Contacts of the strand formed by residues 609 - 614 (chain r) 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 609 (chain r).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    537r  LYS*     3.5    14.6    -      -       +      +
    538r  ILE      6.2     0.2    -      -       -      -
    539r  ILE*     6.0     4.5    -      -       +      +
    605r  TYR*     4.1     3.3    +      -       +      +
    606r  THR*     4.7    13.9    -      -       -      -
    607r  GLN*     3.3     8.0    +      -       -      +
    608r  LEU*     1.3    76.7    -      -       -      +
    610r  ARG*     1.3    61.4    +      -       -      +
    611r  LEU      3.5     7.2    -      -       -      +
    645r  ASP      4.5     3.3    -      -       -      +
    646r  VAL*     4.3    10.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 610 (chain r). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    520r  GLU*     5.4     9.6    -      -       +      -
    536r  PHE*     5.7     7.6    -      -       +      +
    537r  LYS      4.0     3.6    +      -       -      +
    608r  LEU      3.8     4.2    +      -       -      +
    609r  VAL*     1.3    73.4    -      -       -      +
    611r  LEU*     1.3    57.2    +      -       +      +
    645r  ASP      4.7     4.7    -      -       -      +
    646r  VAL*     3.3     8.6    -      -       -      +
    647r  ARG*     2.7    33.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 611 (chain r). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    516r  CYS      5.2     6.5    -      -       -      +
    517r  MET*     6.0     2.9    -      -       -      -
    520r  GLU*     4.9    15.7    -      -       +      -
    537r  LYS      4.3     3.4    +      -       -      +
    538r  ILE*     3.7    16.7    -      -       +      -
    539r  ILE*     3.1    22.9    +      -       -      +
    609r  VAL*     3.5     5.7    -      -       -      +
    610r  ARG*     1.3    82.1    -      -       +      +
    612r  ILE*     1.3    61.8    +      -       -      +
    646r  VAL*     4.8     1.1    -      -       -      +
    647r  ARG*     3.5    13.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 612 (chain r). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    539r  ILE*     3.2    17.7    -      -       +      +
    611r  LEU*     1.3    76.1    -      -       -      +
    613r  ILE*     1.3    62.0    +      -       -      +
    614r  LEU      3.9     0.3    +      -       -      -
    646r  VAL*     5.5     1.5    -      -       +      +
    647r  ARG      3.1     9.0    +      -       -      +
    648r  LEU*     3.5     7.8    -      -       +      +
    649r  ILE*     3.1    23.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 613 (chain r). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    513r  ALA*     5.0    13.7    -      -       +      -
    539r  ILE      2.8    13.7    +      -       -      +
    540r  TYR*     4.1    13.9    -      -       +      -
    541r  ILE*     2.8    34.1    +      -       -      +
    612r  ILE*     1.3    73.8    -      -       -      +
    614r  LEU*     1.3    60.6    +      -       -      +
    615r  ASP*     3.7     4.5    -      -       +      +
    649r  ILE*     3.6    14.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 614 (chain r). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    541r  ILE*     4.0     7.6    -      -       +      -
    612r  ILE      3.9     1.6    +      -       -      -
    613r  ILE*     1.3    72.8    -      -       -      +
    615r  ASP*     1.3    60.5    +      -       -      +
    617r  ILE*     4.1    17.6    -      -       +      +
    649r  ILE      2.9    14.0    +      -       -      +
    650r  GLY*     4.4     4.5    -      -       -      -
    651r  LEU*     2.8    28.6    +      -       -      +
----------------------------------------------------------
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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