
#######################################################
#                                                     #
#                        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  108 (  108),  selected  108 , name T0291TS168_4-D1
# Molecule2: number of CA atoms  100 (  781),  selected  100 , name T0291_D1.pdb
# PARAMETERS: T0291TS168_4-D1.T0291_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    T       1      T       1           #
LGA    Y       2      Y       2          4.994
LGA    V       3      V       3          4.498
LGA    D       4      D       4          4.893
LGA    P       5      P       5          3.127
LGA    H       6      H       6          4.902
LGA    T       7      -       -           -
LGA    Y       8      -       -           -
LGA    E       9      -       -           -
LGA    D      10      -       -           -
LGA    P      11      -       -           -
LGA    T      12      -       -           -
LGA    Q      13      -       -           -
LGA    A      14      -       -           -
LGA    V      15      V      15          2.560
LGA    H      16      H      16          2.766
LGA    E      17      E      17          3.549
LGA    F      18      F      18          3.321
LGA    A      19      A      19          2.191
LGA    K      20      K      20          3.777
LGA    E      21      E      21          1.977
LGA    L      22      L      22          1.667
LGA    D      23      D      23          1.428
LGA    A      24      A      24          1.725
LGA    T      25      T      25          2.296
LGA    N      26      N      26          1.634
LGA    I      27      I      27          4.794
LGA    S      28      S      28          1.297
LGA    I      29      I      29          2.307
LGA    D      30      D      30          1.877
LGA    K      31      K      31          1.450
LGA    V      32      V      32          1.588
LGA    V      33      V      33          2.242
LGA    G      34      G      34          2.611
LGA    A      35      A      35          3.075
LGA    G      36      G      36          2.762
LGA    E      37      E      37          3.296
LGA    F      38      F      38          2.806
LGA    G      39      G      39          1.688
LGA    E      40      E      40          1.375
LGA    V      41      V      41          1.576
LGA    C      42      C      42          3.391
LGA    S      43      S      43          1.843
LGA    G      44      G      44          1.101
LGA    R      45      R      45          0.855
LGA    L      46      L      46          1.243
LGA    K      47      K      47          1.600
LGA    L      48      L      48          2.371
LGA    P      49      P      49          2.087
LGA    S      50      S      50          3.978
LGA    K      51      K      51          2.311
LGA    K      52      K      52          2.827
LGA    E      53      E      53          1.549
LGA    I      54      I      54          1.055
LGA    S      55      S      55          0.696
LGA    V      56      V      56          0.323
LGA    A      57      A      57          1.695
LGA    I      58      I      58          1.575
LGA    K      59      K      59          0.966
LGA    T      60      T      60          1.647
LGA    L      61      L      61          0.494
LGA    K      62      K      62          1.099
LGA    V      63      V      63          1.467
LGA    G      64      G      64          2.025
LGA    Y      65      Y      65          0.855
LGA    T      66      T      66          0.968
LGA    E      67      E      67          1.731
LGA    K      68      K      68          0.830
LGA    Q      69      Q      69          0.803
LGA    R      70      R      70          1.011
LGA    R      71      R      71          0.568
LGA    D      72      D      72          0.577
LGA    F      73      F      73          1.238
LGA    L      74      L      74          1.248
LGA    G      75      G      75          1.106
LGA    E      76      E      76          0.983
LGA    A      77      A      77          0.615
LGA    S      78      S      78          0.677
LGA    I      79      I      79          0.763
LGA    M      80      M      80          0.762
LGA    G      81      G      81          1.184
LGA    Q      82      Q      82          1.571
LGA    F      83      F      83          2.969
LGA    D      84      D      84          4.866
LGA    H      85      H      85          3.980
LGA    P      86      P      86          2.400
LGA    N      87      N      87          1.590
LGA    I      88      I      88          1.813
LGA    I      89      I      89          1.515
LGA    R      90      R      90          1.084
LGA    L      91      L      91          1.388
LGA    E      92      E      92          1.571
LGA    G      93      G      93          1.339
LGA    V      94      V      94          1.529
LGA    V      95      V      95          1.679
LGA    T      96      T      96          1.072
LGA    K      97      K      97          1.081
LGA    S      98      S      98          3.337
LGA    K      99      K      99          1.072
LGA    P     100      P     100          0.745
LGA    V     101      V     101          0.641
LGA    M     102      M     102          0.532
LGA    I     103      I     103          2.327
LGA    V     104      V     104          2.905
LGA    T     105      T     105          0.622
LGA    E     106      E     106          0.472
LGA    Y     107      Y     107          1.160
LGA    M     108      M     108          2.134

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  108  100    5.0     99    2.21   100.00     83.325     4.287

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.776841 * X  +  -0.055407 * Y  +   0.627255 * Z  +  -2.027560
  Y_new =  -0.303196 * X  +  -0.840137 * Y  +  -0.449713 * Z  +   9.953679
  Z_new =   0.551897 * X  +  -0.539537 * Y  +   0.635854 * Z  +  56.206711 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.703636    2.437956  [ DEG:   -40.3154    139.6846 ]
  Theta =  -0.584637   -2.556955  [ DEG:   -33.4972   -146.5027 ]
  Phi   =  -2.769481    0.372111  [ DEG:  -158.6796     21.3204 ]
 
# 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: T0291TS168_4-D1                               
REMARK     2: T0291_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0291TS168_4-D1.T0291_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  108  100   5.0   99   2.21  100.00  83.325
REMARK  ---------------------------------------------------------- 
MOLECULE T0291TS168_4-D1
PFRMAT TS
TARGET T0291
MODEL 4
PARENT N/A
ATOM      1  CA  THR     1      -4.648  35.909  46.616  1.00 25.00           C
ATOM      2  CA  TYR     2      -5.192  32.405  47.881  1.00 25.00           C
ATOM      3  CA  VAL     3      -8.288  30.198  48.310  1.00 25.00           C
ATOM      4  CA  ASP     4     -10.203  30.346  51.625  1.00 25.00           C
ATOM      5  CA  PRO     5     -13.422  29.251  53.303  1.00 25.00           C
ATOM      6  CA  HIS     6     -12.683  31.484  56.281  1.00 25.00           C
ATOM      7  CA  THR     7     -13.578  35.137  56.531  1.00 25.00           C
ATOM      8  CA  TYR     8     -16.711  34.078  54.675  1.00 25.00           C
ATOM      9  CA  GLU     9     -19.335  36.032  56.717  1.00 25.00           C
ATOM     10  CA  ASP    10     -21.990  34.056  54.783  1.00 25.00           C
ATOM     11  CA  PRO    11     -20.452  30.833  55.985  1.00 25.00           C
ATOM     12  CA  THR    12     -22.336  27.789  54.624  1.00 25.00           C
ATOM     13  CA  GLN    13     -23.104  29.683  51.385  1.00 25.00           C
ATOM     14  CA  ALA    14     -19.412  30.645  51.044  1.00 25.00           C
ATOM     15  CA  VAL    15     -18.386  26.993  51.573  1.00 25.00           C
ATOM     16  CA  HIS    16     -20.894  25.876  48.902  1.00 25.00           C
ATOM     17  CA  GLU    17     -19.508  28.492  46.473  1.00 25.00           C
ATOM     18  CA  PHE    18     -15.942  27.276  47.159  1.00 25.00           C
ATOM     19  CA  ALA    19     -17.026  23.660  46.523  1.00 25.00           C
ATOM     20  CA  LYS    20     -18.675  24.707  43.229  1.00 25.00           C
ATOM     21  CA  GLU    21     -20.629  21.522  42.459  1.00 25.00           C
ATOM     22  CA  LEU    22     -20.836  17.852  41.512  1.00 25.00           C
ATOM     23  CA  ASP    23     -24.298  16.275  41.098  1.00 25.00           C
ATOM     24  CA  ALA    24     -26.199  13.595  42.886  1.00 25.00           C
ATOM     25  CA  THR    25     -27.845  12.440  39.718  1.00 25.00           C
ATOM     26  CA  ASN    26     -24.758  10.295  39.252  1.00 25.00           C
ATOM     27  CA  ILE    27     -26.241   6.795  39.339  1.00 25.00           C
ATOM     28  CA  SER    28     -23.242   5.085  40.962  1.00 25.00           C
ATOM     29  CA  ILE    29     -23.267   2.450  43.681  1.00 25.00           C
ATOM     30  CA  ASP    30     -21.389  -0.820  44.173  1.00 25.00           C
ATOM     31  CA  LYS    31     -19.464  -1.660  47.303  1.00 25.00           C
ATOM     32  CA  VAL    32     -17.899  -1.854  50.746  1.00 25.00           C
ATOM     33  CA  VAL    33     -14.391  -0.613  51.380  1.00 25.00           C
ATOM     34  CA  GLY    34     -15.047   0.796  54.891  1.00 25.00           C
ATOM     35  CA  ALA    35     -15.307   0.757  58.740  1.00 25.00           C
ATOM     36  CA  GLY    36     -13.793   4.267  59.130  1.00 25.00           C
ATOM     37  CA  GLU    37     -15.192   6.198  62.131  1.00 25.00           C
ATOM     38  CA  PHE    38     -16.447   9.093  60.045  1.00 25.00           C
ATOM     39  CA  GLY    39     -19.454   6.875  59.298  1.00 25.00           C
ATOM     40  CA  GLU    40     -18.847   4.233  56.596  1.00 25.00           C
ATOM     41  CA  VAL    41     -17.890   4.541  52.932  1.00 25.00           C
ATOM     42  CA  CYS    42     -20.087   4.724  49.787  1.00 25.00           C
ATOM     43  CA  SER    43     -17.399   2.894  47.785  1.00 25.00           C
ATOM     44  CA  GLY    44     -18.208   3.892  44.209  1.00 25.00           C
ATOM     45  CA  ARG    45     -18.172   5.313  40.731  1.00 25.00           C
ATOM     46  CA  LEU    46     -18.549   9.028  40.243  1.00 25.00           C
ATOM     47  CA  LYS    47     -19.802   8.537  36.683  1.00 25.00           C
ATOM     48  CA  LEU    48     -19.212  12.281  36.353  1.00 25.00           C
ATOM     49  CA  PRO    49     -19.417  13.553  32.825  1.00 25.00           C
ATOM     50  CA  SER    50     -15.648  12.797  32.712  1.00 25.00           C
ATOM     51  CA  LYS    51     -16.707  10.715  29.676  1.00 25.00           C
ATOM     52  CA  LYS    52     -17.018   7.033  30.745  1.00 25.00           C
ATOM     53  CA  GLU    53     -16.389   5.614  34.187  1.00 25.00           C
ATOM     54  CA  ILE    54     -14.393   7.462  36.924  1.00 25.00           C
ATOM     55  CA  SER    55     -12.849   5.550  39.869  1.00 25.00           C
ATOM     56  CA  VAL    56     -13.826   6.964  43.199  1.00 25.00           C
ATOM     57  CA  ALA    57     -12.852   5.539  46.637  1.00 25.00           C
ATOM     58  CA  ILE    58     -15.337   7.697  48.542  1.00 25.00           C
ATOM     59  CA  LYS    59     -16.984   9.293  51.577  1.00 25.00           C
ATOM     60  CA  THR    60     -19.507   9.655  54.322  1.00 25.00           C
ATOM     61  CA  LEU    61     -21.882  11.847  56.294  1.00 25.00           C
ATOM     62  CA  LYS    62     -24.345   9.559  58.132  1.00 25.00           C
ATOM     63  CA  VAL    63     -27.787  11.191  58.445  1.00 25.00           C
ATOM     64  CA  GLY    64     -27.573  10.882  62.287  1.00 25.00           C
ATOM     65  CA  TYR    65     -26.239  14.431  62.686  1.00 25.00           C
ATOM     66  CA  THR    66     -25.761  17.408  65.007  1.00 25.00           C
ATOM     67  CA  GLU    67     -24.676  19.287  61.907  1.00 25.00           C
ATOM     68  CA  LYS    68     -21.329  20.131  63.565  1.00 25.00           C
ATOM     69  CA  GLN    69     -19.762  16.975  62.065  1.00 25.00           C
ATOM     70  CA  ARG    70     -21.102  17.926  58.605  1.00 25.00           C
ATOM     71  CA  ARG    71     -19.652  21.450  58.985  1.00 25.00           C
ATOM     72  CA  ASP    72     -16.264  19.974  59.990  1.00 25.00           C
ATOM     73  CA  PHE    73     -16.339  17.661  56.938  1.00 25.00           C
ATOM     74  CA  LEU    74     -17.149  20.639  54.670  1.00 25.00           C
ATOM     75  CA  GLY    75     -14.241  22.617  56.186  1.00 25.00           C
ATOM     76  CA  GLU    76     -11.888  19.651  55.605  1.00 25.00           C
ATOM     77  CA  ALA    77     -13.061  19.402  51.968  1.00 25.00           C
ATOM     78  CA  SER    78     -12.454  23.154  51.489  1.00 25.00           C
ATOM     79  CA  ILE    79      -8.940  22.798  52.970  1.00 25.00           C
ATOM     80  CA  MET    80      -8.215  19.870  50.611  1.00 25.00           C
ATOM     81  CA  GLY    81      -9.429  21.940  47.626  1.00 25.00           C
ATOM     82  CA  GLN    82      -7.180  24.849  48.699  1.00 25.00           C
ATOM     83  CA  PHE    83      -4.185  22.494  48.961  1.00 25.00           C
ATOM     84  CA  ASP    84      -1.893  20.405  46.784  1.00 25.00           C
ATOM     85  CA  HIS    85       1.034  18.160  45.787  1.00 25.00           C
ATOM     86  CA  PRO    86       1.269  15.321  43.193  1.00 25.00           C
ATOM     87  CA  ASN    87       0.826  13.063  46.266  1.00 25.00           C
ATOM     88  CA  ILE    88      -2.400  14.078  48.028  1.00 25.00           C
ATOM     89  CA  ILE    89      -5.923  12.545  48.104  1.00 25.00           C
ATOM     90  CA  ARG    90      -7.225  14.555  45.148  1.00 25.00           C
ATOM     91  CA  LEU    91     -10.216  16.716  46.100  1.00 25.00           C
ATOM     92  CA  GLU    92     -12.306  15.488  43.205  1.00 25.00           C
ATOM     93  CA  GLY    93     -15.354  16.940  44.865  1.00 25.00           C
ATOM     94  CA  VAL    94     -17.993  17.632  47.497  1.00 25.00           C
ATOM     95  CA  VAL    95     -21.531  16.620  46.678  1.00 25.00           C
ATOM     96  CA  THR    96     -24.088  18.489  48.858  1.00 25.00           C
ATOM     97  CA  LYS    97     -27.897  18.962  48.925  1.00 25.00           C
ATOM     98  CA  SER    98     -30.787  17.810  51.112  1.00 25.00           C
ATOM     99  CA  LYS    99     -29.618  14.187  51.550  1.00 25.00           C
ATOM    100  CA  PRO   100     -27.096  12.030  53.423  1.00 25.00           C
ATOM    101  CA  VAL   101     -24.079  13.845  52.058  1.00 25.00           C
ATOM    102  CA  MET   102     -21.017  12.728  50.004  1.00 25.00           C
ATOM    103  CA  ILE   103     -17.903  12.641  47.830  1.00 25.00           C
ATOM    104  CA  VAL   104     -14.253  13.249  48.726  1.00 25.00           C
ATOM    105  CA  THR   105     -12.146  11.239  46.200  1.00 25.00           C
ATOM    106  CA  GLU   106      -9.310   9.821  44.085  1.00 25.00           C
ATOM    107  CA  TYR   107      -8.755   6.096  43.692  1.00 25.00           C
ATOM    108  CA  MET   108      -7.682   3.149  45.819  1.00 25.00           C
TER
END
