Contacts of the strand formed by residues 69 - 74 (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 VAL 69 (chain F).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     65F  HIS*     5.0    11.7    -      -       +      -
     67F  GLY      3.5     3.2    +      -       -      +
     68F  GLU*     1.3    76.6    -      -       -      +
     70F  TYR*     1.3    61.3    +      -       -      +
     71F  CYS      4.8     2.2    -      -       -      +
     83F  SER*     5.9     4.0    -      -       -      -
     84F  ALA      4.0    11.2    -      -       -      +
     85F  GLY*     4.1     1.3    -      -       -      +
    331F  ASN*     3.6    13.9    -      -       -      +
    345F  ALA*     4.5    11.1    -      -       +      -
    346F  SER*     3.3    33.4    +      -       -      +
    347F  SER*     4.3     0.7    +      -       -      -
    349F  LYS*     4.9     6.0    -      -       -      +
    350F  ARG      5.8     1.3    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with TYR 70 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     68F  GLU*     5.1     1.3    -      -       +      +
     69F  VAL*     1.3    73.7    -      -       -      +
     71F  CYS*     1.3    64.3    +      -       -      +
     84F  ALA      3.0     5.9    +      -       -      -
     85F  GLY*     3.7     5.4    -      -       -      -
     86F  PHE      5.4     0.2    -      -       -      +
    112F  VAL      3.8    22.0    -      -       -      +
    113F  MET*     4.4    10.2    -      -       -      +
    331F  ASN*     3.6    22.3    -      -       +      +
    332F  GLU*     3.9     7.9    -      -       -      +
    345F  ALA*     5.3     1.1    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with CYS 71 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     69F  VAL*     3.6     2.5    -      -       -      +
     70F  TYR*     1.3    83.8    -      -       +      +
     72F  CYS*     1.3    64.7    +      -       -      +
     83F  SER*     3.5     2.3    -      -       -      -
     84F  ALA*     3.0    31.7    +      -       +      +
    112F  VAL      5.5     0.4    -      -       -      +
    113F  MET      4.2    15.9    -      -       -      +
    114F  GLU*     4.4     1.3    -      -       +      -
    115F  LEU*     4.2    24.5    -      -       +      +
    332F  GLU*     4.2     9.2    -      -       +      -
    345F  ALA*     4.6     5.7    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with CYS 72 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     71F  CYS*     1.3    79.7    -      -       -      +
     73F  LYS*     1.3    62.1    +      -       -      +
     82F  ALA      3.1    12.8    -      -       -      +
     83F  SER*     4.2     9.4    -      -       -      -
    115F  LEU*     5.5     3.4    -      -       -      -
    332F  GLU*     4.4    11.5    -      -       +      +
    334F  ALA*     4.0    14.4    -      -       +      +
    343F  ILE*     5.3    14.8    -      -       +      +
    345F  ALA*     4.1    18.2    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LYS 73 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     72F  CYS*     1.3    75.8    -      -       -      +
     74F  PHE*     1.3    65.0    +      -       -      +
     81F  LEU*     3.4     6.6    -      -       -      +
     82F  ALA*     2.8    38.4    +      -       +      +
    115F  LEU*     4.7    22.4    -      -       +      +
    116F  HIS*     5.1     6.3    -      -       -      -
    117F  TYR*     5.2     6.1    -      -       +      +
    334F  ALA*     4.6     7.6    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 74 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     73F  LYS*     1.3    80.2    -      -       -      +
     75F  HIS*     1.3    69.9    +      -       -      +
     76F  PRO*     3.5     1.9    -      -       -      +
     78F  GLY*     5.7     3.4    -      -       -      -
     80F  THR      3.8     5.2    -      -       -      +
     81F  LEU*     4.6     2.0    -      -       +      +
    117F  TYR*     4.9     6.7    -      -       -      +
    334F  ALA*     4.9     6.5    -      -       +      +
    335F  PHE      4.3    19.1    -      -       -      +
    336F  HIS*     4.6    11.2    -      -       +      +
    337F  PRO*     5.2     3.1    -      -       +      -
----------------------------------------------------------
 Back to top of page


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