Contacts of the strand formed by residues 217 - 221 (chain F) in PDB entry 6FF7


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 ILE 217 (chain F).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    209F  ILE*     6.4     1.8    -      -       +      -
    210F  SER      3.4    11.9    -      -       -      +
    211F  GLY*     4.7     5.2    -      -       -      -
    215F  ASN      4.3     0.6    -      -       -      -
    216F  ASP*     1.3    72.0    -      -       -      +
    218F  LYS*     1.3    59.0    +      -       -      +
    229F  TYR      4.1     0.3    -      -       -      +
    230F  THR*     3.5     3.5    -      -       -      -
    231F  MET*     2.8    49.8    +      -       +      +
----------------------------------------------------------
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Residues in contact with LYS 218 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    208F  ILE      3.4     2.8    -      -       -      +
    209F  ILE*     3.4     2.4    -      -       -      +
    210F  SER*     2.8    47.6    +      -       -      +
    216F  ASP      3.5     4.9    +      -       -      +
    217F  ILE*     1.3    75.4    -      -       -      +
    219F  VAL*     1.3    61.9    +      -       -      +
    220F  TRP*     4.2     0.4    -      -       -      +
    227F  LEU*     6.1     4.3    -      -       +      -
    229F  TYR      3.6     7.4    -      -       -      +
    230F  THR*     5.5     2.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 219 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    207F  GLN*     5.5     7.2    -      -       +      -
    208F  ILE      3.4     6.1    -      -       -      +
    209F  ILE*     4.7     3.4    -      -       +      +
    217F  ILE      4.3     0.2    +      -       -      -
    218F  LYS*     1.3    75.9    -      -       -      +
    220F  TRP*     1.3    59.8    -      -       -      +
    227F  LEU*     3.8     3.5    -      -       -      -
    228F  THR*     2.9    31.6    +      -       -      -
    229F  TYR*     3.0    32.4    +      -       +      +
----------------------------------------------------------
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Residues in contact with TRP 220 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    190F  PHE*     5.7     8.1    -      -       +      -
    207F  GLN*     3.3    10.7    -      -       -      +
    208F  ILE*     2.9    47.2    +      -       +      +
    218F  LYS      4.2     0.2    +      -       -      -
    219F  VAL*     1.3    73.9    -      -       -      +
    221F  ASP*     1.3    61.8    +      -       -      +
    222F  LEU      3.7     1.0    +      -       -      -
    225F  ASN*     6.1     1.8    -      -       -      -
    226F  LYS      3.7     7.9    -      -       -      +
    227F  LEU*     5.1     0.9    -      -       -      +
    228F  THR*     4.9     1.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with ASP 221 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    206F  ASP      4.0     3.8    -      -       -      -
    207F  GLN*     5.2     0.7    -      -       -      +
    219F  VAL      4.3     0.2    +      -       -      -
    220F  TRP*     1.3    71.7    -      -       -      +
    222F  LEU*     1.3    58.5    +      -       -      +
    223F  ARG*     4.5     1.1    -      -       +      +
    224F  GLN*     4.1    23.1    -      -       +      +
    225F  ASN*     2.7    35.2    +      -       -      -
    226F  LYS*     3.3    14.5    +      -       +      +
    228F  THR*     4.6    12.1    -      -       -      -
----------------------------------------------------------
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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