
#######################################################
#                                                     #
#                        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   25 (  108),  selected   25 , name T0319AL381_2
# Molecule2: number of CA atoms  135 ( 1055),  selected  135 , name T0319.pdb
# PARAMETERS: T0319AL381_2.T0319.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

# WARNING! The change of the parameter DIST cutoff may give you better result.

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      M       1           -
LGA    -       -      K       2           -
LGA    -       -      F       3           -
LGA    -       -      L       4           -
LGA    -       -      T       5           -
LGA    -       -      T       6           -
LGA    -       -      N       7           -
LGA    E     109      F       8          1.941
LGA    M     110      L       9          2.095
LGA    K     111      K      10          2.354
LGA    C     112      C      11          0.741
LGA    R     113      S      12          1.535
LGA    N     114      V      13          3.250
LGA    -       -      K      14           -
LGA    -       -      A      15           -
LGA    C     115      C      16          2.239
LGA    G     116      D      17          3.196
LGA    -       -      T      18           -
LGA    -       -      S      19           -
LGA    -       -      N      20           -
LGA    -       -      D      21           -
LGA    H     117      N      22          1.929
LGA    I     118      F      23          3.424
LGA    Y     119      P      24          3.697
LGA    Y     120      L      25           -
LGA    -       -      Q      26           -
LGA    -       -      Y      27           -
LGA    -       -      D      28           -
LGA    -       -      G      29           -
LGA    -       -      S      30           -
LGA    -       -      K      31           -
LGA    -       -      C      32           -
LGA    -       -      Q      33           -
LGA    -       -      L      34           -
LGA    -       -      V      35           -
LGA    -       -      Q      36           -
LGA    -       -      D      37           -
LGA    -       -      E      38           -
LGA    -       -      S      39           -
LGA    -       -      I      40           -
LGA    -       -      E      41           -
LGA    -       -      F      42           -
LGA    -       -      N      43           -
LGA    -       -      P      44           -
LGA    -       -      E      45           -
LGA    -       -      F      46           -
LGA    -       -      L      47           -
LGA    -       -      L      48           -
LGA    -       -      N      49           -
LGA    -       -      I      50           -
LGA    -       -      V      51           -
LGA    -       -      D      52           -
LGA    I     121      R      53           #
LGA    K     122      V      54          2.449
LGA    N     123      D      55          2.962
LGA    -       -      W      56           -
LGA    -       -      P      57           -
LGA    G     124      A      58          3.383
LGA    I     125      V      59          4.703
LGA    P     126      L      60          2.391
LGA    N     127      T      61          3.623
LGA    L     128      V      62           #
LGA    -       -      A      63           -
LGA    L     129      A      64          1.199
LGA    L     130      E      65          4.626
LGA    -       -      L      66           -
LGA    -       -      G      67           -
LGA    -       -      N      68           -
LGA    -       -      N      69           -
LGA    -       -      A      70           -
LGA    P     131      L      71           #
LGA    P     132      P      72           -
LGA    -       -      P      73           -
LGA    -       -      T      74           -
LGA    -       -      K      75           -
LGA    -       -      P      76           -
LGA    -       -      S      77           -
LGA    -       -      F      78           -
LGA    -       -      P      79           -
LGA    -       -      S      80           -
LGA    -       -      S      81           -
LGA    -       -      I      82           -
LGA    -       -      Q      83           -
LGA    -       -      E      84           -
LGA    -       -      L      85           -
LGA    -       -      T      86           -
LGA    -       -      D      87           -
LGA    -       -      D      88           -
LGA    -       -      D      89           -
LGA    -       -      M      90           -
LGA    -       -      A      91           -
LGA    -       -      I      92           -
LGA    -       -      L      93           -
LGA    -       -      N      94           -
LGA    -       -      D      95           -
LGA    -       -      L      96           -
LGA    -       -      H      97           -
LGA    -       -      T      98           -
LGA    -       -      L      99           -
LGA    H     133      L     100          3.945
LGA    -       -      L     101           -
LGA    -       -      Q     102           -
LGA    -       -      T     103           -
LGA    -       -      S     104           -
LGA    -       -      I     105           -
LGA    -       -      A     106           -
LGA    -       -      E     107           -
LGA    -       -      G     108           -
LGA    -       -      E     109           -
LGA    -       -      M     110           -
LGA    -       -      K     111           -
LGA    -       -      C     112           -
LGA    -       -      R     113           -
LGA    -       -      N     114           -
LGA    -       -      C     115           -
LGA    -       -      G     116           -
LGA    -       -      H     117           -
LGA    -       -      I     118           -
LGA    -       -      Y     119           -
LGA    -       -      Y     120           -
LGA    -       -      I     121           -
LGA    -       -      K     122           -
LGA    -       -      N     123           -
LGA    -       -      G     124           -
LGA    -       -      I     125           -
LGA    -       -      P     126           -
LGA    -       -      N     127           -
LGA    -       -      L     128           -
LGA    -       -      L     129           -
LGA    -       -      L     130           -
LGA    -       -      P     131           -
LGA    -       -      P     132           -
LGA    -       -      H     133           -
LGA    -       -      L     134           -
LGA    -       -      V     135           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   25  135    5.0     20    2.98    15.00      9.968     0.650

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.499513 * X  +  -0.167113 * Y  +   0.850035 * Z  +   8.510013
  Y_new =   0.865110 * X  +  -0.044663 * Y  +   0.499590 * Z  +  -1.468179
  Z_new =  -0.045523 * X  +   0.984926 * Y  +   0.166881 * Z  +  -2.903498 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.402956   -1.738637  [ DEG:    80.3834    -99.6166 ]
  Theta =   0.045538    3.096054  [ DEG:     2.6092    177.3909 ]
  Phi   =   2.094431   -1.047161  [ DEG:   120.0021    -59.9979 ]
 
# 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: T0319AL381_2                                  
REMARK     2: T0319.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0319AL381_2.T0319.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   25  135   5.0   20   2.98   15.00   9.968
REMARK  ---------------------------------------------------------- 
MOLECULE T0319AL381_2
REMARK Aligment from pdb entry: 1yk4A
ATOM      1  N   GLU   109      14.100  -3.554  18.060  1.00  0.00              
ATOM      2  CA AGLU   109      13.032  -3.567  17.108  1.00  0.00              
ATOM      3  CA BGLU   109      13.051  -3.515  17.045  1.00  0.00              
ATOM      4  C   GLU   109      12.004  -2.481  17.411  1.00  0.00              
ATOM      5  O   GLU   109      11.685  -2.279  18.591  1.00  0.00              
ATOM      6  N   MET   110      11.461  -1.851  16.361  1.00  0.00              
ATOM      7  CA  MET   110      10.477  -0.788  16.520  1.00  0.00              
ATOM      8  C   MET   110       9.326  -1.017  15.539  1.00  0.00              
ATOM      9  O   MET   110       9.534  -1.230  14.349  1.00  0.00              
ATOM     10  N   LYS   111       8.097  -0.921  16.047  1.00  0.00              
ATOM     11  CA  LYS   111       6.918  -1.042  15.194  1.00  0.00              
ATOM     12  C   LYS   111       6.510   0.302  14.621  1.00  0.00              
ATOM     13  O   LYS   111       6.432   1.305  15.341  1.00  0.00              
ATOM     14  N   CYS   112       6.177   0.312  13.315  1.00  0.00              
ATOM     15  CA  CYS   112       5.458   1.447  12.736  1.00  0.00              
ATOM     16  C   CYS   112       4.056   1.462  13.328  1.00  0.00              
ATOM     17  O   CYS   112       3.344   0.439  13.290  1.00  0.00              
ATOM     18  N   ARG   113       3.609   2.599  13.878  1.00  0.00              
ATOM     19  CA  ARG   113       2.291   2.637  14.487  1.00  0.00              
ATOM     20  C  AARG   113       1.155   2.447  13.417  1.00  0.00              
ATOM     21  C  BARG   113       1.204   2.450  13.532  1.00  0.00              
ATOM     22  O  AARG   113       0.087   2.126  13.814  1.00  0.00              
ATOM     23  O  BARG   113       0.086   1.931  13.866  1.00  0.00              
ATOM     24  N  AASN   114       1.484   2.779  12.167  1.00  0.00              
ATOM     25  N  BASN   114       1.314   2.844  12.272  1.00  0.00              
ATOM     26  CA AASN   114       0.493   3.064  11.126  1.00  0.00              
ATOM     27  CA BASN   114       0.140   2.790  11.390  1.00  0.00              
ATOM     28  C  AASN   114       0.359   1.869  10.159  1.00  0.00              
ATOM     29  C  BASN   114       0.218   1.768  10.269  1.00  0.00              
ATOM     30  O  AASN   114      -0.643   1.818   9.402  1.00  0.00              
ATOM     31  O  BASN   114      -0.576   1.827   9.303  1.00  0.00              
ATOM     32  N  ACYS   115       1.307   0.956  10.176  1.00  0.00              
ATOM     33  N  BCYS   115       1.085   0.765  10.288  1.00  0.00              
ATOM     34  CA  CYS   115       1.128  -0.287   9.348  1.00  0.00              
ATOM     35  C   CYS   115       1.841  -1.457  10.047  1.00  0.00              
ATOM     36  O   CYS   115       2.360  -1.322  11.135  1.00  0.00              
ATOM     37  N   GLY   116       1.905  -2.602   9.348  1.00  0.00              
ATOM     38  CA  GLY   116       2.492  -3.794   9.952  1.00  0.00              
ATOM     39  C   GLY   116       4.027  -3.864   9.932  1.00  0.00              
ATOM     40  O   GLY   116       4.588  -4.839  10.450  1.00  0.00              
ATOM     41  N   HIS   117       4.685  -2.864   9.378  1.00  0.00              
ATOM     42  CA  HIS   117       6.148  -2.898   9.307  1.00  0.00              
ATOM     43  C   HIS   117       6.782  -2.831  10.709  1.00  0.00              
ATOM     44  O   HIS   117       6.286  -2.127  11.616  1.00  0.00              
ATOM     45  N   ILE   118       7.921  -3.520  10.812  1.00  0.00              
ATOM     46  CA  ILE   118       8.794  -3.521  11.977  1.00  0.00              
ATOM     47  C   ILE   118      10.209  -3.205  11.478  1.00  0.00              
ATOM     48  O   ILE   118      10.725  -3.925  10.605  1.00  0.00              
ATOM     49  N   TYR   119      10.806  -2.128  12.021  1.00  0.00              
ATOM     50  CA  TYR   119      12.215  -1.833  11.771  1.00  0.00              
ATOM     51  C   TYR   119      13.059  -2.595  12.799  1.00  0.00              
ATOM     52  O   TYR   119      12.990  -2.317  14.007  1.00  0.00              
ATOM     53  N   TYR   120      13.839  -3.564  12.311  1.00  0.00              
ATOM     54  CA  TYR   120      14.769  -4.295  13.167  1.00  0.00              
ATOM     55  C   TYR   120      16.161  -3.744  12.854  1.00  0.00              
ATOM     56  O   TYR   120      16.596  -3.795  11.680  1.00  0.00              
ATOM     57  N   ILE   121      16.846  -3.183  13.855  1.00  0.00              
ATOM     58  CA  ILE   121      18.182  -2.640  13.630  1.00  0.00              
ATOM     59  C   ILE   121      19.130  -3.658  13.000  1.00  0.00              
ATOM     60  O   ILE   121      20.038  -3.282  12.242  1.00  0.00              
ATOM     61  N   LYS   122      18.956  -4.958  13.311  1.00  0.00              
ATOM     62  CA  LYS   122      19.789  -5.994  12.715  1.00  0.00              
ATOM     63  C   LYS   122      19.461  -6.293  11.243  1.00  0.00              
ATOM     64  O   LYS   122      20.257  -6.959  10.554  1.00  0.00              
ATOM     65  N   ASN   123      18.293  -5.842  10.769  1.00  0.00              
ATOM     66  CA  ASN   123      17.928  -5.942   9.357  1.00  0.00              
ATOM     67  C   ASN   123      18.273  -4.695   8.537  1.00  0.00              
ATOM     68  O   ASN   123      18.534  -4.803   7.329  1.00  0.00              
ATOM     69  N   GLY   124      18.209  -3.511   9.166  1.00  0.00              
ATOM     70  CA  GLY   124      18.272  -2.294   8.367  1.00  0.00              
ATOM     71  C   GLY   124      17.063  -2.180   7.428  1.00  0.00              
ATOM     72  O   GLY   124      16.013  -2.782   7.647  1.00  0.00              
ATOM     73  N   ILE   125      17.253  -1.355   6.380  1.00  0.00              
ATOM     74  CA  ILE   125      16.242  -1.104   5.349  1.00  0.00              
ATOM     75  C   ILE   125      17.014  -1.079   4.015  1.00  0.00              
ATOM     76  O   ILE   125      17.181  -0.027   3.372  1.00  0.00              
ATOM     77  N   PRO   126      17.546  -2.245   3.630  1.00  0.00              
ATOM     78  CA  PRO   126      18.560  -2.257   2.552  1.00  0.00              
ATOM     79  C   PRO   126      18.005  -1.836   1.201  1.00  0.00              
ATOM     80  O   PRO   126      18.779  -1.293   0.378  1.00  0.00              
ATOM     81  N   ASN   127      16.739  -2.105   0.915  1.00  0.00              
ATOM     82  CA  ASN   127      16.228  -1.752  -0.405  1.00  0.00              
ATOM     83  C   ASN   127      16.233  -0.238  -0.629  1.00  0.00              
ATOM     84  O   ASN   127      16.271   0.241  -1.771  1.00  0.00              
ATOM     85  N   LEU   128      16.194   0.531   0.473  1.00  0.00              
ATOM     86  CA  LEU   128      16.187   1.979   0.427  1.00  0.00              
ATOM     87  C   LEU   128      17.537   2.581   0.888  1.00  0.00              
ATOM     88  O   LEU   128      17.623   3.772   1.165  1.00  0.00              
ATOM     89  N   LEU   129      18.585   1.773   0.958  1.00  0.00              
ATOM     90  CA  LEU   129      19.942   2.265   1.203  1.00  0.00              
ATOM     91  C   LEU   129      20.398   2.356   2.655  1.00  0.00              
ATOM     92  O   LEU   129      21.379   3.054   2.937  1.00  0.00              
ATOM     93  N   LEU   130      19.724   1.637   3.560  1.00  0.00              
ATOM     94  CA  LEU   130      20.102   1.589   4.977  1.00  0.00              
ATOM     95  C   LEU   130      20.646   0.179   5.267  1.00  0.00              
ATOM     96  O   LEU   130      19.909  -0.818   5.227  1.00  0.00              
ATOM     97  N   PRO   131      21.942   0.099   5.566  1.00  0.00              
ATOM     98  CA  PRO   131      22.563  -1.204   5.774  1.00  0.00              
ATOM     99  C   PRO   131      22.042  -1.898   7.031  1.00  0.00              
ATOM    100  O   PRO   131      21.716  -1.258   8.054  1.00  0.00              
ATOM    101  N   PRO   132      22.056  -3.235   7.021  1.00  0.00              
ATOM    102  CA  PRO   132      21.826  -3.985   8.270  1.00  0.00              
ATOM    103  C   PRO   132      22.768  -3.496   9.358  1.00  0.00              
ATOM    104  O   PRO   132      23.947  -3.198   9.105  1.00  0.00              
ATOM    105  N   HIS   133      22.251  -3.461  10.604  1.00  0.00              
ATOM    106  CA  HIS   133      22.992  -3.024  11.751  1.00  0.00              
ATOM    107  C   HIS   133      22.854  -1.510  12.031  1.00  0.00              
ATOM    108  O   HIS   133      23.363  -1.009  13.051  1.00  0.00              
END
