Contacts of the strand formed by residues 869 - 876 (chain B) 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 TYR 869 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    836B  VAL      3.4     1.2    -      -       -      +
    837B  GLN*     3.3     5.1    -      -       -      -
    838B  ALA*     2.9    32.7    +      -       -      +
    861B  ALA      3.3    14.8    -      -       -      +
    862B  PRO*     3.7    16.6    -      -       +      -
    863B  ILE*     3.8     9.0    -      -       -      +
    867B  PRO      3.5     6.5    +      -       -      +
    868B  LEU*     1.3    75.9    -      -       -      +
    870B  THR*     1.3    62.4    +      -       -      +
    871B  ILE*     5.6     0.3    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with THR 870 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    835B  GLU*     6.1     3.6    -      -       -      -
    836B  VAL      3.1     9.0    -      -       -      -
    837B  GLN*     4.6     1.8    -      -       -      +
    859B  GLN      3.7     0.6    -      -       -      +
    860B  ASP*     3.6     3.1    -      -       -      +
    861B  ALA*     2.9    48.1    +      -       -      -
    863B  ILE*     5.4     5.6    -      -       -      +
    869B  TYR*     1.3    74.4    -      -       -      +
    871B  ILE*     1.3    62.0    +      -       -      +
    872B  LYS*     4.2     0.9    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 871 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    834B  VAL      3.3     5.4    -      -       -      +
    835B  GLU*     3.4     2.1    -      -       -      -
    836B  VAL*     2.8    48.4    +      -       +      +
    846B  VAL*     5.9     5.6    -      -       +      -
    859B  GLN      3.4     5.8    -      -       -      +
    860B  ASP*     4.8     4.3    -      -       +      +
    870B  THR*     1.3    75.6    -      -       -      +
    872B  LYS*     1.3    59.9    +      -       -      +
    873B  ALA*     4.0     4.5    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LYS 872 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    834B  VAL      3.3     6.5    -      -       -      +
    835B  GLU*     4.7     4.7    -      -       +      +
    857B  VAL*     4.3     0.9    -      -       -      +
    858B  THR*     2.9    27.9    +      -       -      -
    859B  GLN*     2.8    35.5    +      -       +      +
    870B  THR*     4.2     1.1    -      -       -      -
    871B  ILE*     1.3    72.1    -      -       -      +
    873B  ALA*     1.3    59.3    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA 873 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    833B  PHE*     3.4     6.6    -      -       -      +
    834B  VAL*     2.9    38.4    +      -       +      +
    850B  LEU*     5.6     9.4    -      -       +      -
    856B  HIS      3.8     6.3    -      -       -      +
    857B  VAL*     3.8    22.7    -      -       +      +
    858B  THR*     4.1     2.9    -      -       -      +
    871B  ILE*     5.2     4.5    -      -       +      +
    872B  LYS*     1.3    75.0    -      -       -      +
    874B  PHE*     1.3    63.5    +      -       -      +
    875B  ILE*     6.3     0.4    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 874 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    831B  TYR*     4.8    12.6    -      -       +      -
    832B  TYR      3.6     5.4    -      -       -      +
    833B  PHE*     4.8     0.9    -      -       -      +
    854B  ARG      4.1     1.2    -      -       -      +
    855B  GLY*     3.4     6.4    -      -       -      -
    856B  HIS*     3.1    40.7    +      -       +      +
    873B  ALA*     1.3    77.2    -      -       -      +
    875B  ILE*     1.3    60.6    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 875 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    831B  TYR*     3.2     6.9    -      -       -      -
    832B  TYR*     2.8    38.8    +      -       +      +
    834B  VAL*     5.7     6.7    -      -       +      +
    850B  LEU*     5.9     5.6    -      -       +      -
    853B  ARG*     4.9     9.9    -      -       +      +
    854B  ARG      4.5     5.6    -      -       -      -
    855B  GLY*     5.1     3.6    -      -       -      -
    873B  ALA*     6.3     0.7    -      -       +      -
    874B  PHE*     1.3    74.8    -      -       -      +
    876B  PRO*     1.3    67.2    -      -       -      +
    879B  ASP*     5.9     2.5    -      -       +      +
    880B  SER*     6.0     2.9    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with PRO 876 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    829B  GLU*     6.0     4.5    -      -       +      -
    830B  PRO      3.9     7.0    -      -       -      +
    831B  TYR*     4.5     1.3    -      -       +      -
    832B  TYR      4.8     0.2    -      -       -      -
    853B  ARG      4.5     9.1    -      -       -      +
    854B  ARG*     4.6     7.7    -      -       +      +
    875B  ILE*     1.3    77.8    -      -       -      +
    877B  ALA*     1.3    65.0    +      -       -      +
    878B  ILE*     3.3     5.8    -      -       +      +
    879B  ASP*     3.2    26.0    +      -       +      +
    880B  SER*     3.2    12.2    +      -       -      -
----------------------------------------------------------
 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