
#######################################################
#                                                     #
#                        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   30 (  120),  selected   30 , name T0328AL381_5
# Molecule2: number of CA atoms  307 ( 2453),  selected  307 , name T0328.pdb
# PARAMETERS: T0328AL381_5.T0328.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    S      57      N       5           -
LGA    A      58      M       6           -
LGA    -       -      P       7           -
LGA    -       -      R       8           -
LGA    -       -      E       9           -
LGA    -       -      Q      10           -
LGA    -       -      L      11           -
LGA    -       -      G      12           -
LGA    -       -      V      13           -
LGA    -       -      C      14           -
LGA    -       -      A      15           -
LGA    -       -      E      16           -
LGA    -       -      G      17           -
LGA    -       -      N      18           -
LGA    -       -      L      19           -
LGA    -       -      H      20           -
LGA    -       -      S      21           -
LGA    -       -      V      22           -
LGA    -       -      Y      23           -
LGA    -       -      L      24           -
LGA    -       -      M      25           -
LGA    -       -      F      26           -
LGA    -       -      N      27           -
LGA    F      59      A      28          3.622
LGA    N      60      N      29          3.285
LGA    -       -      D      30           -
LGA    -       -      N      31           -
LGA    -       -      V      32           -
LGA    G      61      E      33          2.710
LGA    -       -      S      34           -
LGA    -       -      Q      35           -
LGA    F      62      L      36          3.199
LGA    V      63      R      37          1.944
LGA    A      64      P      38          1.928
LGA    -       -      C      39           -
LGA    I      65      I      40          1.802
LGA    G      66      A      41          2.820
LGA    -       -      N      42           -
LGA    -       -      V      43           -
LGA    -       -      A      44           -
LGA    A      67      Q      45          1.437
LGA    N      68      Y      46          3.434
LGA    Y      69      I      47          1.869
LGA    -       -      Y      48           -
LGA    -       -      E      49           -
LGA    W      70      L      50          1.299
LGA    D      71      T      51          2.859
LGA    -       -      D      52           -
LGA    -       -      Q      53           -
LGA    S      72      Y      54          2.657
LGA    L      73      S      55          0.123
LGA    -       -      D      56           -
LGA    -       -      S      57           -
LGA    -       -      A      58           -
LGA    Y      74      F      59           #
LGA    P      75      -       -           -
LGA    E      76      -       -           -
LGA    S      77      N      60          5.401
LGA    R      78      G      61          2.326
LGA    P      79      F      62          2.129
LGA    E      80      V      63          1.185
LGA    M      81      A      64          2.155
LGA    L      82      I      65          3.362
LGA    K      83      G      66           -
LGA    -       -      A      67           -
LGA    -       -      N      68           -
LGA    -       -      Y      69           -
LGA    -       -      W      70           -
LGA    -       -      D      71           -
LGA    -       -      S      72           -
LGA    P      84      L      73          4.250
LGA    F      85      Y      74          3.294
LGA    P      86      P      75           -
LGA    -       -      E      76           -
LGA    -       -      S      77           -
LGA    -       -      R      78           -
LGA    -       -      P      79           -
LGA    -       -      E      80           -
LGA    -       -      M      81           -
LGA    -       -      L      82           -
LGA    -       -      K      83           -
LGA    -       -      P      84           -
LGA    -       -      F      85           -
LGA    -       -      P      86           -
LGA    -       -      A      87           -
LGA    -       -      M      88           -
LGA    -       -      Q      89           -
LGA    -       -      E      90           -
LGA    -       -      G      91           -
LGA    -       -      N      92           -
LGA    -       -      R      93           -
LGA    -       -      E      94           -
LGA    -       -      A      95           -
LGA    -       -      P      96           -
LGA    -       -      A      97           -
LGA    -       -      I      98           -
LGA    -       -      E      99           -
LGA    -       -      Y     100           -
LGA    -       -      D     101           -
LGA    -       -      L     102           -
LGA    -       -      F     103           -
LGA    -       -      V     104           -
LGA    -       -      H     105           -
LGA    -       -      L     106           -
LGA    -       -      R     107           -
LGA    -       -      C     108           -
LGA    -       -      D     109           -
LGA    -       -      R     110           -
LGA    -       -      Y     111           -
LGA    -       -      D     112           -
LGA    -       -      I     113           -
LGA    -       -      L     114           -
LGA    -       -      H     115           -
LGA    -       -      L     116           -
LGA    -       -      V     117           -
LGA    -       -      A     118           -
LGA    -       -      N     119           -
LGA    -       -      E     120           -
LGA    -       -      I     121           -
LGA    -       -      S     122           -
LGA    -       -      Q     123           -
LGA    -       -      M     124           -
LGA    -       -      F     125           -
LGA    -       -      E     126           -
LGA    -       -      D     127           -
LGA    -       -      L     128           -
LGA    -       -      V     129           -
LGA    -       -      E     130           -
LGA    -       -      L     131           -
LGA    -       -      V     132           -
LGA    -       -      E     133           -
LGA    -       -      E     134           -
LGA    -       -      E     135           -
LGA    -       -      R     136           -
LGA    -       -      G     137           -
LGA    -       -      F     138           -
LGA    -       -      R     139           -
LGA    -       -      F     140           -
LGA    -       -      M     141           -
LGA    -       -      D     142           -
LGA    -       -      S     143           -
LGA    -       -      R     144           -
LGA    -       -      D     145           -
LGA    -       -      L     146           -
LGA    -       -      T     147           -
LGA    -       -      G     148           -
LGA    -       -      F     149           -
LGA    -       -      V     150           -
LGA    -       -      D     151           -
LGA    -       -      G     152           -
LGA    -       -      T     153           -
LGA    -       -      E     154           -
LGA    -       -      N     155           -
LGA    -       -      P     156           -
LGA    -       -      K     157           -
LGA    -       -      G     158           -
LGA    -       -      R     159           -
LGA    -       -      H     160           -
LGA    -       -      R     161           -
LGA    -       -      Q     162           -
LGA    -       -      E     163           -
LGA    -       -      V     164           -
LGA    -       -      A     165           -
LGA    -       -      L     166           -
LGA    -       -      V     167           -
LGA    -       -      G     168           -
LGA    -       -      S     169           -
LGA    -       -      E     170           -
LGA    -       -      D     171           -
LGA    -       -      P     172           -
LGA    -       -      E     173           -
LGA    -       -      F     174           -
LGA    -       -      K     175           -
LGA    -       -      G     176           -
LGA    -       -      G     177           -
LGA    -       -      S     178           -
LGA    -       -      Y     179           -
LGA    -       -      I     180           -
LGA    -       -      H     181           -
LGA    -       -      V     182           -
LGA    -       -      Q     183           -
LGA    -       -      K     184           -
LGA    -       -      Y     185           -
LGA    -       -      A     186           -
LGA    -       -      H     187           -
LGA    -       -      N     188           -
LGA    -       -      L     189           -
LGA    -       -      S     190           -
LGA    -       -      K     191           -
LGA    -       -      W     192           -
LGA    -       -      H     193           -
LGA    -       -      R     194           -
LGA    -       -      L     195           -
LGA    -       -      P     196           -
LGA    -       -      L     197           -
LGA    -       -      K     198           -
LGA    -       -      K     199           -
LGA    -       -      Q     200           -
LGA    -       -      E     201           -
LGA    -       -      D     202           -
LGA    -       -      I     203           -
LGA    -       -      I     204           -
LGA    -       -      G     205           -
LGA    -       -      R     206           -
LGA    -       -      T     207           -
LGA    -       -      K     208           -
LGA    -       -      Q     209           -
LGA    -       -      D     210           -
LGA    -       -      N     211           -
LGA    -       -      I     212           -
LGA    -       -      E     213           -
LGA    -       -      Y     214           -
LGA    -       -      E     215           -
LGA    -       -      S     216           -
LGA    -       -      E     217           -
LGA    -       -      D     218           -
LGA    -       -      K     219           -
LGA    -       -      P     220           -
LGA    -       -      L     221           -
LGA    -       -      T     222           -
LGA    -       -      S     223           -
LGA    -       -      H     224           -
LGA    -       -      I     225           -
LGA    -       -      K     226           -
LGA    -       -      R     227           -
LGA    -       -      V     228           -
LGA    -       -      N     229           -
LGA    -       -      L     230           -
LGA    -       -      K     231           -
LGA    -       -      D     232           -
LGA    -       -      E     233           -
LGA    -       -      N     234           -
LGA    -       -      G     235           -
LGA    -       -      K     236           -
LGA    -       -      S     237           -
LGA    -       -      I     238           -
LGA    -       -      E     239           -
LGA    -       -      I     240           -
LGA    -       -      L     241           -
LGA    -       -      R     242           -
LGA    -       -      Q     243           -
LGA    -       -      S     244           -
LGA    -       -      M     245           -
LGA    -       -      P     246           -
LGA    -       -      Y     247           -
LGA    -       -      G     248           -
LGA    -       -      S     249           -
LGA    -       -      L     250           -
LGA    -       -      K     251           -
LGA    -       -      E     252           -
LGA    -       -      Q     253           -
LGA    -       -      G     254           -
LGA    -       -      L     255           -
LGA    -       -      M     256           -
LGA    -       -      F     257           -
LGA    -       -      I     258           -
LGA    -       -      S     259           -
LGA    -       -      T     260           -
LGA    -       -      C     261           -
LGA    -       -      R     262           -
LGA    -       -      T     263           -
LGA    -       -      P     264           -
LGA    -       -      D     265           -
LGA    -       -      H     266           -
LGA    -       -      F     267           -
LGA    -       -      E     268           -
LGA    -       -      K     269           -
LGA    -       -      M     270           -
LGA    -       -      L     271           -
LGA    -       -      H     272           -
LGA    -       -      S     273           -
LGA    -       -      M     274           -
LGA    -       -      V     275           -
LGA    -       -      F     276           -
LGA    -       -      G     277           -
LGA    -       -      D     278           -
LGA    -       -      G     279           -
LGA    -       -      A     280           -
LGA    -       -      G     281           -
LGA    -       -      N     282           -
LGA    -       -      H     283           -
LGA    -       -      D     284           -
LGA    -       -      H     285           -
LGA    -       -      L     286           -
LGA    -       -      M     287           -
LGA    -       -      H     288           -
LGA    -       -      F     289           -
LGA    -       -      T     290           -
LGA    -       -      S     291           -
LGA    -       -      A     292           -
LGA    -       -      L     293           -
LGA    -       -      T     294           -
LGA    -       -      G     295           -
LGA    -       -      S     296           -
LGA    -       -      S     297           -
LGA    -       -      F     298           -
LGA    -       -      F     299           -
LGA    -       -      A     300           -
LGA    -       -      P     301           -
LGA    -       -      S     302           -
LGA    -       -      L     303           -
LGA    -       -      D     304           -
LGA    -       -      F     305           -
LGA    -       -      L     306           -
LGA    -       -      M     307           -
LGA    -       -      Q     308           -
LGA    -       -      F     309           -
LGA    -       -      D     310           -
LGA    -       -      N     311           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   30  307    5.0     23    2.80     8.70      4.785     0.794

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.809505 * X  +   0.483614 * Y  +   0.332894 * Z  + -37.344723
  Y_new =   0.221479 * X  +  -0.273570 * Y  +   0.936006 * Z  +  20.689747
  Z_new =   0.543736 * X  +   0.831431 * Y  +   0.114345 * Z  +  33.684826 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.434125   -1.707468  [ DEG:    82.1693    -97.8307 ]
  Theta =  -0.574882   -2.566711  [ DEG:   -32.9383   -147.0617 ]
  Phi   =   2.874530   -0.267063  [ DEG:   164.6984    -15.3016 ]
 
# 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: T0328AL381_5                                  
REMARK     2: T0328.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0328AL381_5.T0328.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   30  307   5.0   23   2.80    8.70   4.785
REMARK  ---------------------------------------------------------- 
MOLECULE T0328AL381_5
REMARK Aligment from pdb entry: 1p3hA
ATOM      1  N   SER    57      50.079  29.361  51.773  1.00  0.00              
ATOM      2  CA  SER    57      49.527  28.779  50.553  1.00  0.00              
ATOM      3  C   SER    57      50.602  28.761  49.462  1.00  0.00              
ATOM      4  O   SER    57      51.603  29.461  49.581  1.00  0.00              
ATOM      5  N   ALA    58      50.400  27.952  48.415  1.00  0.00              
ATOM      6  CA  ALA    58      51.360  27.871  47.320  1.00  0.00              
ATOM      7  C   ALA    58      50.715  27.869  45.953  1.00  0.00              
ATOM      8  O   ALA    58      49.498  27.843  45.809  1.00  0.00              
ATOM      9  N   PHE    59      51.568  27.899  44.942  1.00  0.00              
ATOM     10  CA  PHE    59      51.114  27.864  43.568  1.00  0.00              
ATOM     11  C   PHE    59      51.778  26.643  42.917  1.00  0.00              
ATOM     12  O   PHE    59      52.959  26.368  43.129  1.00  0.00              
ATOM     13  N   ASN    60      51.010  25.896  42.138  1.00  0.00              
ATOM     14  CA  ASN    60      51.572  24.729  41.483  1.00  0.00              
ATOM     15  C   ASN    60      50.758  24.301  40.286  1.00  0.00              
ATOM     16  O   ASN    60      49.843  24.997  39.873  1.00  0.00              
ATOM     17  N   GLY    61      51.082  23.150  39.733  1.00  0.00              
ATOM     18  CA  GLY    61      50.360  22.642  38.579  1.00  0.00              
ATOM     19  C   GLY    61      49.712  21.298  38.877  1.00  0.00              
ATOM     20  O   GLY    61      50.341  20.403  39.404  1.00  0.00              
ATOM     21  N   PHE    62      48.439  21.174  38.537  1.00  0.00              
ATOM     22  CA  PHE    62      47.729  19.932  38.745  1.00  0.00              
ATOM     23  C   PHE    62      48.301  18.896  37.792  1.00  0.00              
ATOM     24  O   PHE    62      48.321  19.084  36.588  1.00  0.00              
ATOM     25  N   VAL    63      48.765  17.793  38.345  1.00  0.00              
ATOM     26  CA  VAL    63      49.349  16.729  37.549  1.00  0.00              
ATOM     27  C   VAL    63      48.397  15.547  37.364  1.00  0.00              
ATOM     28  O   VAL    63      48.411  14.885  36.321  1.00  0.00              
ATOM     29  N   ALA    64      47.583  15.273  38.372  1.00  0.00              
ATOM     30  CA  ALA    64      46.643  14.171  38.325  1.00  0.00              
ATOM     31  C   ALA    64      45.473  14.475  39.246  1.00  0.00              
ATOM     32  O   ALA    64      45.650  15.070  40.291  1.00  0.00              
ATOM     33  N   ILE    65      44.276  14.068  38.853  1.00  0.00              
ATOM     34  CA  ILE    65      43.111  14.319  39.677  1.00  0.00              
ATOM     35  C   ILE    65      42.367  13.033  39.998  1.00  0.00              
ATOM     36  O   ILE    65      42.328  12.103  39.202  1.00  0.00              
ATOM     37  N   GLY    66      41.776  12.987  41.174  1.00  0.00              
ATOM     38  CA  GLY    66      41.039  11.809  41.552  1.00  0.00              
ATOM     39  C   GLY    66      39.700  11.780  40.856  1.00  0.00              
ATOM     40  O   GLY    66      39.294  12.744  40.215  1.00  0.00              
ATOM     41  N   ALA    67      38.988  10.660  40.956  1.00  0.00              
ATOM     42  CA  ALA    67      37.681  10.567  40.307  1.00  0.00              
ATOM     43  C   ALA    67      36.682  11.532  40.933  1.00  0.00              
ATOM     44  O   ALA    67      35.800  12.048  40.260  1.00  0.00              
ATOM     45  N   ASN    68      36.832  11.768  42.228  1.00  0.00              
ATOM     46  CA  ASN    68      35.935  12.656  42.946  1.00  0.00              
ATOM     47  C   ASN    68      35.283  11.879  44.073  1.00  0.00              
ATOM     48  O   ASN    68      35.385  10.661  44.119  1.00  0.00              
ATOM     49  N   TYR    69      34.617  12.567  44.985  1.00  0.00              
ATOM     50  CA  TYR    69      33.948  11.886  46.088  1.00  0.00              
ATOM     51  C   TYR    69      32.513  11.443  45.735  1.00  0.00              
ATOM     52  O   TYR    69      31.780  12.140  45.014  1.00  0.00              
ATOM     53  N   TRP    70      32.113  10.286  46.254  1.00  0.00              
ATOM     54  CA  TRP    70      30.787   9.758  45.987  1.00  0.00              
ATOM     55  C   TRP    70      29.778  10.596  46.715  1.00  0.00              
ATOM     56  O   TRP    70      30.046  11.035  47.829  1.00  0.00              
ATOM     57  N   ASP    71      28.624  10.809  46.093  1.00  0.00              
ATOM     58  CA  ASP    71      27.549  11.585  46.719  1.00  0.00              
ATOM     59  C   ASP    71      26.938  10.806  47.906  1.00  0.00              
ATOM     60  O   ASP    71      27.371   9.700  48.231  1.00  0.00              
ATOM     61  N   SER    72      25.952  11.402  48.565  1.00  0.00              
ATOM     62  CA  SER    72      25.284  10.782  49.716  1.00  0.00              
ATOM     63  C   SER    72      24.958   9.313  49.484  1.00  0.00              
ATOM     64  O   SER    72      25.492   8.426  50.167  1.00  0.00              
ATOM     65  N   LEU    73      24.043   9.088  48.540  1.00  0.00              
ATOM     66  CA  LEU    73      23.579   7.761  48.160  1.00  0.00              
ATOM     67  C   LEU    73      24.756   6.893  47.646  1.00  0.00              
ATOM     68  O   LEU    73      24.986   5.783  48.124  1.00  0.00              
ATOM     69  N   TYR    74      25.502   7.407  46.674  1.00  0.00              
ATOM     70  CA  TYR    74      26.629   6.662  46.127  1.00  0.00              
ATOM     71  C   TYR    74      26.485   6.285  44.651  1.00  0.00              
ATOM     72  O   TYR    74      27.135   5.348  44.175  1.00  0.00              
ATOM     73  N   PRO    75      25.636   7.012  43.923  1.00  0.00              
ATOM     74  CA  PRO    75      25.422   6.727  42.508  1.00  0.00              
ATOM     75  C   PRO    75      26.082   7.707  41.561  1.00  0.00              
ATOM     76  O   PRO    75      26.035   7.512  40.350  1.00  0.00              
ATOM     77  N   GLU    76      26.673   8.760  42.113  1.00  0.00              
ATOM     78  CA  GLU    76      27.368   9.760  41.316  1.00  0.00              
ATOM     79  C   GLU    76      28.610  10.343  41.980  1.00  0.00              
ATOM     80  O   GLU    76      28.594  10.644  43.176  1.00  0.00              
ATOM     81  N   SER    77      29.671  10.524  41.190  1.00  0.00              
ATOM     82  CA  SER    77      30.904  11.141  41.690  1.00  0.00              
ATOM     83  C   SER    77      30.781  12.627  41.357  1.00  0.00              
ATOM     84  O   SER    77      30.605  13.007  40.188  1.00  0.00              
ATOM     85  N   ARG    78      30.868  13.471  42.369  1.00  0.00              
ATOM     86  CA  ARG    78      30.804  14.891  42.114  1.00  0.00              
ATOM     87  C   ARG    78      32.146  15.272  41.504  1.00  0.00              
ATOM     88  O   ARG    78      33.155  15.310  42.206  1.00  0.00              
ATOM     89  N   PRO    79      32.176  15.598  40.195  1.00  0.00              
ATOM     90  CA  PRO    79      33.408  15.982  39.473  1.00  0.00              
ATOM     91  C   PRO    79      34.138  17.132  40.174  1.00  0.00              
ATOM     92  O   PRO    79      33.491  18.004  40.744  1.00  0.00              
ATOM     93  N   GLU    80      35.463  17.179  40.042  1.00  0.00              
ATOM     94  CA  GLU    80      36.248  18.197  40.731  1.00  0.00              
ATOM     95  C   GLU    80      36.266  19.435  39.866  1.00  0.00              
ATOM     96  O   GLU    80      35.865  19.383  38.703  1.00  0.00              
ATOM     97  N   MET    81      36.727  20.549  40.413  1.00  0.00              
ATOM     98  CA  MET    81      36.751  21.768  39.621  1.00  0.00              
ATOM     99  C   MET    81      38.126  22.115  39.111  1.00  0.00              
ATOM    100  O   MET    81      38.385  23.254  38.745  1.00  0.00              
ATOM    101  N   LEU    82      39.012  21.131  39.100  1.00  0.00              
ATOM    102  CA  LEU    82      40.361  21.345  38.600  1.00  0.00              
ATOM    103  C   LEU    82      40.667  20.238  37.622  1.00  0.00              
ATOM    104  O   LEU    82      40.050  19.174  37.664  1.00  0.00              
ATOM    105  N   LYS    83      41.609  20.497  36.729  1.00  0.00              
ATOM    106  CA  LYS    83      41.983  19.520  35.723  1.00  0.00              
ATOM    107  C   LYS    83      43.474  19.561  35.541  1.00  0.00              
ATOM    108  O   LYS    83      44.135  20.480  35.996  1.00  0.00              
ATOM    109  N   PRO    84      44.005  18.561  34.859  1.00  0.00              
ATOM    110  CA  PRO    84      45.434  18.511  34.642  1.00  0.00              
ATOM    111  C   PRO    84      45.845  19.747  33.895  1.00  0.00              
ATOM    112  O   PRO    84      45.129  20.200  33.016  1.00  0.00              
ATOM    113  N   PHE    85      46.991  20.299  34.266  1.00  0.00              
ATOM    114  CA  PHE    85      47.483  21.493  33.597  1.00  0.00              
ATOM    115  C   PHE    85      47.075  22.779  34.285  1.00  0.00              
ATOM    116  O   PHE    85      47.737  23.808  34.120  1.00  0.00              
ATOM    117  N   PRO    86      45.980  22.734  35.040  1.00  0.00              
ATOM    118  CA  PRO    86      45.521  23.916  35.742  1.00  0.00              
ATOM    119  C   PRO    86      46.558  24.362  36.734  1.00  0.00              
ATOM    120  O   PRO    86      47.186  23.551  37.402  1.00  0.00              
END
