Contacts of the strand formed by residues 703 - 712 (chain D) in PDB entry 1DQ8


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 GLY 703 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    585D  ALA*     3.7     1.7    -      -       -      +
    586D  ASP*     3.2     5.3    +      -       -      -
    587D  GLY      2.8    42.9    +      -       -      +
    588D  MET*     4.0    18.5    -      -       -      +
    648D  GLN*     5.0     0.9    +      -       -      -
    702D  ARG*     1.3    77.2    +      -       -      +
    704D  LYS*     1.3    68.4    +      -       -      -
    705D  SER*     4.1     0.7    +      -       -      -
    800D  ILE      3.5     8.3    -      -       -      -
    801D  GLU*     4.6     0.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 704 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    583D  VAL*     4.5    10.8    -      -       +      -
    585D  ALA      3.4     8.7    -      -       -      +
    586D  ASP*     3.0    35.2    +      -       -      +
    651D  SER*     5.3     2.4    +      -       -      -
    652D  GLY      4.7     6.5    +      -       -      -
    654D  ALA      4.8     5.1    +      -       -      -
    655D  MET      5.7     1.2    +      -       -      -
    702D  ARG      3.2     0.6    +      -       -      -
    703D  GLY*     1.3    75.6    -      -       -      -
    705D  SER*     1.3    60.9    +      -       -      +
    706D  VAL*     3.8     5.0    +      -       +      +
    797D  MET      3.4     5.2    -      -       -      +
    798D  PRO      3.7     1.9    -      -       -      -
    800D  ILE*     2.7    45.4    +      -       -      +
    802D  ILE*     3.9    16.9    +      -       +      +
    832D  GLY      4.9     0.2    -      -       -      -
    835D  ALA*     3.9    26.5    -      -       -      +
    836D  ARG*     4.0    17.7    -      -       -      +
    839D  ALA*     3.7    27.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 705 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    606A  LYS*     6.3     0.2    -      -       -      -
    583D  VAL*     3.5     2.3    -      -       -      -
    584D  LEU*     2.7    43.3    +      -       -      -
    585D  ALA*     3.0    31.1    +      -       -      +
    700D  GLU      5.1     0.2    +      -       -      -
    701D  GLY*     3.8    11.4    -      -       -      -
    702D  ARG      4.5     0.7    +      -       -      -
    703D  GLY      4.1     0.9    +      -       -      -
    704D  LYS*     1.3    70.4    -      -       -      +
    706D  VAL*     1.3    59.2    +      -       -      +
    797D  MET      3.4     5.8    -      -       -      -
    798D  PRO*     2.6    27.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 706 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    581D  SER*     4.7     1.3    -      -       -      -
    582D  ARG      3.4    15.3    -      -       -      +
    583D  VAL*     4.5     9.0    -      -       +      -
    584D  LEU*     4.3     4.2    -      -       -      +
    704D  LYS*     4.0     9.4    -      -       +      -
    705D  SER*     1.3    81.1    -      -       -      +
    707D  VAL*     1.3    68.7    +      -       -      +
    796D  THR*     3.5     5.2    -      -       -      +
    797D  MET      2.8    37.7    +      -       -      +
    800D  ILE*     4.0     9.2    -      -       +      -
    839D  ALA*     3.9    27.8    -      -       +      -
    840D  ARG*     4.2    15.3    -      -       +      -
    843D  CYS*     3.6    29.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 707 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    599A  ALA*     3.8    27.4    -      -       +      +
    638A  ILE*     4.2     4.9    -      -       +      -
    640A  GLY*     3.7    21.8    -      -       -      +
    581D  SER*     3.1     5.6    -      -       -      -
    582D  ARG*     3.0    45.1    +      -       +      +
    584D  LEU*     4.1    25.6    -      -       +      -
    706D  VAL*     1.3    78.6    -      -       -      +
    708D  CYS*     1.3    65.8    +      -       -      +
    795D  CYS      3.4     5.8    -      -       -      +
    796D  THR*     3.3    23.6    -      -       -      +
    843D  CYS*     4.2     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with CYS 708 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    599A  ALA*     5.3     0.4    -      -       -      -
    546D  LEU*     3.7    26.2    -      -       -      -
    579D  ALA*     4.1     1.3    -      -       -      -
    580D  SER      3.3    13.0    -      -       -      -
    581D  SER*     3.8     5.2    -      -       -      -
    707D  VAL*     1.3    76.7    -      -       -      +
    709D  GLU*     1.3    71.7    +      -       -      +
    794D  SER*     3.2     6.6    -      -       -      -
    795D  CYS      2.9    30.0    +      -       -      +
    843D  CYS*     3.8    22.7    -      -       -      +
    844D  GLY*     3.7    12.6    -      -       -      +
    847D  MET*     3.7    26.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 709 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    598A  ARG*     3.6    17.0    -      -       -      +
    599A  ALA*     2.7    28.9    +      -       +      -
    600A  CYS*     3.1    35.7    +      -       -      -
    579D  ALA*     3.2     3.1    -      -       -      +
    580D  SER*     2.9    45.0    +      -       -      +
    708D  CYS*     1.3    78.3    -      -       -      +
    710D  ALA*     1.3    65.1    +      -       -      +
    792D  TYR*     2.9    27.2    +      -       +      +
    793D  ILE      3.3    13.5    -      -       -      +
    794D  SER*     4.4     0.9    -      -       -      -
    847D  MET*     3.6     4.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 710 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    573D  ILE*     4.5     6.1    -      -       +      +
    578D  GLY      3.9    17.9    -      -       -      +
    579D  ALA*     4.0     4.7    -      -       +      -
    709D  GLU*     1.3    80.2    -      -       -      +
    711D  VAL*     1.3    66.3    +      -       -      +
    712D  ILE*     4.2    16.2    -      -       +      -
    791D  LEU      3.6     0.3    -      -       -      +
    792D  TYR*     3.6     4.7    -      -       -      -
    793D  ILE*     3.1    33.8    +      -       +      +
    847D  MET*     3.7    17.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 711 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    598A  ARG*     4.0    27.1    -      -       -      +
    576D  GLY*     3.5    20.2    +      -       -      +
    578D  GLY      4.9     2.6    +      -       -      -
    710D  ALA*     1.3    79.1    -      -       -      +
    712D  ILE*     1.3    66.3    +      -       -      +
    713D  PRO*     3.5    11.1    -      -       +      +
    784D  SER*     4.4    12.6    -      -       -      +
    785D  GLY*     6.1     0.7    -      -       -      -
    790D  ASP*     3.9    25.4    -      -       +      -
    791D  LEU      3.2     9.6    -      -       -      +
    792D  TYR*     4.1    16.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 712 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    572D  ALA*     3.6    23.8    -      -       +      +
    573D  ILE*     3.7    20.0    -      -       +      -
    710D  ALA*     4.4     7.6    -      -       +      -
    711D  VAL*     1.3    79.5    -      -       -      +
    713D  PRO*     1.4    68.7    -      -       +      +
    716D  VAL*     3.5    33.2    -      -       +      -
    717D  VAL*     3.8    16.4    -      -       +      +
    721D  LEU*     4.5     3.1    -      -       +      -
    790D  ASP*     4.3     1.8    -      -       -      -
    791D  LEU*     2.7    47.0    +      -       +      +
    793D  ILE*     4.8     3.6    -      -       +      -
    851D  LEU*     3.9    33.2    -      -       +      -
----------------------------------------------------------
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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