
#######################################################
#                                                     #
#                        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   44 (  176),  selected   44 , name T0338AL509_1-D1
# Molecule2: number of CA atoms  143 ( 1129),  selected  143 , name T0338_D1.pdb
# PARAMETERS: T0338AL509_1-D1.T0338_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      A       1           -
LGA    -       -      S       2           -
LGA    -       -      S       3           -
LGA    -       -      R       4           -
LGA    -       -      W       5           -
LGA    -       -      F       6           -
LGA    -       -      F       7           -
LGA    -       -      T       8           -
LGA    -       -      R       9           -
LGA    -       -      E      10           -
LGA    -       -      Q      11           -
LGA    -       -      L      12           -
LGA    -       -      E      13           -
LGA    -       -      N      14           -
LGA    -       -      T      15           -
LGA    -       -      P      16           -
LGA    -       -      S      17           -
LGA    -       -      R      18           -
LGA    -       -      R      19           -
LGA    -       -      C      20           -
LGA    -       -      G      21           -
LGA    -       -      V      22           -
LGA    -       -      E      23           -
LGA    -       -      A      24           -
LGA    -       -      D      25           -
LGA    -       -      K      26           -
LGA    -       -      E      27           -
LGA    L      28      L      28          0.232
LGA    S      29      S      29          0.505
LGA    C      30      C      30          0.991
LGA    R      31      R      31          0.867
LGA    Q      32      Q      32          0.593
LGA    Q      33      Q      33          0.850
LGA    A      34      A      34          0.975
LGA    A      35      A      35          0.550
LGA    N      36      N      36          0.503
LGA    L      37      L      37          0.892
LGA    I      38      I      38          0.897
LGA    Q      39      Q      39          0.693
LGA    E      40      E      40          0.579
LGA    M      41      M      41          0.160
LGA    G      42      G      42          0.785
LGA    Q      43      Q      43          1.051
LGA    R      44      R      44          0.723
LGA    L      45      L      45          0.827
LGA    N      46      N      46          0.719
LGA    V      47      V      47          0.985
LGA    S      48      S      48          0.840
LGA    S      78      Q      49          0.598
LGA    T      79      L      50          0.686
LGA    A      80      T      51          0.635
LGA    L      81      I      52          0.667
LGA    F      82      N      53          0.774
LGA    L      83      T      54          0.551
LGA    A      84      A      55          0.688
LGA    A      85      I      56          1.250
LGA    K      86      V      57          1.264
LGA    H      96      Y      58          1.052
LGA    V      97      M      59          1.473
LGA    D     113      H      60          1.698
LGA    A     118      R      61          1.793
LGA    Y     119      F      62          1.726
LGA    L     120      Y      63          1.758
LGA    -       -      M      64           -
LGA    -       -      H      65           -
LGA    -       -      H      66           -
LGA    -       -      S      67           -
LGA    Q     121      F      68          3.066
LGA    Q     122      T      69          5.006
LGA    -       -      K      70           -
LGA    T     123      F      71          1.876
LGA    R     124      N      72          3.169
LGA    E     125      K      73          2.121
LGA    -       -      N      74           -
LGA    L     126      I      75          1.978
LGA    V     127      I      76          1.922
LGA    G     138      S      77          1.832
LGA    -       -      S      78           -
LGA    -       -      T      79           -
LGA    -       -      A      80           -
LGA    -       -      L      81           -
LGA    -       -      F      82           -
LGA    -       -      L      83           -
LGA    -       -      A      84           -
LGA    -       -      A      85           -
LGA    -       -      K      86           -
LGA    -       -      V      87           -
LGA    -       -      E      88           -
LGA    -       -      E      89           -
LGA    -       -      Q      90           -
LGA    -       -      A      91           -
LGA    -       -      R      92           -
LGA    -       -      K      93           -
LGA    -       -      L      94           -
LGA    -       -      E      95           -
LGA    -       -      H      96           -
LGA    -       -      V      97           -
LGA    -       -      I      98           -
LGA    -       -      K      99           -
LGA    -       -      V     100           -
LGA    -       -      A     101           -
LGA    -       -      H     102           -
LGA    -       -      A     103           -
LGA    -       -      C     104           -
LGA    -       -      L     105           -
LGA    -       -      H     106           -
LGA    -       -      P     107           -
LGA    -       -      L     108           -
LGA    -       -      E     109           -
LGA    -       -      P     110           -
LGA    -       -      L     111           -
LGA    -       -      L     112           -
LGA    -       -      D     113           -
LGA    -       -      T     114           -
LGA    -       -      K     115           -
LGA    -       -      C     116           -
LGA    -       -      D     117           -
LGA    -       -      A     118           -
LGA    -       -      Y     119           -
LGA    -       -      L     120           -
LGA    -       -      Q     121           -
LGA    -       -      Q     122           -
LGA    -       -      T     123           -
LGA    -       -      R     124           -
LGA    -       -      E     125           -
LGA    -       -      L     126           -
LGA    -       -      V     127           -
LGA    -       -      I     128           -
LGA    -       -      L     129           -
LGA    -       -      E     130           -
LGA    -       -      T     131           -
LGA    -       -      I     132           -
LGA    -       -      M     133           -
LGA    -       -      L     134           -
LGA    -       -      Q     135           -
LGA    -       -      T     136           -
LGA    -       -      L     137           -
LGA    -       -      G     138           -
LGA    -       -      F     139           -
LGA    -       -      E     140           -
LGA    -       -      I     141           -
LGA    -       -      T     142           -
LGA    -       -      I     143           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   44  143    5.0     44    1.49    50.00     29.254     2.772

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.307699 * X  +   0.951411 * Y  +  -0.011753 * Z  + -61.684021
  Y_new =   0.379967 * X  +  -0.134193 * Y  +  -0.915214 * Z  +  38.284393
  Z_new =  -0.872322 * X  +   0.277145 * Y  +  -0.402796 * Z  + 105.345581 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.538930   -0.602663  [ DEG:   145.4700    -34.5300 ]
  Theta =   1.059932    2.081661  [ DEG:    60.7296    119.2704 ]
  Phi   =   0.890105   -2.251487  [ DEG:    50.9993   -129.0007 ]
 
# 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: T0338AL509_1-D1                               
REMARK     2: T0338_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0338AL509_1-D1.T0338_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   44  143   5.0   44   1.49   50.00  29.254
REMARK  ---------------------------------------------------------- 
MOLECULE T0338AL509_1-D1
REMARK Aligment from pdb entry: 1vin
ATOM      1  N   LEU    28      -4.666  20.400  62.538  1.00  0.00              
ATOM      2  CA  LEU    28      -5.908  20.463  63.331  1.00  0.00              
ATOM      3  C   LEU    28      -5.921  21.744  64.149  1.00  0.00              
ATOM      4  O   LEU    28      -6.954  22.403  64.313  1.00  0.00              
ATOM      5  N   SER    29      -4.754  22.088  64.679  1.00  0.00              
ATOM      6  CA  SER    29      -4.577  23.275  65.488  1.00  0.00              
ATOM      7  C   SER    29      -4.949  24.544  64.728  1.00  0.00              
ATOM      8  O   SER    29      -5.563  25.459  65.280  1.00  0.00              
ATOM      9  N   CYS    30      -4.555  24.600  63.464  1.00  0.00              
ATOM     10  CA  CYS    30      -4.855  25.754  62.634  1.00  0.00              
ATOM     11  C   CYS    30      -6.373  25.817  62.438  1.00  0.00              
ATOM     12  O   CYS    30      -6.992  26.880  62.553  1.00  0.00              
ATOM     13  N   ARG    31      -6.948  24.634  62.209  1.00  0.00              
ATOM     14  CA  ARG    31      -8.379  24.503  61.992  1.00  0.00              
ATOM     15  C   ARG    31      -9.133  24.973  63.230  1.00  0.00              
ATOM     16  O   ARG    31     -10.108  25.711  63.112  1.00  0.00              
ATOM     17  N   GLN    32      -8.631  24.635  64.419  1.00  0.00              
ATOM     18  CA  GLN    32      -9.290  25.030  65.669  1.00  0.00              
ATOM     19  C   GLN    32      -9.390  26.555  65.790  1.00  0.00              
ATOM     20  O   GLN    32     -10.467  27.103  66.103  1.00  0.00              
ATOM     21  N   GLN    33      -8.290  27.245  65.472  1.00  0.00              
ATOM     22  CA  GLN    33      -8.222  28.712  65.536  1.00  0.00              
ATOM     23  C   GLN    33      -9.198  29.310  64.521  1.00  0.00              
ATOM     24  O   GLN    33     -10.007  30.195  64.866  1.00  0.00              
ATOM     25  N   ALA    34      -9.191  28.776  63.303  1.00  0.00              
ATOM     26  CA  ALA    34     -10.101  29.242  62.256  1.00  0.00              
ATOM     27  C   ALA    34     -11.586  29.166  62.682  1.00  0.00              
ATOM     28  O   ALA    34     -12.321  30.147  62.548  1.00  0.00              
ATOM     29  N   ALA    35     -12.007  28.012  63.210  1.00  0.00              
ATOM     30  CA  ALA    35     -13.409  27.808  63.622  1.00  0.00              
ATOM     31  C   ALA    35     -13.802  28.767  64.744  1.00  0.00              
ATOM     32  O   ALA    35     -14.875  29.401  64.724  1.00  0.00              
ATOM     33  N   ASN    36     -12.864  28.940  65.669  1.00  0.00              
ATOM     34  CA  ASN    36     -13.033  29.831  66.808  1.00  0.00              
ATOM     35  C   ASN    36     -13.248  31.256  66.336  1.00  0.00              
ATOM     36  O   ASN    36     -14.055  31.990  66.899  1.00  0.00              
ATOM     37  N   LEU    37     -12.542  31.603  65.264  1.00  0.00              
ATOM     38  CA  LEU    37     -12.611  32.930  64.676  1.00  0.00              
ATOM     39  C   LEU    37     -13.986  33.122  64.004  1.00  0.00              
ATOM     40  O   LEU    37     -14.607  34.178  64.147  1.00  0.00              
ATOM     41  N   ILE    38     -14.500  32.081  63.358  1.00  0.00              
ATOM     42  CA  ILE    38     -15.814  32.166  62.714  1.00  0.00              
ATOM     43  C   ILE    38     -16.903  32.332  63.767  1.00  0.00              
ATOM     44  O   ILE    38     -17.929  32.988  63.535  1.00  0.00              
ATOM     45  N   GLN    39     -16.697  31.701  64.917  1.00  0.00              
ATOM     46  CA  GLN    39     -17.662  31.872  66.004  1.00  0.00              
ATOM     47  C   GLN    39     -17.659  33.369  66.338  1.00  0.00              
ATOM     48  O   GLN    39     -18.721  33.961  66.544  1.00  0.00              
ATOM     49  N   GLU    40     -16.476  33.998  66.362  1.00  0.00              
ATOM     50  CA  GLU    40     -16.379  35.442  66.661  1.00  0.00              
ATOM     51  C   GLU    40     -17.140  36.249  65.606  1.00  0.00              
ATOM     52  O   GLU    40     -17.897  37.179  65.911  1.00  0.00              
ATOM     53  N   MET    41     -16.918  35.886  64.349  1.00  0.00              
ATOM     54  CA  MET    41     -17.566  36.552  63.212  1.00  0.00              
ATOM     55  C   MET    41     -19.093  36.463  63.309  1.00  0.00              
ATOM     56  O   MET    41     -19.794  37.461  63.120  1.00  0.00              
ATOM     57  N   GLY    42     -19.593  35.255  63.568  1.00  0.00              
ATOM     58  CA  GLY    42     -21.019  35.031  63.705  1.00  0.00              
ATOM     59  C   GLY    42     -21.604  35.890  64.820  1.00  0.00              
ATOM     60  O   GLY    42     -22.694  36.445  64.704  1.00  0.00              
ATOM     61  N   GLN    43     -20.849  36.027  65.898  1.00  0.00              
ATOM     62  CA  GLN    43     -21.290  36.843  67.017  1.00  0.00              
ATOM     63  C   GLN    43     -21.455  38.290  66.550  1.00  0.00              
ATOM     64  O   GLN    43     -22.518  38.911  66.715  1.00  0.00              
ATOM     65  N   ARG    44     -20.403  38.779  65.898  1.00  0.00              
ATOM     66  CA  ARG    44     -20.346  40.141  65.396  1.00  0.00              
ATOM     67  C   ARG    44     -21.418  40.519  64.372  1.00  0.00              
ATOM     68  O   ARG    44     -21.957  41.625  64.421  1.00  0.00              
ATOM     69  N   LEU    45     -21.679  39.644  63.408  1.00  0.00              
ATOM     70  CA  LEU    45     -22.708  39.945  62.418  1.00  0.00              
ATOM     71  C   LEU    45     -24.062  39.387  62.850  1.00  0.00              
ATOM     72  O   LEU    45     -25.025  39.420  62.087  1.00  0.00              
ATOM     73  N   ASN    46     -24.121  38.887  64.086  1.00  0.00              
ATOM     74  CA  ASN    46     -25.343  38.336  64.650  1.00  0.00              
ATOM     75  C   ASN    46     -25.928  37.283  63.717  1.00  0.00              
ATOM     76  O   ASN    46     -27.129  37.284  63.395  1.00  0.00              
ATOM     77  N   VAL    47     -25.077  36.353  63.303  1.00  0.00              
ATOM     78  CA  VAL    47     -25.495  35.283  62.412  1.00  0.00              
ATOM     79  C   VAL    47     -26.105  34.118  63.197  1.00  0.00              
ATOM     80  O   VAL    47     -25.845  33.947  64.398  1.00  0.00              
ATOM     81  N   SER    48     -26.975  33.365  62.547  1.00  0.00              
ATOM     82  CA  SER    48     -27.586  32.195  63.162  1.00  0.00              
ATOM     83  C   SER    48     -26.514  31.165  63.473  1.00  0.00              
ATOM     84  O   SER    48     -25.491  31.099  62.791  1.00  0.00              
ATOM     85  N   SER    78     -26.733  30.357  64.504  1.00  0.00              
ATOM     86  CA  SER    78     -25.766  29.321  64.864  1.00  0.00              
ATOM     87  C   SER    78     -25.745  28.285  63.768  1.00  0.00              
ATOM     88  O   SER    78     -24.759  27.573  63.603  1.00  0.00              
ATOM     89  N   THR    79     -26.851  28.179  63.047  1.00  0.00              
ATOM     90  CA  THR    79     -26.953  27.223  61.947  1.00  0.00              
ATOM     91  C   THR    79     -25.929  27.525  60.850  1.00  0.00              
ATOM     92  O   THR    79     -25.343  26.601  60.272  1.00  0.00              
ATOM     93  N   ALA    80     -25.729  28.801  60.566  1.00  0.00              
ATOM     94  CA  ALA    80     -24.788  29.249  59.558  1.00  0.00              
ATOM     95  C   ALA    80     -23.370  28.808  59.909  1.00  0.00              
ATOM     96  O   ALA    80     -22.574  28.405  59.043  1.00  0.00              
ATOM     97  N   LEU    81     -23.061  28.922  61.194  1.00  0.00              
ATOM     98  CA  LEU    81     -21.770  28.550  61.709  1.00  0.00              
ATOM     99  C   LEU    81     -21.542  27.077  61.524  1.00  0.00              
ATOM    100  O   LEU    81     -20.465  26.669  61.075  1.00  0.00              
ATOM    101  N   PHE    82     -22.581  26.280  61.786  1.00  0.00              
ATOM    102  CA  PHE    82     -22.458  24.823  61.633  1.00  0.00              
ATOM    103  C   PHE    82     -22.222  24.447  60.163  1.00  0.00              
ATOM    104  O   PHE    82     -21.348  23.636  59.846  1.00  0.00              
ATOM    105  N   LEU    83     -22.974  25.088  59.267  1.00  0.00              
ATOM    106  CA  LEU    83     -22.902  24.895  57.825  1.00  0.00              
ATOM    107  C   LEU    83     -21.509  25.246  57.265  1.00  0.00              
ATOM    108  O   LEU    83     -20.918  24.488  56.495  1.00  0.00              
ATOM    109  N   ALA    84     -20.951  26.356  57.746  1.00  0.00              
ATOM    110  CA  ALA    84     -19.639  26.839  57.312  1.00  0.00              
ATOM    111  C   ALA    84     -18.578  25.829  57.645  1.00  0.00              
ATOM    112  O   ALA    84     -17.732  25.537  56.783  1.00  0.00              
ATOM    113  N   ALA    85     -18.645  25.286  58.873  1.00  0.00              
ATOM    114  CA  ALA    85     -17.675  24.285  59.302  1.00  0.00              
ATOM    115  C   ALA    85     -17.765  23.060  58.402  1.00  0.00              
ATOM    116  O   ALA    85     -16.737  22.504  57.993  1.00  0.00              
ATOM    117  N   LYS    86     -18.980  22.607  58.134  1.00  0.00              
ATOM    118  CA  LYS    86     -19.169  21.506  57.202  1.00  0.00              
ATOM    119  C   LYS    86     -18.554  21.808  55.803  1.00  0.00              
ATOM    120  O   LYS    86     -17.917  20.950  55.201  1.00  0.00              
ATOM    121  N   HIS    96     -18.756  23.016  55.291  1.00  0.00              
ATOM    122  CA  HIS    96     -18.221  23.365  53.978  1.00  0.00              
ATOM    123  C   HIS    96     -16.692  23.262  54.004  1.00  0.00              
ATOM    124  O   HIS    96     -16.075  22.662  53.101  1.00  0.00              
ATOM    125  N   VAL    97     -16.063  23.879  54.996  1.00  0.00              
ATOM    126  CA  VAL    97     -14.614  23.852  55.152  1.00  0.00              
ATOM    127  C   VAL    97     -14.064  22.432  55.270  1.00  0.00              
ATOM    128  O   VAL    97     -13.025  22.114  54.704  1.00  0.00              
ATOM    129  N   ASP   113     -14.734  21.572  56.028  1.00  0.00              
ATOM    130  CA  ASP   113     -14.243  20.206  56.159  1.00  0.00              
ATOM    131  C   ASP   113     -14.429  19.416  54.881  1.00  0.00              
ATOM    132  O   ASP   113     -13.604  18.573  54.567  1.00  0.00              
ATOM    133  N   ALA   118     -15.512  19.654  54.146  1.00  0.00              
ATOM    134  CA  ALA   118     -15.688  18.919  52.896  1.00  0.00              
ATOM    135  C   ALA   118     -14.673  19.456  51.863  1.00  0.00              
ATOM    136  O   ALA   118     -14.103  18.700  51.078  1.00  0.00              
ATOM    137  N   TYR   119     -14.406  20.758  51.919  1.00  0.00              
ATOM    138  CA  TYR   119     -13.455  21.383  51.016  1.00  0.00              
ATOM    139  C   TYR   119     -12.052  20.825  51.252  1.00  0.00              
ATOM    140  O   TYR   119     -11.399  20.339  50.319  1.00  0.00              
ATOM    141  N   LEU   120     -11.617  20.831  52.508  1.00  0.00              
ATOM    142  CA  LEU   120     -10.290  20.328  52.867  1.00  0.00              
ATOM    143  C   LEU   120     -10.157  18.830  52.678  1.00  0.00              
ATOM    144  O   LEU   120      -9.056  18.293  52.727  1.00  0.00              
ATOM    145  N   GLN   121      -1.495  27.285  54.408  1.00  0.00              
ATOM    146  CA  GLN   121      -1.950  28.027  55.577  1.00  0.00              
ATOM    147  C   GLN   121      -2.315  29.475  55.271  1.00  0.00              
ATOM    148  O   GLN   121      -3.219  30.047  55.898  1.00  0.00              
ATOM    149  N   GLN   122      -1.627  30.054  54.284  1.00  0.00              
ATOM    150  CA  GLN   122      -1.878  31.435  53.888  1.00  0.00              
ATOM    151  C   GLN   122      -3.266  31.680  53.321  1.00  0.00              
ATOM    152  O   GLN   122      -3.745  32.807  53.324  1.00  0.00              
ATOM    153  N   THR   123      -3.908  30.626  52.835  1.00  0.00              
ATOM    154  CA  THR   123      -5.249  30.722  52.269  1.00  0.00              
ATOM    155  C   THR   123      -6.319  30.050  53.144  1.00  0.00              
ATOM    156  O   THR   123      -7.482  29.985  52.743  1.00  0.00              
ATOM    157  N   ARG   124      -5.923  29.519  54.303  1.00  0.00              
ATOM    158  CA  ARG   124      -6.878  28.840  55.180  1.00  0.00              
ATOM    159  C   ARG   124      -7.985  29.786  55.607  1.00  0.00              
ATOM    160  O   ARG   124      -9.167  29.423  55.565  1.00  0.00              
ATOM    161  N   GLU   125      -7.603  31.004  55.989  1.00  0.00              
ATOM    162  CA  GLU   125      -8.565  32.009  56.415  1.00  0.00              
ATOM    163  C   GLU   125      -9.524  32.411  55.295  1.00  0.00              
ATOM    164  O   GLU   125     -10.701  32.696  55.541  1.00  0.00              
ATOM    165  N   LEU   126      -9.032  32.393  54.061  1.00  0.00              
ATOM    166  CA  LEU   126      -9.872  32.753  52.909  1.00  0.00              
ATOM    167  C   LEU   126     -10.892  31.624  52.715  1.00  0.00              
ATOM    168  O   LEU   126     -12.064  31.880  52.447  1.00  0.00              
ATOM    169  N   VAL   127     -10.455  30.381  52.907  1.00  0.00              
ATOM    170  CA  VAL   127     -11.356  29.243  52.767  1.00  0.00              
ATOM    171  C   VAL   127     -12.469  29.425  53.782  1.00  0.00              
ATOM    172  O   VAL   127     -13.658  29.284  53.454  1.00  0.00              
ATOM    173  N   GLY   138     -12.093  29.817  54.996  1.00  0.00              
ATOM    174  CA  GLY   138     -13.069  30.026  56.050  1.00  0.00              
ATOM    175  C   GLY   138     -14.022  31.175  55.740  1.00  0.00              
ATOM    176  O   GLY   138     -15.215  31.043  55.929  1.00  0.00              
END
