
#######################################################
#                                                     #
#                        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   39 (  156),  selected   39 , name T0300AL381_1
# Molecule2: number of CA atoms   89 (  695),  selected   89 , name T0300
# PARAMETERS: T0300AL381_1.T0300  -4  -ie  -d:5  -o1  -sia  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    K       8      D       7           -
LGA    T       9      K       8           -
LGA    Y      10      T       9           -
LGA    -       -      Y      10           -
LGA    -       -      E      11           -
LGA    -       -      E      12           -
LGA    -       -      M      13           -
LGA    -       -      V      14           -
LGA    -       -      K      15           -
LGA    -       -      E      16           -
LGA    -       -      V      17           -
LGA    -       -      E      18           -
LGA    -       -      R      19           -
LGA    -       -      L      20           -
LGA    -       -      K      21           -
LGA    -       -      L      22           -
LGA    -       -      E      23           -
LGA    -       -      N      24           -
LGA    -       -      K      25           -
LGA    -       -      T      26           -
LGA    -       -      L      27           -
LGA    -       -      K      28           -
LGA    -       -      Q      29           -
LGA    -       -      K      30           -
LGA    -       -      V      31           -
LGA    -       -      S      39           -
LGA    -       -      D      40           -
LGA    -       -      D      41           -
LGA    -       -      S      42           -
LGA    -       -      I      43           -
LGA    E      11      L      44          4.305
LGA    E      12      T      45          1.516
LGA    -       -      A      46           -
LGA    M      13      A      47          1.209
LGA    V      14      K      48          1.288
LGA    K      15      R      49          1.575
LGA    E      16      E      50          1.333
LGA    V      17      S      51          1.064
LGA    E      18      I      52          1.177
LGA    R      19      I      53          1.653
LGA    L      20      V      54          1.435
LGA    K      21      S      55          0.802
LGA    L      22      S      56          0.735
LGA    E      23      S      57          0.786
LGA    N      24      R      58          0.768
LGA    K      25      A      59          0.936
LGA    T      26      L      60          1.197
LGA    L      27      G      61          1.406
LGA    K      28      A      62          1.489
LGA    Q      29      V      63          1.306
LGA    K      30      A      64          1.242
LGA    V      31      M      65          1.668
LGA    K      32      R      66          1.377
LGA    S      33      K      67          1.308
LGA    S      34      I      68          1.206
LGA    V      54      E      69          1.289
LGA    S      55      A      70          1.319
LGA    S      56      K      71          1.563
LGA    S      57      V      72          1.681
LGA    R      58      R      73          0.877
LGA    A      59      S      74          0.890
LGA    L      60      R      75          1.729
LGA    G      61      A      76          2.113
LGA    A      62      A      77          1.414
LGA    V      63      K      78          2.656
LGA    A      64      A      79          2.650
LGA    M      65      V      80          4.149
LGA    -       -      T      81           -
LGA    -       -      E      82           -
LGA    -       -      Q      83           -
LGA    -       -      E      84           -
LGA    -       -      L      85           -
LGA    -       -      T      86           -
LGA    -       -      S      87           -
LGA    -       -      L      88           -
LGA    -       -      L      89           -
LGA    -       -      Q      90           -
LGA    -       -      S      91           -
LGA    -       -      L      92           -
LGA    -       -      T      93           -
LGA    -       -      L      94           -
LGA    -       -      R      95           -
LGA    -       -      V      96           -
LGA    -       -      D      97           -
LGA    -       -      V      98           -
LGA    -       -      S      99           -
LGA    -       -      M     100           -
LGA    -       -      E     101           -
LGA    -       -      E     102           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   39   89    5.0     36    1.72    11.11     37.951     1.978

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.519794 * X  +  -0.068134 * Y  +  -0.851570 * Z  +  63.421204
  Y_new =   0.493187 * X  +  -0.837860 * Y  +  -0.234002 * Z  + -27.855921
  Z_new =  -0.697554 * X  +  -0.541616 * Y  +   0.469117 * Z  +  42.223721 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.857005    2.284588  [ DEG:   -49.1027    130.8973 ]
  Theta =   0.771978    2.369615  [ DEG:    44.2311    135.7689 ]
  Phi   =   2.382454   -0.759138  [ DEG:   136.5046    -43.4954 ]
 
# 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: T0300AL381_1                                  
REMARK     2: T0300                                         
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0300AL381_1.T0300 -4 -ie -d:5 -o1 -sia 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   39   89   5.0   36   1.72   11.11  37.951
REMARK  ---------------------------------------------------------- 
MOLECULE T0300AL381_1
REMARK Aligment from pdb entry: 1debA
ATOM      1  N   LYS     8      60.835 -12.834 -14.070  1.00  0.00              
ATOM      2  CA  LYS     8      59.669 -13.270 -14.831  1.00  0.00              
ATOM      3  C   LYS     8      59.467 -12.405 -16.060  1.00  0.00              
ATOM      4  O   LYS     8      59.834 -11.239 -16.065  1.00  0.00              
ATOM      5  N   THR     9      58.884 -12.973 -17.106  1.00  0.00              
ATOM      6  CA  THR     9      58.613 -12.210 -18.311  1.00  0.00              
ATOM      7  C   THR     9      57.412 -11.320 -17.993  1.00  0.00              
ATOM      8  O   THR     9      56.834 -11.395 -16.907  1.00  0.00              
ATOM      9  N   TYR    10      57.027 -10.490 -18.948  1.00  0.00              
ATOM     10  CA  TYR    10      55.882  -9.618 -18.761  1.00  0.00              
ATOM     11  C   TYR    10      54.616 -10.477 -18.641  1.00  0.00              
ATOM     12  O   TYR    10      53.699 -10.144 -17.890  1.00  0.00              
ATOM     13  N   GLU    11      54.574 -11.580 -19.383  1.00  0.00              
ATOM     14  CA  GLU    11      53.413 -12.463 -19.357  1.00  0.00              
ATOM     15  C   GLU    11      53.315 -13.303 -18.086  1.00  0.00              
ATOM     16  O   GLU    11      52.227 -13.611 -17.624  1.00  0.00              
ATOM     17  N   GLU    12      54.452 -13.677 -17.528  1.00  0.00              
ATOM     18  CA  GLU    12      54.439 -14.457 -16.307  1.00  0.00              
ATOM     19  C   GLU    12      53.935 -13.579 -15.169  1.00  0.00              
ATOM     20  O   GLU    12      53.183 -14.025 -14.308  1.00  0.00              
ATOM     21  N   MET    13      54.316 -12.310 -15.193  1.00  0.00              
ATOM     22  CA  MET    13      53.868 -11.386 -14.160  1.00  0.00              
ATOM     23  C   MET    13      52.372 -11.205 -14.278  1.00  0.00              
ATOM     24  O   MET    13      51.646 -11.198 -13.282  1.00  0.00              
ATOM     25  N   VAL    14      51.913 -11.050 -15.511  1.00  0.00              
ATOM     26  CA  VAL    14      50.501 -10.850 -15.726  1.00  0.00              
ATOM     27  C   VAL    14      49.738 -12.003 -15.106  1.00  0.00              
ATOM     28  O   VAL    14      48.687 -11.803 -14.513  1.00  0.00              
ATOM     29  N   LYS    15      50.262 -13.212 -15.240  1.00  0.00              
ATOM     30  CA  LYS    15      49.592 -14.354 -14.650  1.00  0.00              
ATOM     31  C   LYS    15      49.604 -14.288 -13.120  1.00  0.00              
ATOM     32  O   LYS    15      48.637 -14.680 -12.466  1.00  0.00              
ATOM     33  N   GLU    16      50.701 -13.804 -12.549  1.00  0.00              
ATOM     34  CA  GLU    16      50.789 -13.700 -11.100  1.00  0.00              
ATOM     35  C   GLU    16      49.733 -12.721 -10.613  1.00  0.00              
ATOM     36  O   GLU    16      49.018 -12.989  -9.645  1.00  0.00              
ATOM     37  N   VAL    17      49.630 -11.590 -11.304  1.00  0.00              
ATOM     38  CA  VAL    17      48.678 -10.556 -10.930  1.00  0.00              
ATOM     39  C   VAL    17      47.260 -11.093 -10.976  1.00  0.00              
ATOM     40  O   VAL    17      46.469 -10.843 -10.067  1.00  0.00              
ATOM     41  N   GLU    18      46.938 -11.846 -12.019  1.00  0.00              
ATOM     42  CA  GLU    18      45.605 -12.418 -12.138  1.00  0.00              
ATOM     43  C   GLU    18      45.264 -13.329 -10.955  1.00  0.00              
ATOM     44  O   GLU    18      44.167 -13.265 -10.409  1.00  0.00              
ATOM     45  N   ARG    19      46.201 -14.179 -10.562  1.00  0.00              
ATOM     46  CA  ARG    19      45.960 -15.094  -9.452  1.00  0.00              
ATOM     47  C   ARG    19      45.962 -14.334  -8.125  1.00  0.00              
ATOM     48  O   ARG    19      45.193 -14.649  -7.211  1.00  0.00              
ATOM     49  N   LEU    20      46.815 -13.323  -8.021  1.00  0.00              
ATOM     50  CA  LEU    20      46.890 -12.530  -6.792  1.00  0.00              
ATOM     51  C   LEU    20      45.594 -11.754  -6.554  1.00  0.00              
ATOM     52  O   LEU    20      45.093 -11.703  -5.434  1.00  0.00              
ATOM     53  N   LYS    21      45.057 -11.161  -7.619  1.00  0.00              
ATOM     54  CA  LYS    21      43.804 -10.416  -7.549  1.00  0.00              
ATOM     55  C   LYS    21      42.644 -11.330  -7.147  1.00  0.00              
ATOM     56  O   LYS    21      41.735 -10.930  -6.408  1.00  0.00              
ATOM     57  N   LEU    22      42.635 -12.548  -7.659  1.00  0.00              
ATOM     58  CA  LEU    22      41.515 -13.421  -7.324  1.00  0.00              
ATOM     59  C   LEU    22      41.649 -13.830  -5.861  1.00  0.00              
ATOM     60  O   LEU    22      40.681 -13.811  -5.104  1.00  0.00              
ATOM     61  N   GLU    23      42.863 -14.155  -5.459  1.00  0.00              
ATOM     62  CA  GLU    23      43.125 -14.520  -4.089  1.00  0.00              
ATOM     63  C   GLU    23      42.699 -13.353  -3.199  1.00  0.00              
ATOM     64  O   GLU    23      41.975 -13.559  -2.223  1.00  0.00              
ATOM     65  N   ASN    24      43.122 -12.132  -3.542  1.00  0.00              
ATOM     66  CA  ASN    24      42.744 -10.958  -2.759  1.00  0.00              
ATOM     67  C   ASN    24      41.244 -10.830  -2.682  1.00  0.00              
ATOM     68  O   ASN    24      40.725 -10.475  -1.643  1.00  0.00              
ATOM     69  N   LYS    25      40.545 -11.097  -3.777  1.00  0.00              
ATOM     70  CA  LYS    25      39.088 -11.006  -3.746  1.00  0.00              
ATOM     71  C   LYS    25      38.499 -12.079  -2.827  1.00  0.00              
ATOM     72  O   LYS    25      37.517 -11.832  -2.109  1.00  0.00              
ATOM     73  N   THR    26      39.105 -13.264  -2.828  1.00  0.00              
ATOM     74  CA  THR    26      38.595 -14.340  -1.993  1.00  0.00              
ATOM     75  C   THR    26      38.861 -14.078  -0.511  1.00  0.00              
ATOM     76  O   THR    26      37.985 -14.322   0.325  1.00  0.00              
ATOM     77  N   LEU    27      40.055 -13.572  -0.190  1.00  0.00              
ATOM     78  CA  LEU    27      40.384 -13.251   1.189  1.00  0.00              
ATOM     79  C   LEU    27      39.384 -12.216   1.731  1.00  0.00              
ATOM     80  O   LEU    27      38.883 -12.369   2.834  1.00  0.00              
ATOM     81  N   LYS    28      39.071 -11.185   0.946  1.00  0.00              
ATOM     82  CA  LYS    28      38.101 -10.172   1.371  1.00  0.00              
ATOM     83  C   LYS    28      36.736 -10.793   1.629  1.00  0.00              
ATOM     84  O   LYS    28      36.043 -10.429   2.570  1.00  0.00              
ATOM     85  N   GLN    29      36.335 -11.719   0.763  1.00  0.00              
ATOM     86  CA  GLN    29      35.056 -12.402   0.921  1.00  0.00              
ATOM     87  C   GLN    29      35.047 -13.153   2.267  1.00  0.00              
ATOM     88  O   GLN    29      34.065 -13.125   3.027  1.00  0.00              
ATOM     89  N   LYS    30      36.159 -13.808   2.567  1.00  0.00              
ATOM     90  CA  LYS    30      36.277 -14.565   3.800  1.00  0.00              
ATOM     91  C   LYS    30      36.187 -13.689   5.031  1.00  0.00              
ATOM     92  O   LYS    30      35.474 -14.008   5.966  1.00  0.00              
ATOM     93  N   VAL    31      36.934 -12.594   5.030  1.00  0.00              
ATOM     94  CA  VAL    31      36.953 -11.676   6.160  1.00  0.00              
ATOM     95  C   VAL    31      35.549 -11.109   6.365  1.00  0.00              
ATOM     96  O   VAL    31      35.064 -10.983   7.480  1.00  0.00              
ATOM     97  N   LYS    32      34.896 -10.806   5.257  1.00  0.00              
ATOM     98  CA  LYS    32      33.555 -10.261   5.244  1.00  0.00              
ATOM     99  C   LYS    32      32.597 -11.280   5.863  1.00  0.00              
ATOM    100  O   LYS    32      31.754 -10.937   6.690  1.00  0.00              
ATOM    101  N   SER    33      32.746 -12.536   5.458  1.00  0.00              
ATOM    102  CA  SER    33      31.924 -13.648   5.943  1.00  0.00              
ATOM    103  C   SER    33      32.110 -13.771   7.453  1.00  0.00              
ATOM    104  O   SER    33      31.159 -13.724   8.243  1.00  0.00              
ATOM    105  N   SER    34      33.365 -13.913   7.840  1.00  0.00              
ATOM    106  CA  SER    34      33.728 -14.090   9.224  1.00  0.00              
ATOM    107  C   SER    34      33.420 -12.900  10.089  1.00  0.00              
ATOM    108  O   SER    34      33.072 -13.056  11.263  1.00  0.00              
ATOM    109  N   VAL    54      33.529 -11.711   9.520  1.00  0.00              
ATOM    110  CA  VAL    54      33.227 -10.528  10.295  1.00  0.00              
ATOM    111  C   VAL    54      31.728 -10.573  10.587  1.00  0.00              
ATOM    112  O   VAL    54      31.322 -10.374  11.730  1.00  0.00              
ATOM    113  N   SER    55      30.911 -10.890   9.585  1.00  0.00              
ATOM    114  CA  SER    55      29.460 -10.979   9.785  1.00  0.00              
ATOM    115  C   SER    55      29.115 -12.089  10.792  1.00  0.00              
ATOM    116  O   SER    55      28.176 -11.970  11.619  1.00  0.00              
ATOM    117  N   SER    56      29.870 -13.179  10.723  1.00  0.00              
ATOM    118  CA  SER    56      29.665 -14.294  11.632  1.00  0.00              
ATOM    119  C   SER    56      29.940 -13.891  13.093  1.00  0.00              
ATOM    120  O   SER    56      29.218 -14.307  14.000  1.00  0.00              
ATOM    121  N   SER    57      30.963 -13.071  13.328  1.00  0.00              
ATOM    122  CA  SER    57      31.279 -12.628  14.691  1.00  0.00              
ATOM    123  C   SER    57      30.091 -11.827  15.197  1.00  0.00              
ATOM    124  O   SER    57      29.591 -12.045  16.301  1.00  0.00              
ATOM    125  N   ARG    58      29.634 -10.900  14.366  1.00  0.00              
ATOM    126  CA  ARG    58      28.503 -10.063  14.713  1.00  0.00              
ATOM    127  C   ARG    58      27.247 -10.854  15.030  1.00  0.00              
ATOM    128  O   ARG    58      26.535 -10.530  15.982  1.00  0.00              
ATOM    129  N   ALA    59      26.960 -11.878  14.232  1.00  0.00              
ATOM    130  CA  ALA    59      25.776 -12.689  14.486  1.00  0.00              
ATOM    131  C   ALA    59      25.962 -13.507  15.766  1.00  0.00              
ATOM    132  O   ALA    59      25.003 -13.798  16.467  1.00  0.00              
ATOM    133  N   LEU    60      27.196 -13.866  16.088  1.00  0.00              
ATOM    134  CA  LEU    60      27.425 -14.626  17.313  1.00  0.00              
ATOM    135  C   LEU    60      27.182 -13.751  18.545  1.00  0.00              
ATOM    136  O   LEU    60      26.606 -14.191  19.550  1.00  0.00              
ATOM    137  N   GLY    61      27.626 -12.509  18.464  1.00  0.00              
ATOM    138  CA  GLY    61      27.454 -11.593  19.576  1.00  0.00              
ATOM    139  C   GLY    61      25.977 -11.297  19.776  1.00  0.00              
ATOM    140  O   GLY    61      25.494 -11.247  20.907  1.00  0.00              
ATOM    141  N   ALA    62      25.258 -11.100  18.677  1.00  0.00              
ATOM    142  CA  ALA    62      23.835 -10.830  18.757  1.00  0.00              
ATOM    143  C   ALA    62      23.170 -12.009  19.462  1.00  0.00              
ATOM    144  O   ALA    62      22.360 -11.824  20.369  1.00  0.00              
ATOM    145  N   VAL    63      23.508 -13.227  19.057  1.00  0.00              
ATOM    146  CA  VAL    63      22.910 -14.399  19.693  1.00  0.00              
ATOM    147  C   VAL    63      23.230 -14.461  21.185  1.00  0.00              
ATOM    148  O   VAL    63      22.377 -14.797  22.004  1.00  0.00              
ATOM    149  N   ALA    64      24.470 -14.156  21.542  1.00  0.00              
ATOM    150  CA  ALA    64      24.863 -14.206  22.950  1.00  0.00              
ATOM    151  C   ALA    64      24.073 -13.176  23.739  1.00  0.00              
ATOM    152  O   ALA    64      23.550 -13.473  24.799  1.00  0.00              
ATOM    153  N   MET    65      23.940 -11.980  23.187  1.00  0.00              
ATOM    154  CA  MET    65      23.204 -10.912  23.851  1.00  0.00              
ATOM    155  C   MET    65      21.705 -11.154  23.994  1.00  0.00              
ATOM    156  O   MET    65      21.105 -10.769  25.007  1.00  0.00              
END
