Contacts of the strand formed by residues 689 - 693 (chain D) in PDB entry 6T8O


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 689 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    446D  ASP*     4.5    13.2    -      -       +      +
    447D  ILE*     6.5     0.2    -      -       +      -
    452D  ILE*     4.9     9.4    -      -       +      -
    679D  LEU*     4.6     0.7    -      -       -      -
    680D  TYR*     2.7    56.2    +      -       +      +
    682D  PRO*     5.0     6.7    -      -       +      -
    687D  LEU*     4.0    14.4    -      -       +      +
    688D  PRO*     1.3    73.0    -      -       -      +
    690D  ARG*     1.3    68.9    +      -       -      +
    691D  VAL*     3.4    10.6    +      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 690 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    365D  ILE*     3.4    30.7    -      -       -      +
    398D  ARG*     3.6    34.6    -      -       -      +
    412D  GLU*     3.4    28.4    +      -       -      +
    414D  PRO*     5.7     0.2    -      -       -      +
    446D  ASP*     3.5    22.3    -      -       -      +
    447D  ILE*     3.7    25.8    +      -       +      +
    671D  GLN      4.8     2.2    +      -       -      -
    672D  LEU*     3.8    18.5    -      -       +      +
    673D  LEU*     4.0    12.1    -      -       -      +
    677D  ASP*     2.4    39.2    +      -       -      +
    678D  MET      3.7    12.8    -      -       -      +
    679D  LEU*     3.7    13.5    -      -       +      -
    688D  PRO      3.6     4.2    +      -       -      +
    689D  ILE*     1.3    72.6    -      -       -      +
    691D  VAL*     1.3    60.1    +      -       -      +
    692D  HIS*     3.7     5.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 691 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    443D  LEU*     3.9    27.1    -      -       +      -
    444D  GLY      4.0    13.7    -      -       -      +
    445D  HIS      3.4    10.8    -      -       -      +
    446D  ASP*     4.8     0.2    -      -       -      -
    452D  ILE*     4.4    19.5    -      -       +      -
    677D  ASP*     3.6     1.1    -      -       -      +
    678D  MET*     2.7    56.7    +      -       +      +
    680D  TYR*     3.9    14.6    -      -       +      -
    689D  ILE*     3.4    21.3    +      -       +      +
    690D  ARG*     1.3    79.8    -      -       -      +
    692D  HIS*     1.3    64.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with HIS 692 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    363D  PRO*     5.1     5.1    -      -       +      +
    364D  VAL*     3.5    46.1    +      -       +      +
    365D  ILE*     3.8    20.6    +      -       +      +
    421D  VAL*     4.4    14.1    -      -       +      +
    444D  GLY*     3.3    20.1    -      -       -      -
    445D  HIS*     2.9    14.8    +      -       +      +
    446D  ASP      3.5    24.8    +      -       -      -
    447D  ILE*     4.2     7.9    -      -       -      +
    676D  GLY      3.5     6.1    -      -       -      +
    677D  ASP*     2.8    34.6    +      -       -      -
    690D  ARG*     3.7    16.2    -      -       +      -
    691D  VAL*     1.3    70.9    -      -       -      +
    693D  GLY*     1.3    65.4    +      -       -      +
    694D  ALA*     3.5     0.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 693 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    421D  VAL*     4.6     4.9    -      -       -      +
    443D  LEU      3.3    10.1    -      -       -      -
    475D  GLY*     6.5     0.9    -      -       -      -
    652D  PHE*     5.5     0.2    -      -       -      -
    676D  GLY*     2.4    30.0    +      -       -      +
    678D  MET*     4.1    16.7    -      -       -      +
    691D  VAL      3.7     2.8    +      -       -      -
    692D  HIS*     1.3    69.1    -      -       -      +
    694D  ALA*     1.3    62.0    +      -       -      -
    695D  PHE      3.5     0.2    +      -       -      -
    801D  ADP      3.0    24.9    +      -       -      -
----------------------------------------------------------
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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