.00           C
ATOM     80  CA  ALA    80     -11.743  53.925  64.886  1.00 25.00           C
ATOM     81  CA  ALA    81     -11.704  50.808  67.109  1.00 25.00           C
ATOM     82  CA  ILE    82      -8.155  51.653  68.275  1.00 25.00           C
ATOM     83  CA  ASN    83      -9.246  55.234  69.080  1.00 25.00           C
ATOM     84  CA  ALA    84     -12.236  53.903  71.068  1.00 25.00           C
ATOM     85  CA  TYR    85      -9.927  51.541  73.006  1.00 25.00           C
ATOM     86  CA  TYR    86      -9.472  47.847  72.221  1.00 25.00           C
ATOM     87  CA  ASN    87      -5.985  47.888  73.812  1.00 25.00           C
ATOM     88  CA  ASN    88      -5.611  44.313  72.543  1.00 25.00           C
ATOM     89  CA  PRO    89      -8.200  43.406  75.137  1.00 25.00           C
ATOM     90  CA  GLN    90      -5.424  42.782  77.700  1.00 25.00           C
ATOM     91  CA  VAL    91      -7.398  44.722  80.347  1.00 25.00           C
ATOM     92  CA  ALA    92     -10.528  42.659  79.560  1.00 25.00           C
ATOM     93  CA  ARG    93      -8.504  39.423  79.882  1.00 25.00           C
ATOM     94  CA  GLU    94      -7.116  40.597  83.253  1.00 25.00           C
ATOM     95  CA  HIS    95     -10.660  41.411  84.456  1.00 25.00           C
ATOM     96  CA  GLY    96     -13.720  40.176  86.446  1.00 25.00           C
TER
END
