Contacts of the strand formed by residues 65 - 69 (chain n) 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 65 (chain n).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    102h  ARG*     3.6    19.1    -      -       +      +
     17n  ILE*     6.0     5.2    -      -       +      -
     18n  GLU      4.2     3.4    -      -       -      +
     19n  LEU*     4.5     1.6    -      -       -      +
     20n  LYS*     4.4     2.2    -      -       -      +
     36n  MET*     5.8     2.5    -      -       +      +
     61n  ARG      4.2     1.4    +      -       -      +
     62n  GLY*     3.2    16.8    +      -       -      +
     63n  ASN      3.7     8.5    -      -       -      +
     64n  ASN*     1.3    79.0    -      -       -      +
     66n  ARG*     1.3    64.7    +      -       -      +
     67n  TYR*     4.8     4.0    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ARG 66 (chain n). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     48h  ASN*     6.2     4.3    -      -       +      -
    101h  LEU*     3.8     0.9    -      -       -      +
    102h  ARG*     2.8    32.3    +      -       -      +
    105h  SER*     4.9    15.5    -      -       -      -
     18n  GLU*     2.8    24.0    +      -       +      +
     19n  LEU      3.9    15.5    -      -       -      +
     20n  LYS*     3.9     6.0    -      -       +      +
     64n  ASN      3.7     2.4    +      -       -      -
     65n  ILE*     1.3    73.3    -      -       -      +
     67n  TYR*     1.3    62.9    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with TYR 67 (chain n). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    1329  ASP*     6.0     4.3    -      -       +      -
    3389  ARG*     5.1     9.0    -      -       +      -
    100h  PHE      2.9    18.8    -      -       -      +
    101h  LEU*     3.7    11.2    -      -       +      +
    102h  ARG*     4.4     0.9    -      -       -      +
     17n  ILE*     3.3     4.2    -      -       -      +
     18n  GLU*     2.8    36.4    +      -       +      +
     65n  ILE*     3.8     4.6    -      -       -      +
     66n  ARG*     1.3    84.8    -      -       +      +
     68n  PHE*     1.3    60.8    +      -       -      +
     69n  ILE      4.1     0.3    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 68 (chain n). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    1259  GLN*     4.9    11.0    -      -       +      -
    1279  LEU*     1.4   156.1    -      -       +      +
    1289  VAL      4.1     1.1    -      -       -      +
    1329  ASP*     6.4     0.2    -      -       -      -
     99h  MET*     3.1     6.7    -      -       -      +
    100h  PHE*     2.6    52.2    +      -       +      +
     17n  ILE*     4.4     3.8    -      -       +      +
     67n  TYR*     1.3    74.3    -      -       -      +
     69n  ILE*     1.3    52.5    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 69 (chain n). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    1269  ASN      1.2    31.8    -      -       -      +
    1279  LEU*     1.8    35.4    +      -       -      +
    1309  PHE*     1.2    63.0    +      -       +      +
    1319  THR*     2.8    24.2    -      -       -      +
    1329  ASP*     3.8     1.8    -      -       -      +
     98h  LYS      3.9     4.7    -      -       -      +
     99h  MET*     4.1     2.9    -      -       +      -
     16n  THR      2.6     0.8    +      -       -      -
     67n  TYR      4.1     0.6    +      -       -      -
     68n  PHE      1.3    64.0    -      -       -      -
     70n  LEU*     1.3    50.9    -      -       -      +
----------------------------------------------------------
 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