Contacts of the strand formed by residues 205 - 209 (chain F) in PDB entry 3KQG


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 ASN 205 (chain F).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    201F  TYR*     3.3     8.8    -      -       -      -
    202F  PHE      2.8    31.7    +      -       -      -
    203F  LYS      3.6    11.5    +      -       -      -
    204F  GLY*     1.3    81.0    -      -       -      +
    206F  PHE*     1.3    61.8    +      -       -      +
    207F  TYR*     3.2    33.3    +      -       +      +
    238F  GLU*     5.0     1.0    +      -       -      -
    320F  LYS*     3.9    23.5    -      -       +      +
    321F  ARG      3.5     6.1    -      -       -      +
    322F  PRO*     3.1    30.5    -      -       -      +
    323F  TYR      4.0     1.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 206 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    190F  ASP      4.5     1.3    -      -       -      -
    191F  ILE*     4.0    20.2    -      -       -      -
    194F  VAL*     3.3    44.2    -      -       +      -
    195F  VAL      5.2     0.7    -      -       -      -
    199F  TRP*     3.7    17.6    -      -       +      -
    200F  LYS      3.1     9.6    -      -       -      +
    201F  TYR*     3.7    27.1    -      +       +      -
    205F  ASN*     1.3    75.0    -      -       -      +
    207F  TYR*     1.3    63.2    +      -       -      +
    320F  LYS*     3.4     4.7    -      -       -      +
    321F  ARG*     2.8    60.5    +      -       +      +
    322F  PRO      4.2     0.4    -      -       -      -
    323F  TYR*     3.5    48.7    -      +       +      -
    324F  VAL      5.1     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 207 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    199F  TRP*     3.3    10.9    -      -       -      -
    200F  LYS*     2.7    38.0    +      -       -      +
    202F  PHE*     3.7    23.7    +      -       +      -
    205F  ASN*     3.2    45.1    +      -       +      +
    206F  PHE*     1.3    71.2    -      -       -      +
    208F  TYR*     1.3    59.4    +      -       -      +
    209F  PHE*     3.9    21.3    +      -       +      -
    231F  THR*     3.5    23.3    -      -       -      -
    238F  GLU*     2.7    32.8    +      -       +      +
    241F  PHE*     3.5    21.8    -      +       +      -
    242F  LEU*     3.8    19.7    -      -       +      -
    318F  ILE*     4.3     2.5    -      -       +      -
    319F  CYS      3.2     7.4    -      -       -      +
    320F  LYS*     3.6    15.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 208 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    244D  LYS      4.4     6.9    +      -       -      -
    245D  THR*     4.7     6.6    +      -       -      -
    247D  GLY*     3.6    26.0    +      -       -      -
    197F  GLN      5.3     2.2    -      -       -      -
    198F  GLY*     4.1    15.9    -      -       -      -
    199F  TRP*     3.7    48.4    -      +       +      +
    207F  TYR*     1.3    74.0    -      -       -      +
    209F  PHE*     1.3    65.5    +      -       -      +
    210F  SER*     3.4    30.5    -      -       -      -
    211F  LEU*     4.5    11.3    +      -       +      +
    222F  PHE*     3.7    31.6    -      +       -      -
    226F  ARG*     5.4     0.7    -      -       -      -
    317F  PHE*     3.3     3.0    -      +       -      +
    318F  ILE*     3.2     7.0    -      -       -      -
    319F  CYS*     2.8    44.1    +      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 209 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    211E  LEU*     6.2     2.0    -      -       +      -
    200F  LYS*     3.9    33.0    -      -       +      +
    207F  TYR*     3.9    24.0    -      -       +      -
    208F  TYR*     1.3    80.8    -      -       -      +
    210F  SER*     1.3    68.5    +      -       -      +
    211F  LEU*     4.6     6.9    -      -       -      +
    241F  PHE*     4.4     4.9    -      +       -      -
    242F  LEU*     3.9    18.4    -      -       +      -
    245F  THR*     3.5    39.0    -      -       +      -
    246F  ALA*     3.8    11.0    -      -       -      -
    251F  TYR*     3.9    26.7    -      +       +      +
    317F  PHE      3.8     4.3    -      -       -      -
    318F  ILE*     3.3    34.3    -      -       +      -
----------------------------------------------------------
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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