Contacts of the strand formed by residues 687 - 692 (chain q) 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 687 (chain q).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    611q  ASP*     3.5    17.4    -      -       +      +
    612q  ILE      5.1     0.7    -      -       -      -
    613q  LEU*     4.6    19.1    -      -       +      +
    684q  ILE*     3.6    16.2    +      -       +      +
    685q  GLU      3.5     3.4    -      -       -      -
    686q  GLY*     1.3    77.1    -      -       -      +
    688q  ILE*     1.3    59.8    +      -       -      +
    689q  TYR      4.8     2.7    -      -       -      +
    726q  ARG*     3.8    20.5    -      -       +      +
    727q  ALA*     3.5    11.9    -      -       -      +
    729q  ARG*     5.5     1.0    -      -       -      +
    730q  VAL*     5.0    10.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 688 (chain q). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    609q  PRO      4.9     3.8    -      -       -      +
    610q  GLY*     4.1    19.3    -      -       -      -
    611q  ASP      3.0     5.5    +      -       -      -
    686q  GLY      3.3     3.8    +      -       -      +
    687q  ILE*     1.3    74.7    -      -       -      +
    689q  TYR*     1.3    61.4    +      -       +      +
    727q  ALA*     3.3    15.9    -      -       -      +
    730q  VAL*     6.5     0.4    -      -       +      -
    731q  ALA*     5.6     2.2    -      -       +      +
    732q  ALA      4.7     5.6    -      -       -      +
    733q  GLY*     3.3    12.0    -      -       -      -
    734q  LYS      3.1    21.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 689 (chain q). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    603q  ILE*     5.2    13.7    -      -       +      -
    610q  GLY      5.9     0.9    -      -       -      +
    611q  ASP      3.1     8.3    +      -       -      +
    612q  ILE*     3.3    12.2    -      -       +      +
    613q  LEU*     2.8    27.2    +      -       -      +
    687q  ILE*     3.7     2.0    -      -       -      +
    688q  ILE*     1.3    80.7    -      -       +      +
    690q  VAL*     1.3    63.4    +      -       -      +
    727q  ALA*     4.8     1.1    -      -       -      -
    734q  LYS*     3.3    13.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 690 (chain q). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    613q  LEU*     3.3    13.0    -      -       +      +
    688q  ILE      4.3     0.2    -      -       -      -
    689q  TYR*     1.3    78.2    -      -       -      +
    691q  LEU*     1.3    58.1    +      -       -      +
    692q  ASP*     4.1     1.6    -      -       +      -
    723q  ARG*     3.9    25.1    -      -       +      +
    726q  ARG*     5.5     1.6    -      -       +      -
    727q  ALA*     4.6     8.3    -      -       +      +
    734q  LYS      3.0    10.4    +      -       -      +
    735q  CYS*     3.3    12.4    -      -       +      -
    736q  PHE*     2.8    33.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 691 (chain q). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    596q  CYS*     5.2    18.8    -      -       +      +
    599q  SER*     5.2     8.7    -      -       -      -
    600q  VAL*     5.8     4.3    -      -       +      +
    613q  LEU      2.9    10.9    +      -       -      +
    614q  VAL*     4.4    11.9    -      -       +      -
    615q  PHE*     3.2    26.5    +      -       -      +
    690q  VAL*     1.3    75.1    -      -       -      +
    692q  ASP*     1.3    60.7    +      -       -      +
    693q  PRO      3.9     1.7    -      -       -      -
    736q  PHE*     3.5    11.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with ASP 692 (chain q). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    615q  PHE*     5.0     5.2    -      -       +      -
    690q  VAL*     4.1     3.8    -      -       +      -
    691q  LEU*     1.3    72.5    -      -       -      +
    693q  PRO*     1.3    62.3    -      -       -      +
    694q  GLY*     3.2     6.7    +      -       -      +
    720q  ALA*     5.9     3.8    -      -       +      +
    723q  ARG*     4.8    19.5    -      -       +      -
    735q  CYS*     6.0     3.6    -      -       +      -
    736q  PHE      2.7    15.1    +      -       -      +
    737q  ARG*     3.5     8.6    -      -       +      +
    738q  LEU*     2.8    26.3    +      -       -      -
----------------------------------------------------------
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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