Contacts of the strand formed by residues 679 - 686 (chain F) in PDB entry 6BAA


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 679 (chain F).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    678F  CYS*     1.3    79.5    +      -       -      +
    680F  GLN*     1.3    60.1    +      -       -      +
    681F  ILE      4.3     0.2    -      -       -      -
    702F  ARG*     3.5     6.2    -      -       -      +
    703F  ILE*     3.3    46.8    +      -       +      +
    704F  PRO*     4.3     0.9    -      -       -      +
    738F  PHE      3.2    11.9    -      -       -      +
    739F  TRP*     4.5    18.1    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLN 680 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    678F  CYS      3.5     4.5    +      -       -      +
    679F  VAL*     1.3    75.0    -      -       -      +
    681F  ILE*     1.3    58.3    +      -       -      +
    682F  ILE*     4.2     0.4    -      -       -      -
    702F  ARG*     3.5    26.2    -      -       -      +
    736F  ALA      4.1     0.3    -      -       -      +
    737F  VAL*     3.3     1.9    -      -       -      -
    738F  PHE*     2.4    65.7    +      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 681 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    679F  VAL      4.3     0.4    -      -       -      -
    680F  GLN*     1.3    73.7    -      -       -      +
    682F  ILE*     1.3    60.4    +      -       -      +
    683F  GLY      4.3     0.2    -      -       -      -
    684F  GLY*     6.0     2.2    -      -       -      +
    699F  ILE      5.0     4.7    -      -       -      +
    700F  THR*     3.7     2.7    -      -       -      -
    701F  ILE      2.9    45.5    +      -       -      +
    702F  ARG*     3.6     9.0    -      -       -      +
    736F  ALA      3.4     5.6    -      -       -      +
    737F  VAL*     4.2     7.2    -      -       +      +
    738F  PHE      5.7     0.2    -      -       -      +
    739F  TRP*     5.7     7.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 682 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    681F  ILE*     1.3    73.9    -      -       -      +
    683F  GLY*     1.3    63.7    +      -       -      +
    684F  GLY      3.4     2.6    +      -       -      +
    700F  THR*     4.2     4.9    -      -       -      -
    702F  ARG*     3.5    23.3    -      -       -      +
    735F  GLY*     3.3     1.6    -      -       -      -
    736F  ALA*     2.6    55.7    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 683 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    682F  ILE*     1.3    69.6    -      -       -      +
    684F  GLY*     1.3    59.7    +      -       -      +
    685F  PHE*     4.9     0.3    -      -       -      +
    698F  ASN*     3.5    27.8    +      -       -      -
    699F  ILE      3.2     8.0    +      -       -      -
    700F  THR*     3.4    10.1    -      -       -      -
    734F  SER*     2.9    18.9    -      -       -      +
    735F  GLY*     3.2     7.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 684 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    681F  ILE*     6.1     2.0    -      -       -      -
    682F  ILE      3.4     4.4    -      -       -      -
    683F  GLY*     1.3    74.4    -      -       -      +
    685F  PHE*     1.3    59.0    +      -       -      -
    686F  PHE*     4.3     1.4    +      -       -      -
    696F  LEU*     4.4     0.7    -      -       -      +
    697F  SER*     3.7     0.9    -      -       -      -
    698F  ASN      3.1     2.2    +      -       -      -
    699F  ILE*     2.4    53.9    +      -       -      +
    734F  SER      3.7     4.5    -      -       -      -
    735F  GLY*     4.7     1.8    -      -       -      -
    736F  ALA      5.2     3.4    -      -       -      -
    737F  VAL*     6.6     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 685 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    683F  GLY      4.9     0.2    -      -       -      +
    684F  GLY*     1.3    74.1    -      -       -      -
    686F  PHE*     1.3    60.0    +      -       -      +
    694F  PRO*     4.3     3.8    -      -       +      -
    696F  LEU      3.2    11.9    -      -       -      +
    697F  SER*     4.2     3.6    -      -       -      +
    698F  ASN      4.2     8.3    -      -       -      +
    725F  ALA*     5.8     0.2    -      -       -      +
    730F  MET*     5.0     0.7    -      -       -      +
    731F  GLN      3.2    13.9    -      -       -      +
    732F  LYS*     3.2    14.0    -      -       -      +
    733F  VAL*     3.6    32.5    -      -       +      +
    734F  SER*     3.5    12.1    +      -       -      +
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Residues in contact with PHE 686 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    684F  GLY      5.7     0.4    -      -       -      -
    685F  PHE*     1.3    74.6    -      -       -      +
    687F  THR*     1.3    54.9    +      -       -      +
    694F  PRO*     3.2     2.6    -      -       -      +
    695F  THR*     2.6    30.2    +      -       -      -
    696F  LEU*     2.7    38.9    +      -       +      +
    721F  SER*     5.0     5.8    -      -       -      +
    722F  LEU*     6.0     0.4    -      -       -      -
    725F  ALA*     3.7    30.7    -      -       +      -
    730F  MET*     3.8     8.5    -      -       +      -
    731F  GLN      3.9     0.9    -      -       -      -
----------------------------------------------------------
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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