Contacts of the strand formed by residues 409 - 419 (chain A) in PDB entry 5LXX


Residue contacts within the protein are derived with the CSU software (Sobolev V., Sorokine A., Prilusky J., Abola E.E. and Edelman M. (1999) Automated analysis of interatomic contacts in proteins. Bioinformatics, 15, 327-332). A short description of the analytical approach is given at the end of the page.
For CSU analysis of other PDB entry

Note:
Non-standard 3 letter residue codes indicate a heterogroup. To identify and analyse, use LPC software

Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB   - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC   - hydrophobic-hydrophilic contact (destabilizing contact)
+/-  - indicates presence/absence of a specific contacts
*    - indicates residues forming contacts  by their side chain
       (including CA atoms)
Residues in contact with LEU 409 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19A  ILE*     3.7    20.0    -      -       +      -
     35A  ILE*     4.3    14.8    -      -       +      -
     37A  MET*     3.3    33.7    -      -       +      -
     42A  ILE*     4.3    13.0    -      -       +      -
     65A  VAL*     4.4     6.1    -      -       +      -
     66A  ILE      3.4     4.0    -      -       -      +
     68A  GLY      4.0     0.9    -      -       -      +
    102A  THR*     4.5     1.0    -      -       -      +
    401A  ILE*     3.4    39.5    -      -       +      -
    407A  ALA*     4.5     1.1    -      -       -      -
    408A  ASP*     1.3    85.8    -      -       -      +
    410A  VAL*     1.3    71.3    +      -       -      +
    411A  ILE*     6.3     0.2    -      -       +      -
    446A  VAL*     3.6     0.5    -      -       -      +
    447A  ILE*     2.8    45.4    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 410 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     65A  VAL*     3.3     4.0    -      -       -      -
     66A  ILE*     2.9    47.6    +      -       +      +
     68A  GLY*     4.0    11.4    -      -       -      -
    100A  GLY*     3.4    32.8    -      -       -      +
    409A  LEU*     1.3    83.7    -      -       -      +
    411A  ILE*     1.3    76.1    +      -       -      +
    412A  TRP*     3.6    15.9    +      -       +      +
    443A  PRO*     3.8    19.3    -      -       +      -
    445A  VAL      3.3    10.3    -      -       -      +
    446A  VAL*     4.3     9.6    -      -       +      -
    447A  ILE*     6.5     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 411 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19A  ILE*     4.2    21.3    -      -       +      -
     58A  ILE*     3.9    27.8    -      -       +      -
     59A  GLU      5.5     0.2    -      -       -      +
     60A  ALA*     4.3    10.3    -      -       +      -
     63A  ARG*     3.8    32.3    -      -       +      -
     64A  MET      3.3    10.5    -      -       -      +
     65A  VAL*     4.3    15.5    -      -       +      -
    409A  LEU*     6.3     0.2    -      -       +      -
    410A  VAL*     1.3    75.9    -      -       -      +
    412A  TRP*     1.3    56.1    +      -       -      +
    444A  LEU*     2.8    39.8    +      -       +      +
    445A  VAL*     2.9    36.3    +      -       +      +
    447A  ILE*     5.7     1.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with TRP 412 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     63A  ARG*     4.4     7.4    -      -       -      +
     64A  MET*     2.9    54.6    +      -       +      +
     66A  ILE*     4.4    23.1    -      -       +      -
     99A  GLY      4.1     2.7    -      -       -      -
    100A  GLY*     5.1     0.4    -      -       -      -
    362A  MET*     3.6    35.4    -      -       +      -
    363A  SER*     3.7    11.4    -      -       -      -
    366A  TRP*     3.4    40.1    -      +       +      -
    380A  PHE*     4.1     7.4    -      +       -      -
    410A  VAL*     3.6    11.0    +      -       +      -
    411A  ILE*     1.3    73.3    -      -       -      +
    413A  ASP*     1.3    63.8    +      -       -      +
    414A  PRO*     3.4    20.0    -      -       +      +
    441A  GLY*     3.6    17.7    -      -       -      -
    442A  SER      3.6    21.3    -      -       -      -
    443A  PRO*     3.6    24.9    -      -       +      -
    444A  LEU*     4.6     2.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 413 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     63A  ARG*     4.4    13.4    +      -       -      +
    411A  ILE      4.1     0.6    +      -       -      -
    412A  TRP*     1.3    74.0    +      -       -      +
    414A  PRO*     1.3    64.9    -      -       -      +
    415A  ASP*     2.9    21.0    +      -       -      +
    416A  SER*     3.1    26.0    +      -       -      +
    441A  GLY*     3.3     2.6    -      -       -      -
    442A  SER*     2.8    39.7    +      -       -      +
    444A  LEU*     3.6    30.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with PRO 414 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     63A  ARG*     5.3     5.8    -      -       +      +
     64A  MET*     4.1    17.5    -      -       +      +
    366A  TRP*     3.2    44.4    +      -       +      +
    412A  TRP*     3.4    15.9    -      -       +      +
    413A  ASP*     1.3    86.6    -      -       -      +
    415A  ASP*     1.3    75.7    +      -       -      +
    440A  ARG*     2.9    24.9    +      -       -      +
    441A  GLY*     4.4     0.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with ASP 415 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    413A  ASP*     2.9     7.4    +      -       -      +
    414A  PRO*     1.3    94.2    -      -       -      +
    416A  SER*     1.3    67.7    +      -       -      +
    417A  VAL*     3.6     9.7    +      -       -      +
    440A  ARG*     3.1    31.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 416 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    413A  ASP*     3.1    24.1    +      -       -      -
    415A  ASP*     1.3    78.8    -      -       -      +
    417A  VAL*     1.3    58.0    +      -       -      +
    418A  LYS*     4.3    11.8    -      -       -      +
    440A  ARG*     3.1     5.2    -      -       -      -
    441A  GLY      2.9    24.9    +      -       -      -
    442A  SER*     2.6    42.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 417 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    415A  ASP      3.6     7.6    +      -       -      +
    416A  SER*     1.3    77.5    -      -       -      +
    418A  LYS*     1.3    69.6    +      -       -      +
    438A  GLU*     3.7    37.7    -      -       +      +
    439A  CYS      3.4    10.3    -      -       -      +
    440A  ARG*     4.4    16.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 418 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    416A  SER*     4.6     8.5    -      -       -      +
    417A  VAL*     1.3    82.1    -      -       -      +
    419A  THR*     1.3    67.5    +      -       -      +
    420A  ILE*     3.6     2.9    +      -       +      +
    437A  MET      3.4     0.9    -      -       -      +
    438A  GLU*     4.4     3.8    -      -       -      -
    439A  CYS*     2.8    35.1    +      -       +      +
    441A  GLY      6.0     0.2    -      -       -      +
    442A  SER*     3.5    37.5    +      -       -      +
    443A  PRO*     4.6     8.1    +      -       -      +
    444A  LEU*     6.4     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with THR 419 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    418A  LYS*     1.3    76.4    -      -       -      +
    420A  ILE*     1.3    74.8    +      -       -      +
    421A  SER*     3.6     9.0    +      -       -      -
    424A  THR*     4.3     8.3    +      -       -      -
    435A  GLU*     5.8     0.4    -      -       -      +
    436A  GLY*     3.9    19.7    -      -       -      +
    437A  MET      3.2     5.8    -      -       -      +
    438A  GLU*     2.4    31.1    +      -       -      +
----------------------------------------------------------
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A short description of the analytical approach
The contact analysis used in this page is based upon the approach developed in: Sobolev V., Wade R.C., Vriend G. and Edelman M. PROTEINS (1996) 25, 120-129. Contact legitimacy depends on the hydrophobic-hydrophilic properties of the contacting atoms. In order to define it, for each inter-atomic contact, eight atom classes have been introduced:


   I  Hydrophilic      - N and O that can donate and accept hydrogen bonds
                         (e.g., oxygen of hydroxyl group of Ser. or Thr)
  II  Acceptor         - N or O that can only accept a hydrogen bond
 III  Donor            - N that can only donate a hydrogen bond
  IV  Hydrophobic      - Cl, Br, I and all C atoms that are not in
                         aromatic rings and do not have a covalent bond to
                         a N or O atom
   V  Aromatic         - C in aromatic rings irrespective of any other 
                         bonds formed by the atom
  VI  Neutral          - C atoms that have a covalent bond to at least one
                         atom of class I or two or more atoms from class II
                         or III; atoms; S, F, P, and metal atoms in all cases
 VII  Neutral-donor    - C atoms that have a covalent bond with only one
                         atom of class III
VIII  Neutral-acceptor - C atoms that have a covalent bond with only 
                         one atom of class II
For each pair of contacts the state of legitimacy is shown below:

Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
  Atomic class           I  II  III   IV   V   VI  VII  VIII
------------------------------------------------------------
   I  (Hydrophilic)      +   +    +    -   +   +    +    +
  II  (Acceptor)         +   -    +    -   +   +    +    -
 III  (Donor)            +   +    -    -   +   +    -    +
  IV  (Hydrophobic)      -   -    -    +   +   +    +    +
   V  (Aromatic)         +   +    +    +   +   +    +    +
  VI  (Neutral)          +   +    +    +   +   +    +    +
 VII  (Neutral-donor)    +   +    -    +   +   +    -    +
VIII  (Neutral-acceptor) +   -    +    +   +   +    +    -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically assigned based on the atomic coordinates. However, in three cases (see below) the automatic assignment is currently ambiguous. In these cases, the user is advised to manually analyse the full list of contacts using LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are 
   considered "aromatic" (Class V) if the ring is approximately
   planar, and "hydrophobic" (Class IV) or "neutral" (Classes
   VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
   "hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
   "carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).

Please E-mail any questions and/or suggestions concerning this page to Vladimir.Sobolev@weizmann.ac.il