
#######################################################
#                                                     #
#                        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  117 (  117),  selected  117 , name T0350TS599_1
# Molecule2: number of CA atoms  109 ( 1798),  selected  109 , name T0350.pdb
# PARAMETERS: T0350TS599_1.T0350.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      -       -           -
LGA    N       2      -       -           -
LGA    I       3      -       -           -
LGA    E       4      -       -           -
LGA    R       5      -       -           -
LGA    L       6      -       -           -
LGA    T       7      -       -           -
LGA    T       8      -       -           -
LGA    L       9      -       -           -
LGA    Q      10      -       -           -
LGA    P      11      -       -           -
LGA    V      12      -       -           -
LGA    W      13      -       -           -
LGA    D      14      -       -           -
LGA    R      15      -       -           -
LGA    Y      16      -       -           -
LGA    D      17      -       -           -
LGA    T      18      -       -           -
LGA    Q      19      -       -           -
LGA    I      20      -       -           -
LGA    H      21      -       -           -
LGA    N      22      -       -           -
LGA    Q      23      -       -           -
LGA    K      24      -       -           -
LGA    D      25      -       -           -
LGA    N      26      -       -           -
LGA    D      27      -       -           -
LGA    N      28      -       -           -
LGA    E      29      -       -           -
LGA    V      30      -       -           -
LGA    P      31      -       -           -
LGA    V      32      -       -           -
LGA    H      33      -       -           -
LGA    Q      34      -       -           -
LGA    V      35      -       -           -
LGA    S      36      -       -           -
LGA    Y      37      -       -           -
LGA    T      38      -       -           -
LGA    N      39      -       -           -
LGA    L      40      -       -           -
LGA    A      41      -       -           -
LGA    E      42      -       -           -
LGA    M      43      -       -           -
LGA    V      44      M       1           #
LGA    -       -      N       2           -
LGA    -       -      I       3           -
LGA    -       -      E       4           -
LGA    -       -      R       5           -
LGA    -       -      L       6           -
LGA    -       -      T       7           -
LGA    -       -      T       8           -
LGA    -       -      L       9           -
LGA    G      45      Q      10           #
LGA    E      46      P      11          2.395
LGA    M      47      V      12          5.010
LGA    N      48      -       -           -
LGA    K      49      -       -           -
LGA    L      50      W      13           #
LGA    L      51      D      14           -
LGA    E      52      R      15           -
LGA    P      53      Y      16           -
LGA    S      54      D      17           -
LGA    Q      55      T      18           -
LGA    V      56      Q      19           -
LGA    H      57      I      20           -
LGA    L      58      H      21           -
LGA    K      59      N      22           -
LGA    F      60      Q      23           -
LGA    E      61      K      24           -
LGA    -       -      D      25           -
LGA    -       -      N      26           -
LGA    -       -      D      27           -
LGA    -       -      N      28           -
LGA    -       -      E      29           -
LGA    -       -      V      30           -
LGA    -       -      P      31           -
LGA    -       -      V      32           -
LGA    -       -      H      33           -
LGA    -       -      Q      34           -
LGA    -       -      V      35           -
LGA    -       -      S      36           -
LGA    -       -      Y      37           -
LGA    -       -      T      38           -
LGA    -       -      N      39           -
LGA    L      62      L      40          4.857
LGA    H      63      A      41          2.884
LGA    D      64      E      42           #
LGA    K      65      -       -           -
LGA    L      66      -       -           -
LGA    N      67      -       -           -
LGA    E      68      M      43          4.241
LGA    Y      69      V      44          3.518
LGA    Y      70      G      45           #
LGA    -       -      E      46           -
LGA    -       -      M      47           -
LGA    -       -      N      48           -
LGA    -       -      K      49           -
LGA    -       -      L      50           -
LGA    -       -      L      51           -
LGA    -       -      E      52           -
LGA    -       -      P      53           -
LGA    -       -      S      54           -
LGA    -       -      Q      55           -
LGA    -       -      V      56           -
LGA    -       -      H      57           -
LGA    -       -      L      58           -
LGA    -       -      K      59           -
LGA    V      71      F      60          4.587
LGA    -       -      E      61           -
LGA    -       -      L      62           -
LGA    -       -      H      63           -
LGA    -       -      D      64           -
LGA    -       -      K      65           -
LGA    -       -      L      66           -
LGA    -       -      N      67           -
LGA    -       -      E      68           -
LGA    -       -      Y      69           -
LGA    -       -      Y      70           -
LGA    -       -      V      71           -
LGA    K      72      K      72           #
LGA    V      73      V      73          2.972
LGA    I      74      I      74          1.969
LGA    E      75      E      75          1.570
LGA    D      76      D      76          1.764
LGA    S      77      S      77          3.282
LGA    T      78      T      78          2.126
LGA    N      79      N      79          1.766
LGA    E      80      E      80          2.446
LGA    V      81      V      81          3.365
LGA    I      82      -       -           -
LGA    R      83      -       -           -
LGA    E      84      I      82          4.028
LGA    I      85      R      83          2.610
LGA    P      86      E      84          2.812
LGA    P      87      I      85          2.774
LGA    K      88      P      86          2.310
LGA    -       -      P      87           -
LGA    -       -      K      88           -
LGA    R      89      R      89           #
LGA    W      90      W      90           #
LGA    L      91      L      91           #
LGA    D      92      D      92          4.028
LGA    F      93      F      93          3.167
LGA    Y      94      Y      94          3.417
LGA    A      95      A      95          2.940
LGA    A      96      A      96          0.683
LGA    M      97      M      97          0.292
LGA    T      98      T      98          0.969
LGA    E      99      E      99          2.557
LGA    F     100      F     100          2.749
LGA    L     101      L     101          2.545
LGA    G     102      G     102          2.126
LGA    L     103      -       -           -
LGA    F     104      L     103          2.914
LGA    V     105      F     104          4.633
LGA    D     106      -       -           -
LGA    E     107      -       -           -
LGA    K     108      V     105           #
LGA    K     109      D     106          2.991
LGA    L     110      E     107          3.346
LGA    -       -      K     108           -
LGA    E     111      K     109          3.647
LGA    H     112      -       -           -
LGA    H     113      -       -           -
LGA    H     114      -       -           -
LGA    H     115      -       -           -
LGA    H     116      -       -           -
LGA    H     117      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  117  109    5.0     37    3.07    56.76     22.000     1.167

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.274741 * X  +   0.428668 * Y  +  -0.860675 * Z  +   0.171699
  Y_new =   0.956958 * X  +  -0.208982 * Y  +   0.201390 * Z  +   2.997547
  Z_new =  -0.093536 * X  +  -0.878960 * Y  +  -0.467633 * Z  + -14.081131 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.059739    1.081854  [ DEG:  -118.0143     61.9857 ]
  Theta =   0.093673    3.047919  [ DEG:     5.3671    174.6329 ]
  Phi   =   1.291218   -1.850375  [ DEG:    73.9813   -106.0187 ]
 
# 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: T0350TS599_1                                  
REMARK     2: T0350.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0350TS599_1.T0350.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  117  109   5.0   37   3.07   56.76  22.000
REMARK  ---------------------------------------------------------- 
MOLECULE T0350TS599_1
PFRMAT TS                                                                       
TARGET T0350                                                                    
MODEL  1                                                                        
PARENT N/A                                                                      
ATOM      1  CA  MET     1       2.493  13.130 -19.841  1.00  0.00              
ATOM      2  CA  ASN     2       4.093   9.275 -19.319  1.00  0.00              
ATOM      3  CA  ILE     3       0.197   9.839 -19.596  1.00  0.00              
ATOM      4  CA  GLU     4      -2.213   7.378 -18.310  1.00  0.00              
ATOM      5  CA  ARG     5      -3.363   9.483 -15.339  1.00  0.00              
ATOM      6  CA  LEU     6      -4.450  12.511 -17.375  1.00  0.00              
ATOM      7  CA  THR     7      -6.558  10.499 -19.873  1.00  0.00              
ATOM      8  CA  THR     8      -8.360   8.635 -17.072  1.00  0.00              
ATOM      9  CA  LEU     9      -9.269  11.750 -15.065  1.00  0.00              
ATOM     10  CA  GLN    10     -10.823  13.541 -18.053  1.00  0.00              
ATOM     11  CA  PRO    11     -13.133  10.560 -18.708  1.00  0.00              
ATOM     12  CA  VAL    12     -14.083  10.415 -15.007  1.00  0.00              
ATOM     13  CA  TRP    13     -14.869  14.178 -14.802  1.00  0.00              
ATOM     14  CA  ASP    14     -17.250  13.767 -17.683  1.00  0.00              
ATOM     15  CA  ARG    15     -18.973  10.709 -16.217  1.00  0.00              
ATOM     16  CA  TYR    16     -20.187  12.123 -12.969  1.00  0.00              
ATOM     17  CA  ASP    17     -17.801  11.524 -10.155  1.00  0.00              
ATOM     18  CA  THR    18     -20.034   9.071  -8.192  1.00  0.00              
ATOM     19  CA  GLN    19     -20.512   6.858 -11.276  1.00  0.00              
ATOM     20  CA  ILE    20     -16.738   6.772 -11.951  1.00  0.00              
ATOM     21  CA  HIS    21     -15.865   5.835  -8.391  1.00  0.00              
ATOM     22  CA  ASN    22     -18.334   2.975  -8.475  1.00  0.00              
ATOM     23  CA  GLN    23     -16.886   1.806 -11.827  1.00  0.00              
ATOM     24  CA  LYS    24     -13.322   1.880 -10.495  1.00  0.00              
ATOM     25  CA  ASP    25     -14.369  -0.099  -7.379  1.00  0.00              
ATOM     26  CA  ASN    26     -16.143  -2.822  -9.267  1.00  0.00              
ATOM     27  CA  ASP    27     -13.479  -3.056 -11.910  1.00  0.00              
ATOM     28  CA  ASN    28     -11.094  -3.775  -9.229  1.00  0.00              
ATOM     29  CA  GLU    29     -12.757  -6.123  -6.968  1.00  0.00              
ATOM     30  CA  VAL    30     -13.787  -8.993  -9.143  1.00  0.00              
ATOM     31  CA  PRO    31     -10.406  -8.591 -10.768  1.00  0.00              
ATOM     32  CA  VAL    32      -8.821  -9.203  -7.329  1.00  0.00              
ATOM     33  CA  HIS    33     -11.008 -12.200  -6.582  1.00  0.00              
ATOM     34  CA  GLN    34     -10.437 -13.817 -10.026  1.00  0.00              
ATOM     35  CA  VAL    35      -6.636 -13.416  -9.589  1.00  0.00              
ATOM     36  CA  SER    36      -6.306 -14.694  -6.017  1.00  0.00              
ATOM     37  CA  TYR    37      -5.583 -12.395  -3.101  1.00  0.00              
ATOM     38  CA  THR    38      -2.044 -13.612  -2.639  1.00  0.00              
ATOM     39  CA  ASN    39      -1.291 -13.129  -6.361  1.00  0.00              
ATOM     40  CA  LEU    40      -2.745  -9.608  -6.315  1.00  0.00              
ATOM     41  CA  ALA    41      -0.727  -8.634  -3.316  1.00  0.00              
ATOM     42  CA  GLU    42       2.415  -9.974  -5.051  1.00  0.00              
ATOM     43  CA  MET    43       1.513  -7.980  -8.194  1.00  0.00              
ATOM     44  CA  VAL    44       1.185  -4.754  -6.105  1.00  0.00              
ATOM     45  CA  GLY    45       4.584  -5.344  -4.431  1.00  0.00              
ATOM     46  CA  GLU    46       6.151  -5.900  -7.898  1.00  0.00              
ATOM     47  CA  MET    47       4.482  -2.689  -9.084  1.00  0.00              
ATOM     48  CA  ASN    48       5.830  -0.738  -6.135  1.00  0.00              
ATOM     49  CA  LYS    49       9.295  -2.019  -7.119  1.00  0.00              
ATOM     50  CA  LEU    50       8.729  -0.952 -10.725  1.00  0.00              
ATOM     51  CA  LEU    51       7.678   2.556  -9.603  1.00  0.00              
ATOM     52  CA  GLU    52      10.780   2.895  -7.450  1.00  0.00              
ATOM     53  CA  PRO    53      12.916   1.883 -10.452  1.00  0.00              
ATOM     54  CA  SER    54      11.087   4.432 -12.670  1.00  0.00              
ATOM     55  CA  GLN    55      11.585   7.167 -10.115  1.00  0.00              
ATOM     56  CA  VAL    56      15.378   6.544 -10.489  1.00  0.00              
ATOM     57  CA  HIS    57      15.438   7.810 -14.043  1.00  0.00              
ATOM     58  CA  LEU    58      12.082   7.955 -15.822  1.00  0.00              
ATOM     59  CA  LYS    59      11.569   9.663 -19.118  1.00  0.00              
ATOM     60  CA  PHE    60       8.002  10.424 -20.243  1.00  0.00              
ATOM     61  CA  GLU    61       7.084  10.834 -23.866  1.00  0.00              
ATOM     62  CA  LEU    62       3.628  11.971 -24.804  1.00  0.00              
ATOM     63  CA  HIS    63       2.412  11.561 -28.282  1.00  0.00              
ATOM     64  CA  ASP    64      -0.046  14.232 -29.187  1.00  0.00              
ATOM     65  CA  LYS    65      -1.494  12.593 -32.225  1.00  0.00              
ATOM     66  CA  LEU    66      -2.216   9.246 -30.726  1.00  0.00              
ATOM     67  CA  ASN    67      -2.973  10.500 -27.233  1.00  0.00              
ATOM     68  CA  GLU    68      -0.522   7.872 -26.070  1.00  0.00              
ATOM     69  CA  TYR    69       1.921   7.958 -23.251  1.00  0.00              
ATOM     70  CA  TYR    70       5.350   6.480 -23.758  1.00  0.00              
ATOM     71  CA  VAL    71       7.538   5.788 -20.805  1.00  0.00              
ATOM     72  CA  LYS    72      11.234   5.457 -21.276  1.00  0.00              
ATOM     73  CA  VAL    73      13.308   3.924 -18.567  1.00  0.00              
ATOM     74  CA  ILE    74      16.895   4.908 -18.365  1.00  0.00              
ATOM     75  CA  GLU    75      19.282   3.406 -15.695  1.00  0.00              
ATOM     76  CA  ASP    76      21.170   6.539 -14.772  1.00  0.00              
ATOM     77  CA  SER    77      24.520   5.279 -14.042  1.00  0.00              
ATOM     78  CA  THR    78      25.031   2.766 -16.795  1.00  0.00              
ATOM     79  CA  ASN    79      22.252   3.487 -19.327  1.00  0.00              
ATOM     80  CA  GLU    80      21.339  -0.151 -19.373  1.00  0.00              
ATOM     81  CA  VAL    81      17.622  -0.662 -19.158  1.00  0.00              
ATOM     82  CA  ILE    82      16.822   1.827 -21.898  1.00  0.00              
ATOM     83  CA  ARG    83      19.383   0.236 -24.242  1.00  0.00              
ATOM     84  CA  GLU    84      18.045  -3.268 -23.705  1.00  0.00              
ATOM     85  CA  ILE    85      14.501  -2.618 -24.299  1.00  0.00              
ATOM     86  CA  PRO    86      12.702  -3.383 -27.586  1.00  0.00              
ATOM     87  CA  PRO    87      10.087  -0.647 -27.941  1.00  0.00              
ATOM     88  CA  LYS    88       7.171  -3.096 -27.634  1.00  0.00              
ATOM     89  CA  ARG    89       8.345  -4.472 -24.339  1.00  0.00              
ATOM     90  CA  TRP    90       8.784  -1.006 -22.814  1.00  0.00              
ATOM     91  CA  LEU    91       5.209  -0.037 -23.813  1.00  0.00              
ATOM     92  CA  ASP    92       3.864  -3.282 -22.288  1.00  0.00              
ATOM     93  CA  PHE    93       5.711  -2.737 -19.022  1.00  0.00              
ATOM     94  CA  TYR    94       4.430   0.880 -18.868  1.00  0.00              
ATOM     95  CA  ALA    95       0.854  -0.317 -19.473  1.00  0.00              
ATOM     96  CA  ALA    96       1.256  -2.904 -16.708  1.00  0.00              
ATOM     97  CA  MET    97       2.585  -0.321 -14.314  1.00  0.00              
ATOM     98  CA  THR    98      -0.215   2.110 -14.917  1.00  0.00              
ATOM     99  CA  GLU    99      -2.854  -0.471 -14.302  1.00  0.00              
ATOM    100  CA  PHE   100      -1.268  -1.621 -11.079  1.00  0.00              
ATOM    101  CA  LEU   101      -0.172   1.454  -9.113  1.00  0.00              
ATOM    102  CA  GLY   102      -3.354   3.200 -10.022  1.00  0.00              
ATOM    103  CA  LEU   103      -5.532   0.280  -9.144  1.00  0.00              
ATOM    104  CA  PHE   104      -3.911  -0.382  -5.761  1.00  0.00              
ATOM    105  CA  VAL   105      -3.422   3.180  -4.668  1.00  0.00              
ATOM    106  CA  ASP   106      -3.123   4.417  -1.150  1.00  0.00              
ATOM    107  CA  GLU   107      -5.208   7.546  -1.065  1.00  0.00              
ATOM    108  CA  LYS   108      -2.211   9.742  -0.146  1.00  0.00              
ATOM    109  CA  LYS   109      -0.304   8.697  -3.295  1.00  0.00              
ATOM    110  CA  LEU   110      -3.338   9.245  -5.567  1.00  0.00              
ATOM    111  CA  GLU   111      -3.983  12.669  -4.008  1.00  0.00              
ATOM    112  CA  HIS   112      -0.405  13.727  -4.406  1.00  0.00              
ATOM    113  CA  HIS   113      -0.219  12.692  -8.088  1.00  0.00              
ATOM    114  CA  HIS   114      -3.054  14.980  -9.117  1.00  0.00              
ATOM    115  CA  HIS   115      -5.917  12.853  -9.930  1.00  0.00              
ATOM    116  CA  HIS   116      -9.685  11.300  -8.892  1.00  0.00              
ATOM    117  CA  HIS   117     -11.645  14.926  -9.624  1.00  0.00              
TER                                                                             
END
