Contacts of the helix formed by residues 31 - 39 (chain G) in PDB entry 4QOC


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 LYS 31 (chain G).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     65A  ARG*     4.9    12.9    +      -       -      +
     66A  LEU      5.6     1.2    +      -       -      -
     68A  ASP*     6.3     0.6    -      -       -      +
     71A  GLN*     4.9    12.5    -      -       +      +
     76A  TYR*     3.8    54.3    -      -       +      +
     29G  ARG      4.5     0.2    -      -       -      -
     30G  PRO*     1.3    74.3    -      -       -      +
     32G  PRO*     1.3    78.2    -      -       +      +
     33G  LEU*     3.3     3.4    +      -       +      +
     34G  LEU      3.3     2.8    +      -       -      +
     35G  LEU*     3.0    19.2    +      -       -      +
    105G  ARG      3.1    26.3    +      -       -      +
    106G  ASN*     2.9    25.1    +      -       +      +
    107G  LEU*     3.7    23.4    +      -       -      +
    108G  VAL*     4.2     3.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with PRO 32 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     71A  GLN*     5.5     4.9    -      -       +      +
     72A  GLN*     3.0    38.6    -      -       +      +
     74A  ILE*     6.3     1.8    -      -       +      -
     76A  TYR*     3.6    16.8    -      -       -      +
     30G  PRO      4.8     0.2    -      -       -      +
     31G  LYS*     1.3    87.6    -      -       +      +
     33G  LEU*     1.3    57.2    +      -       -      +
     35G  LEU*     3.2    10.3    +      -       +      +
     36G  LYS*     2.9    28.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 33 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     70A  LYS*     4.4    21.5    -      -       +      +
     71A  GLN*     6.1     3.9    -      -       +      +
     72A  GLN*     3.7    19.9    +      -       -      +
     31G  LYS*     3.5     2.7    -      -       +      +
     32G  PRO*     1.3    78.9    -      -       -      +
     34G  LEU*     1.3    62.0    +      -       -      +
     36G  LYS*     3.2    22.6    +      -       +      +
     37G  LEU*     3.1    16.6    +      -       -      +
     81G  LEU*     4.2    17.7    -      -       +      +
     84G  ASP*     5.1     7.2    -      -       +      -
     85G  LEU*     2.6    44.1    -      -       +      +
    106G  ASN*     5.1     1.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 34 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     30G  PRO*     3.8    20.4    -      -       +      -
     31G  LYS*     3.3     8.0    +      -       -      +
     33G  LEU*     1.3    75.6    -      -       -      +
     35G  LEU*     1.3    60.6    +      -       -      +
     37G  LEU*     3.1     5.3    +      -       +      -
     38G  LEU*     2.8    48.7    +      -       +      +
     53G  VAL*     4.7    11.9    -      -       +      -
     57G  LEU*     4.0    28.0    -      -       +      -
     85G  LEU*     3.1    19.1    -      -       +      +
     86G  PHE*     5.9     3.6    -      -       +      -
    103G  ILE*     4.8     5.8    -      -       +      +
    106G  ASN*     3.6    40.7    -      -       +      +
    107G  LEU*     4.7     6.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 35 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     30G  PRO*     4.1    18.8    -      -       +      +
     31G  LYS      3.0    13.9    +      -       -      +
     32G  PRO*     3.4    12.8    -      -       +      +
     34G  LEU*     1.3    76.6    -      -       -      +
     36G  LYS*     1.3    64.1    +      -       -      +
     38G  LEU*     4.3     5.8    -      -       +      -
     39G  LYS*     2.9    24.8    +      -       -      +
     44G  GLN*     2.6    47.1    -      -       +      +
     45G  LYS      4.2    11.9    -      -       -      +
     48G  TYR*     3.7    23.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with LYS 36 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     32G  PRO      2.9    13.6    +      -       -      +
     33G  LEU*     3.3    25.3    -      -       +      +
     34G  LEU      3.2     0.2    -      -       -      -
     35G  LEU*     1.3    78.4    -      -       -      +
     37G  LEU*     1.3    63.4    +      -       -      +
     39G  LYS*     3.7    26.0    +      -       -      +
     40G  SER*     3.5    16.6    +      -       -      -
     81G  LEU*     4.5    18.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 37 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33G  LEU      3.1     8.5    +      -       -      +
     34G  LEU*     3.1    10.8    +      -       +      +
     36G  LYS*     1.3    79.5    -      -       -      +
     38G  LEU*     1.3    71.8    +      -       +      +
     40G  SER*     2.6    27.9    +      -       -      -
     41G  VAL*     4.0     1.2    +      -       -      +
     56G  TYR      4.7     1.6    -      -       -      +
     57G  LEU*     4.0    18.6    -      -       +      -
     60G  TYR*     3.5    57.8    -      -       +      -
     81G  LEU*     4.0    24.1    -      -       +      +
     82G  LEU*     4.0    23.1    -      -       +      -
     85G  LEU*     4.6     7.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 38 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     30G  PRO*     3.6    33.4    -      -       +      -
     34G  LEU*     2.8    39.9    +      -       +      +
     35G  LEU*     3.2     9.2    +      -       +      +
     37G  LEU*     1.3    83.6    -      -       +      +
     39G  LYS*     1.3    57.3    +      -       -      +
     41G  VAL*     2.8    30.9    +      -       -      +
     42G  GLY*     2.9     7.4    +      -       -      -
     48G  TYR*     4.2    25.4    -      -       +      +
     53G  VAL*     4.2    19.5    -      -       +      +
     56G  TYR*     3.5    29.6    -      -       +      +
     57G  LEU*     4.5     3.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 39 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     35G  LEU      2.9    11.4    +      -       -      +
     36G  LYS*     3.8    30.5    -      -       -      +
     38G  LEU*     1.3    72.0    -      -       -      +
     40G  SER*     1.3    60.1    +      -       -      +
     41G  VAL      2.8     6.5    +      -       -      -
     42G  GLY      3.3    18.0    +      -       -      +
     44G  GLN*     2.5    53.2    -      -       +      +
     48G  TYR*     5.4     0.4    +      -       -      -
----------------------------------------------------------
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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