Contacts of the strand formed by residues 71 - 76 (chain D) in PDB entry 2QXU


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 71 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4D  ASN*     4.1     0.4    -      -       -      -
      5D  PRO*     3.4    15.9    -      -       +      +
      7D  VAL*     4.0    13.9    -      -       +      -
     59D  VAL*     4.0    19.7    -      -       +      -
     62D  VAL*     3.9    25.4    -      -       +      -
     63D  LEU*     3.5    26.5    -      -       +      -
     70D  LYS*     1.3    75.5    -      -       -      +
     72D  ASP*     1.3    73.3    +      -       -      +
     73D  ILE*     4.1    15.3    -      -       +      -
     95D  LYS      3.0    14.5    +      -       -      +
     96D  VAL*     3.4     4.1    -      -       +      +
     97D  ALA      3.0    22.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with ASP 72 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      3D  HIS*     5.6     1.0    -      -       -      -
      4D  ASN*     3.2    32.3    +      -       -      +
      5D  PRO      2.9    10.8    +      -       -      +
      6D  VAL*     4.4     9.1    -      -       +      +
      7D  VAL      2.9    24.2    +      -       -      -
     31D  TRP*     5.5     2.1    +      -       -      -
     71D  VAL*     1.3    75.9    -      -       -      +
     73D  ILE*     1.3    66.4    +      -       -      +
     97D  ALA*     3.3     1.0    -      -       -      +
     98D  ASN*     3.0    51.5    +      -       -      +
    173D  LEU*     3.6    28.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 73 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7D  VAL*     3.2    18.8    -      -       +      +
      9D  VAL*     3.8    10.1    -      -       +      -
     55D  LEU*     5.0     4.7    -      -       +      -
     59D  VAL*     4.8     5.8    -      -       +      -
     71D  VAL*     4.1    11.2    -      -       +      -
     72D  ASP*     1.3    80.8    -      -       -      +
     74D  VAL*     1.3    73.1    +      -       -      +
     75D  ALA*     4.1     2.2    -      -       +      +
     83D  THR*     3.6    41.7    -      -       +      +
     86D  TYR*     4.6    12.3    -      -       +      -
     96D  VAL*     3.8    29.4    -      -       +      -
     98D  ASN      2.8    14.3    +      -       -      +
     99D  VAL*     3.5     5.8    -      -       +      -
    100D  VAL*     2.8    27.7    +      -       -      +
    173D  LEU*     4.8     0.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 74 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6D  VAL*     3.9    19.3    -      -       +      +
      7D  VAL      3.1     4.8    +      -       -      -
      8D  MET*     3.2    16.4    -      -       +      +
      9D  VAL      2.8    23.2    +      -       -      -
     19D  PHE*     4.0    12.4    -      -       +      -
     22D  ILE*     4.6     6.1    -      -       +      -
     26D  LEU*     5.3     1.3    -      -       +      -
     73D  ILE*     1.3    78.7    -      -       -      +
     75D  ALA*     1.3    60.5    +      -       -      +
    100D  VAL*     3.2    10.5    -      -       +      +
    102D  LEU*     4.1    26.2    -      -       +      -
    169D  ILE*     4.3    31.2    -      -       +      -
    173D  LEU*     4.4    12.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 75 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      9D  VAL*     3.4     9.0    -      -       +      +
     19D  PHE*     4.9     0.4    -      -       -      -
     73D  ILE*     4.0     4.0    -      -       +      -
     74D  VAL*     1.3    74.7    -      -       -      +
     76D  HIS*     1.3    54.1    +      -       -      +
     79D  GLY      3.5    28.0    -      -       -      +
     80D  GLY*     3.7     8.5    -      -       -      +
     83D  THR*     3.6    15.0    -      -       +      +
    100D  VAL      2.8    11.7    +      -       -      +
    101D  THR*     3.2    10.7    -      -       +      -
    102D  LEU*     2.7    36.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with HIS 76 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      9D  VAL      2.9     7.9    +      -       -      +
     10D  HIS*     4.8     0.2    -      -       -      -
     11D  GLY*     3.3    17.1    +      -       -      +
     18D  ASN*     5.1     7.1    +      -       -      +
     19D  PHE*     4.1    19.3    -      -       +      -
     75D  ALA*     1.3    73.6    -      -       -      +
     77D  SER*     1.3    87.2    +      -       -      +
     79D  GLY*     2.8    20.7    +      -       -      -
    102D  LEU*     3.4    27.1    -      -       +      -
    156D  HIS*     2.9    38.0    +      +       -      -
    157D  ILE*     5.0     6.5    -      -       +      -
    159D  LEU*     4.1     5.9    -      -       +      +
    160D  LEU*     3.9    37.1    -      -       +      +
----------------------------------------------------------
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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