Contacts of the strand formed by residues 680 - 684 (chain A) in PDB entry 1D0N


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 680 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    673A  LEU*     4.4    15.7    -      -       +      -
    674A  LEU      3.8     5.2    -      -       -      +
    675A  ASP*     3.9    19.7    -      -       -      +
    679A  GLN*     1.3    81.6    -      -       -      +
    681A  PHE*     1.3    71.2    +      -       -      +
    682A  VAL      3.9     0.2    +      -       -      -
    700A  ALA*     4.4    11.9    -      -       +      -
    703A  TYR*     4.4    16.2    -      -       +      -
    704A  ILE*     3.6    31.0    -      -       +      -
    711A  ARG*     4.2     3.6    -      -       -      +
    715A  THR*     4.1     7.4    -      -       +      -
    716A  PRO      3.2     8.1    +      -       -      +
    717A  ILE*     3.6     6.9    -      -       +      +
    718A  THR*     3.0    24.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 681 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    673A  LEU*     3.2     8.7    -      -       -      +
    674A  LEU*     2.8    64.9    +      -       +      +
    676A  THR*     4.1    15.5    -      -       -      -
    679A  GLN*     3.3    31.2    -      -       +      -
    680A  VAL*     1.3    76.0    -      -       -      +
    682A  VAL*     1.3    59.1    +      -       -      +
    683A  TRP      4.0     0.2    -      -       -      -
    718A  THR*     3.4    25.1    -      -       +      -
    720A  VAL*     3.9    16.8    -      -       +      -
    726A  PRO*     4.3     3.6    -      -       +      -
    728A  SER*     3.6    39.3    -      -       -      -
    729A  PHE*     3.6    30.5    -      +       +      -
    732A  TRP*     5.2     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 682 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    671A  VAL*     3.7    26.7    -      -       +      -
    672A  MET      3.2     3.4    -      -       -      -
    673A  LEU*     3.6    17.3    -      -       +      -
    681A  PHE*     1.3    73.1    -      -       -      +
    683A  TRP*     1.3    60.1    +      -       -      +
    684A  VAL*     4.0     3.5    +      -       +      -
    696A  ALA*     3.9    26.2    -      -       +      +
    700A  ALA*     5.0     2.0    -      -       +      -
    717A  ILE*     4.5    11.4    -      -       +      -
    718A  THR      2.9    10.7    +      -       -      +
    719A  VAL*     3.2    32.6    -      -       +      +
    720A  VAL*     2.9    27.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with TRP 683 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    666A  LEU*     3.8    36.6    -      -       +      +
    667A  ALA      3.5    15.9    -      -       -      -
    668A  THR*     4.2     0.7    -      -       -      -
    670A  ASP      3.9     1.8    -      -       -      -
    671A  VAL*     3.3     4.7    -      -       -      +
    672A  MET*     2.7    62.5    +      -       +      +
    674A  LEU      6.1     0.4    -      -       -      +
    681A  PHE      4.0     1.0    -      -       -      -
    682A  VAL*     1.3    71.6    -      -       -      +
    684A  VAL*     1.3    60.9    +      -       -      +
    685A  GLY*     3.5    27.1    -      -       -      -
    720A  VAL*     3.7    12.6    -      -       +      -
    722A  GLN*     3.5    37.3    -      -       +      +
    725A  GLU*     2.7    37.4    +      -       +      +
    729A  PHE*     3.6    28.9    -      +       +      -
    741A  TRP*     3.8    15.0    -      +       -      -
----------------------------------------------------------
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Residues in contact with VAL 684 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    670A  ASP      4.1     1.8    -      -       -      -
    671A  VAL*     4.2    14.1    -      -       +      +
    682A  VAL*     4.2     9.4    -      -       +      +
    683A  TRP*     1.3    80.5    -      -       -      +
    685A  GLY*     1.3    64.2    +      -       -      +
    686A  LYS*     3.6     0.5    +      -       -      -
    688A  SER*     4.5     2.5    -      -       -      +
    693A  LYS*     4.3    26.5    -      -       +      +
    696A  ALA*     4.2    25.4    -      -       +      -
    719A  VAL*     4.6     6.3    -      -       +      -
    720A  VAL      3.1    17.8    +      -       -      +
    721A  LYS*     4.1    19.0    -      -       +      +
    722A  GLN      3.4    17.8    +      -       -      -
----------------------------------------------------------
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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