Contacts of the strand formed by residues 675 - 680 (chain A) in PDB entry 6DBU


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 ARG 675 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    585A  ALA*     3.1    33.3    +      -       -      +
    588A  ASP*     4.4     3.8    +      -       -      +
    589A  LEU*     6.1     3.2    -      -       -      +
    643A  SER*     3.2     1.5    -      -       -      -
    644A  PHE*     2.9    57.2    +      -       +      +
    645A  THR*     4.6     5.6    -      -       -      -
    646A  ILE*     4.9     7.0    -      -       -      +
    673A  SER*     4.6     8.5    -      -       -      +
    674A  CYS*     1.3    75.9    -      -       -      +
    676A  PRO*     1.3    68.4    -      -       -      +
    677A  LEU      3.7     0.2    +      -       -      -
   1014A  TRP*     3.2    52.1    -      -       +      -
   1017A  THR*     2.5    45.6    +      -       -      +
   1018A  SER*     3.6    20.8    +      -       -      +
   1019A  LYS*     5.2     1.9    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with PRO 676 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    576A  PHE*     4.4     1.9    -      -       -      -
    641A  ARG*     4.7     6.3    -      -       -      -
    642A  PHE      3.7     6.5    -      -       -      +
    643A  SER*     3.9     5.6    -      -       -      -
    674A  CYS      3.3    10.3    -      -       -      +
    675A  ARG*     1.3    85.7    -      -       +      +
    677A  LEU*     1.3    60.3    +      -       -      +
    679A  LEU*     4.2    19.3    -      -       +      -
   1010A  LEU*     4.1    12.9    -      -       +      +
   1013A  HIS*     3.3    44.9    -      -       +      +
   1014A  TRP*     3.7    25.0    -      -       -      +
   1017A  THR*     3.8    15.3    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 677 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    575A  ARG*     3.1    18.4    -      -       -      +
    576A  PHE*     3.1    24.5    +      -       +      +
    578A  TYR*     3.4    52.5    -      -       +      +
    581A  ALA*     3.9    11.0    -      -       +      -
    642A  PHE*     2.9    29.7    +      -       +      +
    643A  SER*     5.0     0.2    -      -       -      -
    644A  PHE*     3.6    35.0    -      -       +      -
    675A  ARG      4.5     0.4    -      -       -      +
    676A  PRO*     1.3    76.3    -      -       -      +
    678A  CYS*     1.3    66.5    +      -       +      +
    697A  VAL*     4.2    11.0    -      -       +      -
   1010A  LEU*     4.9     4.3    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with CYS 678 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    556A  GLY*     6.5     0.2    -      -       -      -
    573A  SER*     5.5     0.9    -      -       -      -
    574A  ARG      3.8     1.1    -      -       -      -
    575A  ARG*     3.5    32.8    -      -       +      -
    640A  VAL      4.1     0.2    -      -       -      +
    641A  ARG*     3.7     0.3    -      -       -      -
    642A  PHE*     3.0    42.6    +      -       +      +
    677A  LEU*     1.3    86.8    -      -       +      +
    679A  LEU*     1.3    74.9    +      -       -      +
    680A  MET*     3.7    31.6    -      -       -      -
    693A  ILE*     5.1     3.1    -      -       -      -
    694A  LEU*     4.7     8.1    -      -       -      -
    697A  VAL*     4.8     4.7    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 679 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    573A  SER*     3.1     5.2    -      -       -      -
    574A  ARG*     2.9    38.3    +      -       +      +
    639A  ALA*     6.3     0.9    -      -       +      -
    640A  VAL      3.6     9.6    -      -       -      +
    641A  ARG*     4.2    16.4    -      -       +      -
    676A  PRO*     4.2    24.5    -      -       +      -
    678A  CYS*     1.3    87.4    -      -       -      +
    680A  MET*     1.3    61.7    +      -       -      +
    990A  PHE*     3.3    40.8    -      -       +      -
   1006A  LEU*     3.6    25.2    -      -       +      +
   1009A  ILE*     4.4     6.1    -      -       +      -
   1010A  LEU*     4.4    18.8    -      -       +      +
   1013A  HIS*     5.8     2.0    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with MET 680 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    572A  ILE      3.8     0.4    -      -       -      -
    573A  SER*     3.6    18.6    -      -       -      -
    639A  ALA*     3.5     3.1    -      -       -      +
    640A  VAL*     2.9    63.2    +      -       +      +
    642A  PHE*     6.3     0.7    -      -       +      +
    678A  CYS*     3.7    13.5    -      -       -      -
    679A  LEU*     1.3    82.0    -      -       -      +
    681A  PHE*     1.3    59.8    +      -       -      +
    682A  VAL*     3.0    20.9    +      -       +      -
    690A  LEU*     3.6    15.9    -      -       +      -
    693A  ILE*     3.4    26.5    -      -       +      -
    694A  LEU*     3.2    36.3    -      -       +      -
   1006A  LEU*     5.0     1.5    -      -       -      +
----------------------------------------------------------
 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