
#######################################################
#                                                     #
#                        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  125 (  125),  selected  125 , name T0285TS168_3
# Molecule2: number of CA atoms   99 (  800),  selected   99 , name T0285.pdb
# PARAMETERS: T0285TS168_3.T0285.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    A       1      -       -           -
LGA    Y       2      -       -           -
LGA    L       3      -       -           -
LGA    P       4      -       -           -
LGA    D       5      -       -           -
LGA    D       6      -       -           -
LGA    S       7      -       -           -
LGA    P       8      S       7          2.605
LGA    A       9      P       8          2.239
LGA    K      10      A       9          1.896
LGA    R      11      K      10          1.717
LGA    L      12      R      11          1.250
LGA    L      13      L      12          0.943
LGA    F      14      L      13          0.669
LGA    Q      15      F      14          0.865
LGA    M      16      Q      15          0.285
LGA    V      17      M      16          0.487
LGA    G      18      V      17          0.527
LGA    N      19      G      18          0.843
LGA    A      20      N      19          0.984
LGA    I      21      A      20          0.405
LGA    N      22      I      21          2.012
LGA    R      23      N      22          3.200
LGA    N      24      R      23          2.250
LGA    T      25      N      24          4.560
LGA    Q      26      -       -           -
LGA    Q      27      -       -           -
LGA    L      28      -       -           -
LGA    T      29      -       -           -
LGA    Q      30      -       -           -
LGA    D      31      -       -           -
LGA    L      32      -       -           -
LGA    R      33      -       -           -
LGA    A      34      -       -           -
LGA    M      35      -       -           -
LGA    P      36      -       -           -
LGA    N      37      -       -           -
LGA    W      38      -       -           -
LGA    S      39      -       -           -
LGA    L      40      -       -           -
LGA    R      41      T      25          4.890
LGA    F      42      -       -           -
LGA    V      43      -       -           -
LGA    Y      44      -       -           -
LGA    I      45      -       -           -
LGA    V      46      -       -           -
LGA    D      47      -       -           -
LGA    R      48      -       -           -
LGA    N      49      -       -           -
LGA    N      50      -       -           -
LGA    Q      51      -       -           -
LGA    D      52      -       -           -
LGA    L      53      -       -           -
LGA    L      54      -       -           -
LGA    K      55      -       -           -
LGA    R      56      -       -           -
LGA    P      57      -       -           -
LGA    L      58      -       -           -
LGA    P      59      -       -           -
LGA    P      60      Q      26          2.939
LGA    G      61      Q      27          4.830
LGA    I      62      L      28          2.132
LGA    M      63      T      29          2.362
LGA    -       -      Q      30           -
LGA    -       -      D      31           -
LGA    -       -      L      32           -
LGA    -       -      R      33           -
LGA    -       -      A      34           -
LGA    -       -      M      35           -
LGA    -       -      P      36           -
LGA    -       -      N      37           -
LGA    -       -      W      38           -
LGA    -       -      S      39           -
LGA    -       -      L      40           -
LGA    -       -      R      41           -
LGA    -       -      F      42           -
LGA    -       -      V      43           -
LGA    V      64      Y      44          5.418
LGA    L      65      I      45          3.399
LGA    A      66      -       -           -
LGA    P      67      -       -           -
LGA    R      68      -       -           -
LGA    L      69      -       -           -
LGA    T      70      -       -           -
LGA    A      71      -       -           -
LGA    K      72      -       -           -
LGA    H      73      -       -           -
LGA    P      74      -       -           -
LGA    Y      75      -       -           -
LGA    D      76      -       -           -
LGA    K      77      -       -           -
LGA    V      78      -       -           -
LGA    Q      79      -       -           -
LGA    D      80      -       -           -
LGA    R      81      -       -           -
LGA    N      82      -       -           -
LGA    R      83      -       -           -
LGA    K      84      -       -           -
LGA    L      85      -       -           -
LGA    Y      86      -       -           -
LGA    G      87      -       -           -
LGA    R      88      -       -           -
LGA    H      89      -       -           -
LGA    I      90      V      46           #
LGA    T      91      D      47          4.175
LGA    -       -      R      48           -
LGA    -       -      N      49           -
LGA    -       -      N      50           -
LGA    -       -      Q      51           -
LGA    L      92      D      52          2.880
LGA    N      93      L      53          3.483
LGA    -       -      L      54           -
LGA    D      94      K      55          1.890
LGA    G      95      R      56          4.989
LGA    N      96      P      57           #
LGA    S      97      L      58           -
LGA    V      98      P      59           -
LGA    K      99      P      60           -
LGA    V     100      G      61           -
LGA    V     101      I      62           -
LGA    T     102      M      63           -
LGA    I     103      V      64           -
LGA    S     104      L      65           -
LGA    -       -      A      66           -
LGA    -       -      P      67           -
LGA    -       -      R      68           -
LGA    -       -      L      69           -
LGA    A     105      T      70           #
LGA    G     106      -       -           -
LGA    R     107      A      71          2.282
LGA    D     108      K      72          1.052
LGA    E     109      H      73          2.626
LGA    G     110      P      74           #
LGA    P     111      Y      75          3.632
LGA    D     112      D      76          5.106
LGA    -       -      K      77           -
LGA    -       -      V      78           -
LGA    -       -      Q      79           -
LGA    -       -      D      80           -
LGA    -       -      R      81           -
LGA    -       -      N      82           -
LGA    -       -      R      83           -
LGA    -       -      K      84           -
LGA    -       -      L      85           -
LGA    -       -      Y      86           -
LGA    -       -      G      87           -
LGA    R     113      R      88          1.801
LGA    -       -      H      89           -
LGA    -       -      I      90           -
LGA    -       -      T      91           -
LGA    -       -      L      92           -
LGA    -       -      N      93           -
LGA    -       -      D      94           -
LGA    -       -      G      95           -
LGA    -       -      N      96           -
LGA    -       -      S      97           -
LGA    D     114      V      98           #
LGA    I     115      K      99          3.905
LGA    I     116      V     100          2.945
LGA    W     117      V     101          2.039
LGA    E     118      -       -           -
LGA    M     119      -       -           -
LGA    F     120      T     102          3.124
LGA    L     121      I     103          3.590
LGA    E     122      S     104           #
LGA    N     123      A     105           -
LGA    L     124      -       -           -
LGA    E     125      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  125   99    5.0     41    2.90     7.32     27.107     1.368

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.135696 * X  +  -0.959963 * Y  +  -0.245067 * Z  +  19.183983
  Y_new =   0.008724 * X  +   0.248503 * Y  +  -0.968592 * Z  +   4.123937
  Z_new =   0.990712 * X  +   0.129296 * Y  +   0.042096 * Z  +  77.477318 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.256044   -1.885548  [ DEG:    71.9660   -108.0340 ]
  Theta =  -1.434398   -1.707195  [ DEG:   -82.1850    -97.8150 ]
  Phi   =   0.064202   -3.077390  [ DEG:     3.6785   -176.3215 ]
 
# 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: T0285TS168_3                                  
REMARK     2: T0285.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0285TS168_3.T0285.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  125   99   5.0   41   2.90    7.32  27.107
REMARK  ---------------------------------------------------------- 
MOLECULE T0285TS168_3
PFRMAT TS
TARGET T0285
MODEL 3
PARENT N/A
ATOM      1  CA  ALA     1      25.910  25.122 100.462  1.00 25.00           C
ATOM      2  CA  TYR     2      24.620  25.962  97.031  1.00 25.00           C
ATOM      3  CA  LEU     3      20.889  26.224  96.388  1.00 25.00           C
ATOM      4  CA  PRO     4      20.169  26.740  92.725  1.00 25.00           C
ATOM      5  CA  ASP     5      16.643  26.782  91.329  1.00 25.00           C
ATOM      6  CA  ASP     6      14.329  27.479  88.324  1.00 25.00           C
ATOM      7  CA  SER     7      16.145  24.851  86.205  1.00 25.00           C
ATOM      8  CA  PRO     8      16.271  21.174  85.389  1.00 25.00           C
ATOM      9  CA  ALA     9      19.863  19.886  85.057  1.00 25.00           C
ATOM     10  CA  LYS    10      18.604  16.270  85.195  1.00 25.00           C
ATOM     11  CA  ARG    11      16.010  17.046  82.486  1.00 25.00           C
ATOM     12  CA  LEU    12      18.728  18.622  80.298  1.00 25.00           C
ATOM     13  CA  LEU    13      20.938  15.530  80.774  1.00 25.00           C
ATOM     14  CA  PHE    14      18.011  13.258  79.805  1.00 25.00           C
ATOM     15  CA  GLN    15      17.377  15.369  76.673  1.00 25.00           C
ATOM     16  CA  MET    16      21.084  15.138  75.737  1.00 25.00           C
ATOM     17  CA  VAL    17      20.989  11.337  76.203  1.00 25.00           C
ATOM     18  CA  GLY    18      17.875  11.118  73.984  1.00 25.00           C
ATOM     19  CA  ASN    19      19.610  13.225  71.298  1.00 25.00           C
ATOM     20  CA  ALA    20      22.681  10.943  71.457  1.00 25.00           C
ATOM     21  CA  ILE    21      20.438   7.859  71.096  1.00 25.00           C
ATOM     22  CA  ASN    22      18.705   9.443  68.070  1.00 25.00           C
ATOM     23  CA  ARG    23      22.110  10.207  66.490  1.00 25.00           C
ATOM     24  CA  ASN    24      23.220   6.588  67.073  1.00 25.00           C
ATOM     25  CA  THR    25      19.990   5.312  65.459  1.00 25.00           C
ATOM     26  CA  GLN    26      20.561   7.604  62.444  1.00 25.00           C
ATOM     27  CA  GLN    27      24.152   6.315  62.113  1.00 25.00           C
ATOM     28  CA  LEU    28      22.893   2.700  62.250  1.00 25.00           C
ATOM     29  CA  THR    29      20.299   3.475  59.542  1.00 25.00           C
ATOM     30  CA  GLN    30      23.018   5.051  57.353  1.00 25.00           C
ATOM     31  CA  ASP    31      25.228   1.959  57.830  1.00 25.00           C
ATOM     32  CA  LEU    32      22.300  -0.312  56.861  1.00 25.00           C
ATOM     33  CA  ARG    33      21.667   1.799  53.728  1.00 25.00           C
ATOM     34  CA  ALA    34      18.164   1.569  55.220  1.00 25.00           C
ATOM     35  CA  MET    35      17.262  -0.811  58.038  1.00 25.00           C
ATOM     36  CA  PRO    36      18.655  -4.372  58.193  1.00 25.00           C
ATOM     37  CA  ASN    37      15.679  -5.061  60.350  1.00 25.00           C
ATOM     38  CA  TRP    38      15.110  -2.545  63.078  1.00 25.00           C
ATOM     39  CA  SER    39      14.775  -4.626  66.224  1.00 25.00           C
ATOM     40  CA  LEU    40      17.222  -2.124  67.709  1.00 25.00           C
ATOM     41  CA  ARG    41      17.227   1.252  69.487  1.00 25.00           C
ATOM     42  CA  PHE    42      18.148   3.434  72.441  1.00 25.00           C
ATOM     43  CA  VAL    43      16.887   6.060  74.888  1.00 25.00           C
ATOM     44  CA  TYR    44      20.393   6.361  76.236  1.00 25.00           C
ATOM     45  CA  ILE    45      23.835   5.824  74.752  1.00 25.00           C
ATOM     46  CA  VAL    46      25.581   8.788  76.304  1.00 25.00           C
ATOM     47  CA  ASP    47      28.690  11.035  76.150  1.00 25.00           C
ATOM     48  CA  ARG    48      28.778  10.698  72.306  1.00 25.00           C
ATOM     49  CA  ASN    49      30.869  12.248  69.478  1.00 25.00           C
ATOM     50  CA  ASN    50      28.867   9.779  67.337  1.00 25.00           C
ATOM     51  CA  GLN    51      32.039   8.844  65.503  1.00 25.00           C
ATOM     52  CA  ASP    52      34.977   9.070  67.949  1.00 25.00           C
ATOM     53  CA  LEU    53      32.873   7.387  70.670  1.00 25.00           C
ATOM     54  CA  LEU    54      31.614   4.089  69.237  1.00 25.00           C
ATOM     55  CA  LYS    55      34.887   4.102  67.253  1.00 25.00           C
ATOM     56  CA  ARG    56      35.717   0.431  67.767  1.00 25.00           C
ATOM     57  CA  PRO    57      33.520  -2.688  67.322  1.00 25.00           C
ATOM     58  CA  LEU    58      30.770  -0.918  69.291  1.00 25.00           C
ATOM     59  CA  PRO    59      29.489  -3.640  71.614  1.00 25.00           C
ATOM     60  CA  PRO    60      26.225  -4.552  69.994  1.00 25.00           C
ATOM     61  CA  GLY    61      23.605  -1.980  70.835  1.00 25.00           C
ATOM     62  CA  ILE    62      23.997   1.155  72.957  1.00 25.00           C
ATOM     63  CA  MET    63      25.623   1.387  76.390  1.00 25.00           C
ATOM     64  CA  VAL    64      22.404   2.122  78.178  1.00 25.00           C
ATOM     65  CA  LEU    65      22.331   2.088  82.023  1.00 25.00           C
ATOM     66  CA  ALA    66      21.845   0.355  85.404  1.00 25.00           C
ATOM     67  CA  PRO    67      18.456   0.646  87.202  1.00 25.00           C
ATOM     68  CA  ARG    68      15.951  -0.197  89.899  1.00 25.00           C
ATOM     69  CA  LEU    69      18.190  -0.214  93.044  1.00 25.00           C
ATOM     70  CA  THR    70      16.929   1.330  96.320  1.00 25.00           C
ATOM     71  CA  ALA    71      13.536   1.054  94.751  1.00 25.00           C
ATOM     72  CA  LYS    72      11.581  -2.037  95.944  1.00 25.00           C
ATOM     73  CA  HIS    73      12.498  -3.543  92.575  1.00 25.00           C
ATOM     74  CA  PRO    74      10.674  -2.694  89.346  1.00 25.00           C
ATOM     75  CA  TYR    75      10.710  -6.331  88.446  1.00 25.00           C
ATOM     76  CA  ASP    76      14.182  -6.720  86.988  1.00 25.00           C
ATOM     77  CA  LYS    77      15.137  -8.351  83.657  1.00 25.00           C
ATOM     78  CA  VAL    78      15.472 -11.751  85.390  1.00 25.00           C
ATOM     79  CA  GLN    79      12.029 -11.293  87.005  1.00 25.00           C
ATOM     80  CA  ASP    80      10.521 -10.407  83.599  1.00 25.00           C
ATOM     81  CA  ARG    81      12.117 -13.526  82.053  1.00 25.00           C
ATOM     82  CA  ASN    82      10.701 -15.682  84.884  1.00 25.00           C
ATOM     83  CA  ARG    83       7.227 -14.169  84.333  1.00 25.00           C
ATOM     84  CA  LYS    84       7.479 -14.892  80.580  1.00 25.00           C
ATOM     85  CA  LEU    85       8.721 -11.706  78.852  1.00 25.00           C
ATOM     86  CA  TYR    86       5.829  -9.758  77.289  1.00 25.00           C
ATOM     87  CA  GLY    87       5.807  -7.132  80.119  1.00 25.00           C
ATOM     88  CA  ARG    88       7.959  -4.283  81.454  1.00 25.00           C
ATOM     89  CA  HIS    89       9.449  -0.848  80.770  1.00 25.00           C
ATOM     90  CA  ILE    90      12.208   0.759  78.742  1.00 25.00           C
ATOM     91  CA  THR    91      15.865   1.067  79.799  1.00 25.00           C
ATOM     92  CA  LEU    92      18.841  -1.176  80.482  1.00 25.00           C
ATOM     93  CA  ASN    93      21.868  -3.244  81.556  1.00 25.00           C
ATOM     94  CA  ASP    94      23.629  -5.632  84.014  1.00 25.00           C
ATOM     95  CA  GLY    95      27.210  -6.672  83.107  1.00 25.00           C
ATOM     96  CA  ASN    96      28.176  -3.834  85.464  1.00 25.00           C
ATOM     97  CA  SER    97      28.907  -2.031  82.150  1.00 25.00           C
ATOM     98  CA  VAL    98      26.284  -2.245  79.402  1.00 25.00           C
ATOM     99  CA  LYS    99      24.520  -3.582  76.300  1.00 25.00           C
ATOM    100  CA  VAL   100      20.988  -2.266  76.097  1.00 25.00           C
ATOM    101  CA  VAL   101      18.720  -2.302  73.095  1.00 25.00           C
ATOM    102  CA  THR   102      16.093  -0.484  75.133  1.00 25.00           C
ATOM    103  CA  ILE   103      13.488   1.676  73.469  1.00 25.00           C
ATOM    104  CA  SER   104      12.659   5.255  72.338  1.00 25.00           C
ATOM    105  CA  ALA   105      10.354   7.999  70.963  1.00 25.00           C
ATOM    106  CA  GLY   106       6.584   8.355  70.604  1.00 25.00           C
ATOM    107  CA  ARG   107       4.974   5.994  73.158  1.00 25.00           C
ATOM    108  CA  ASP   108       2.566   6.419  76.079  1.00 25.00           C
ATOM    109  CA  GLU   109       2.038   6.079  79.803  1.00 25.00           C
ATOM    110  CA  GLY   110       2.998   9.767  80.376  1.00 25.00           C
ATOM    111  CA  PRO   111       6.158   8.178  81.757  1.00 25.00           C
ATOM    112  CA  ASP   112       9.623   7.715  80.246  1.00 25.00           C
ATOM    113  CA  ARG   113      13.474   7.872  80.271  1.00 25.00           C
ATOM    114  CA  ASP   114      14.422   5.023  82.649  1.00 25.00           C
ATOM    115  CA  ILE   115      17.748   4.560  80.807  1.00 25.00           C
ATOM    116  CA  ILE   116      18.444   8.317  81.071  1.00 25.00           C
ATOM    117  CA  TRP   117      17.675   8.221  84.821  1.00 25.00           C
ATOM    118  CA  GLU   118      20.046   5.244  85.257  1.00 25.00           C
ATOM    119  CA  MET   119      22.790   7.121  83.356  1.00 25.00           C
ATOM    120  CA  PHE   120      22.266  10.192  85.582  1.00 25.00           C
ATOM    121  CA  LEU   121      22.503   7.996  88.711  1.00 25.00           C
ATOM    122  CA  GLU   122      25.744   6.435  87.399  1.00 25.00           C
ATOM    123  CA  ASN   123      27.180   9.920  86.728  1.00 25.00           C
ATOM    124  CA  LEU   124      30.239   8.556  88.545  1.00 25.00           C
ATOM    125  CA  GLU   125      32.226   9.210  91.749  1.00 25.00           C
TER
END
