
#######################################################
#                                                     #
#                        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   21 (   21),  selected   21 , name T0365TS464_2_2-D1
# Molecule2: number of CA atoms  207 ( 1594),  selected  207 , name T0365_D1.pdb
# PARAMETERS: T0365TS464_2_2-D1.T0365_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      P      14           -
LGA    -       -      I      15           -
LGA    -       -      K      16           -
LGA    -       -      P      17           -
LGA    -       -      L      18           -
LGA    -       -      Q      19           -
LGA    -       -      E      20           -
LGA    -       -      H      21           -
LGA    -       -      M      22           -
LGA    -       -      D      23           -
LGA    -       -      K      24           -
LGA    -       -      V      25           -
LGA    -       -      Y      26           -
LGA    -       -      D      27           -
LGA    -       -      C      28           -
LGA    -       -      A      29           -
LGA    -       -      S      30           -
LGA    -       -      L      31           -
LGA    -       -      L      32           -
LGA    -       -      V      33           -
LGA    -       -      P      34           -
LGA    -       -      F      35           -
LGA    -       -      F      36           -
LGA    -       -      E      37           -
LGA    -       -      A      38           -
LGA    -       -      T      39           -
LGA    -       -      I      40           -
LGA    -       -      T      41           -
LGA    -       -      G      42           -
LGA    -       -      N      43           -
LGA    -       -      W      44           -
LGA    -       -      D      45           -
LGA    -       -      D      46           -
LGA    -       -      A      47           -
LGA    -       -      V      48           -
LGA    -       -      Q      49           -
LGA    -       -      I      50           -
LGA    -       -      R      51           -
LGA    -       -      K      52           -
LGA    -       -      Q      53           -
LGA    -       -      I      54           -
LGA    -       -      S      55           -
LGA    -       -      L      56           -
LGA    -       -      A      57           -
LGA    -       -      E      58           -
LGA    -       -      K      59           -
LGA    -       -      Q      60           -
LGA    -       -      G      61           -
LGA    -       -      D      62           -
LGA    -       -      S      63           -
LGA    -       -      L      64           -
LGA    -       -      K      65           -
LGA    -       -      R      66           -
LGA    -       -      E      67           -
LGA    -       -      I      68           -
LGA    -       -      R      69           -
LGA    -       -      L      70           -
LGA    -       -      T      71           -
LGA    -       -      L      72           -
LGA    -       -      F      77           -
LGA    -       -      M      78           -
LGA    -       -      P      79           -
LGA    -       -      V      80           -
LGA    -       -      E      81           -
LGA    -       -      R      82           -
LGA    -       -      T      83           -
LGA    -       -      D      84           -
LGA    -       -      L      85           -
LGA    -       -      L      86           -
LGA    -       -      E      87           -
LGA    -       -      L      88           -
LGA    -       -      L      89           -
LGA    -       -      T      90           -
LGA    -       -      Q      91           -
LGA    -       -      Q      92           -
LGA    -       -      D      93           -
LGA    -       -      K      94           -
LGA    -       -      I      95           -
LGA    -       -      A      96           -
LGA    -       -      N      97           -
LGA    -       -      K      98           -
LGA    -       -      A      99           -
LGA    -       -      K     100           -
LGA    -       -      D     101           -
LGA    -       -      I     102           -
LGA    -       -      S     103           -
LGA    -       -      G     104           -
LGA    -       -      R     105           -
LGA    -       -      V     106           -
LGA    -       -      I     107           -
LGA    -       -      G     108           -
LGA    -       -      R     109           -
LGA    -       -      Q     110           -
LGA    -       -      L     111           -
LGA    -       -      L     112           -
LGA    -       -      I     113           -
LGA    -       -      P     114           -
LGA    -       -      Q     115           -
LGA    -       -      A     116           -
LGA    -       -      L     117           -
LGA    -       -      Q     118           -
LGA    -       -      V     119           -
LGA    -       -      P     120           -
LGA    -       -      F     121           -
LGA    -       -      I     122           -
LGA    -       -      A     123           -
LGA    -       -      Y     124           -
LGA    -       -      L     125           -
LGA    -       -      Q     126           -
LGA    -       -      R     127           -
LGA    -       -      C     128           -
LGA    -       -      I     129           -
LGA    P      14      D     130          2.804
LGA    I      15      A     131          1.895
LGA    K      16      V     132          0.780
LGA    P      17      G     133          0.993
LGA    L      18      L     134          0.793
LGA    Q      19      A     135          1.105
LGA    E      20      Q     136          1.310
LGA    H      21      Q     137          0.874
LGA    M      22      V     138          0.497
LGA    D      23      I     139          0.983
LGA    K      24      N     140          1.376
LGA    V      25      E     141          1.348
LGA    Y      26      L     142          1.062
LGA    D      27      D     143          1.275
LGA    C      28      D     144          0.983
LGA    A      29      L     145          0.585
LGA    -       -      L     146           -
LGA    -       -      E     147           -
LGA    -       -      A     148           -
LGA    -       -      R     151           -
LGA    -       -      G     152           -
LGA    -       -      R     153           -
LGA    -       -      E     154           -
LGA    -       -      V     155           -
LGA    -       -      D     156           -
LGA    -       -      F     157           -
LGA    -       -      V     158           -
LGA    -       -      A     159           -
LGA    -       -      K     160           -
LGA    -       -      M     161           -
LGA    -       -      I     162           -
LGA    -       -      N     163           -
LGA    -       -      E     164           -
LGA    -       -      L     165           -
LGA    -       -      D     166           -
LGA    -       -      I     167           -
LGA    -       -      I     168           -
LGA    -       -      E     169           -
LGA    -       -      E     170           -
LGA    -       -      D     171           -
LGA    -       -      T     172           -
LGA    -       -      D     173           -
LGA    -       -      D     174           -
LGA    -       -      L     175           -
LGA    -       -      Q     176           -
LGA    -       -      I     177           -
LGA    -       -      Q     178           -
LGA    -       -      L     179           -
LGA    -       -      R     180           -
LGA    -       -      R     181           -
LGA    -       -      Q     182           -
LGA    -       -      L     183           -
LGA    -       -      F     184           -
LGA    -       -      A     185           -
LGA    -       -      L     186           -
LGA    -       -      E     187           -
LGA    -       -      S     188           -
LGA    -       -      E     189           -
LGA    -       -      L     190           -
LGA    -       -      N     191           -
LGA    -       -      P     192           -
LGA    -       -      V     193           -
LGA    -       -      D     194           -
LGA    -       -      V     195           -
LGA    -       -      M     196           -
LGA    -       -      F     197           -
LGA    -       -      L     198           -
LGA    -       -      Y     199           -
LGA    -       -      K     200           -
LGA    -       -      T     201           -
LGA    -       -      I     202           -
LGA    -       -      E     203           -
LGA    -       -      W     204           -
LGA    -       -      V     205           -
LGA    -       -      G     206           -
LGA    -       -      G     207           -
LGA    -       -      L     208           -
LGA    -       -      A     209           -
LGA    -       -      D     210           -
LGA    -       -      L     211           -
LGA    -       -      A     212           -
LGA    -       -      E     213           -
LGA    -       -      R     214           -
LGA    -       -      V     215           -
LGA    -       -      G     216           -
LGA    A     159      S     217          1.522
LGA    K     160      R     218          2.301
LGA    M     161      L     219          1.255
LGA    I     162      E     220          2.288
LGA    N     163      L     221          1.855
LGA    -       -      M     222           -
LGA    -       -      L     223           -
LGA    -       -      A     224           -
LGA    -       -      R     225           -
LGA    -       -      V     226           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   21  207    5.0     21    1.45     9.52      9.562     1.354

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.397485 * X  +   0.482019 * Y  +   0.780809 * Z  +  16.064445
  Y_new =   0.779829 * X  +  -0.625903 * Y  +  -0.010595 * Z  +  16.012733
  Z_new =   0.483604 * X  +   0.613109 * Y  +  -0.624679 * Z  +  48.016865 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.365541   -0.776051  [ DEG:   135.5355    -44.4645 ]
  Theta =  -0.504767   -2.636826  [ DEG:   -28.9210   -151.0790 ]
  Phi   =   1.099413   -2.042179  [ DEG:    62.9917   -117.0083 ]
 
# 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: T0365TS464_2_2-D1                             
REMARK     2: T0365_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0365TS464_2_2-D1.T0365_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   21  207   5.0   21   1.45    9.52   9.562
REMARK  ---------------------------------------------------------- 
MOLECULE T0365TS464_2_2-D1
REMARK PARENT number 2
PFRMAT TS
TARGET T0365
PARENT N/A
ATOM     14  CA  PRO    14      30.715  28.497  44.889  1.00  0.00
ATOM     15  CA  ILE    15      32.876  28.810  41.745  1.00  0.00
ATOM     16  CA  LYS    16      31.630  25.320  40.836  1.00  0.00
ATOM     17  CA  PRO    17      28.155  26.777  40.188  1.00  0.00
ATOM     18  CA  LEU    18      29.676  29.067  37.568  1.00  0.00
ATOM     19  CA  GLN    19      31.617  26.086  36.179  1.00  0.00
ATOM     20  CA  GLU    20      28.523  24.041  35.300  1.00  0.00
ATOM     21  CA  HIS    21      26.794  26.959  33.559  1.00  0.00
ATOM     22  CA  MET    22      30.039  27.991  31.832  1.00  0.00
ATOM     23  CA  ASP    23      30.371  24.544  30.230  1.00  0.00
ATOM     24  CA  LYS    24      26.757  24.695  29.041  1.00  0.00
ATOM     25  CA  VAL    25      27.230  28.112  27.404  1.00  0.00
ATOM     26  CA  TYR    26      30.634  27.121  25.988  1.00  0.00
ATOM     27  CA  ASP    27      29.070  24.181  24.133  1.00  0.00
ATOM     28  CA  CYS    28      26.360  26.453  22.682  1.00  0.00
ATOM     29  CA  ALA    29      29.035  28.730  21.198  1.00  0.00
ATOM     30  CA  ALA   159      39.135  33.570  32.929  1.00  0.00
ATOM     31  CA  LYS   160      39.133  29.797  32.191  1.00  0.00
ATOM     32  CA  MET   161      37.194  28.201  29.319  1.00  0.00
ATOM     33  CA  ILE   162      36.444  31.488  27.529  1.00  0.00
ATOM     34  CA  ASN   163      40.053  32.663  27.990  1.00  0.00
TER
END
