Contacts of the helix formed by residues 79 - 85 (chain D) in PDB entry 3G3B


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 PRO 79 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     64D  CYS*     4.4     0.2    -      -       -      -
     65D  ASN*     3.3    12.6    -      -       +      +
     77D  ASN      4.9     0.2    -      -       -      +
     78D  ILE*     1.3    97.8    -      -       +      +
     80D  CYS*     1.3    64.0    +      -       -      +
     81D  SER*     3.8    18.2    -      -       -      +
     82D  ALA*     3.2    23.6    +      -       +      +
     83D  LEU*     4.0     2.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with CYS 80 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     53D  TYR*     3.4    39.4    -      -       +      +
     60D  SER*     3.6     2.9    -      -       -      -
     64D  CYS*     2.0    63.9    -      -       -      -
     65D  ASN      2.9    19.2    +      -       -      -
     66D  ASP*     3.5    11.4    -      -       +      +
     79D  PRO*     1.3    70.8    -      -       -      +
     81D  SER*     1.3    57.1    +      -       -      +
     83D  LEU*     2.9    27.5    +      -       -      +
     84D  LEU*     3.6     6.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 81 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     53D  TYR*     5.3     0.8    -      -       -      -
     66D  ASP*     5.8     0.2    -      -       -      +
     79D  PRO*     3.8    14.1    -      -       -      +
     80D  CYS*     1.3    79.1    -      -       -      +
     82D  ALA*     1.3    57.2    +      -       -      +
     83D  LEU      3.2     0.2    -      -       -      -
     84D  LEU*     3.2    34.9    +      -       -      +
     85D  SER*     3.8     4.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 82 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     78D  ILE*     4.3    11.4    -      -       +      -
     79D  PRO*     3.2    24.0    +      -       +      +
     80D  CYS      3.1     0.4    -      -       -      -
     81D  SER*     1.3    79.8    +      -       -      +
     83D  LEU*     1.3    58.9    +      -       -      +
     84D  LEU      3.2     2.7    -      -       -      -
     85D  SER*     3.3    25.0    -      -       -      -
     87D  ASP      4.6     1.9    -      -       -      +
     90D  ALA*     3.7    25.4    -      -       +      +
     91D  SER      5.0     0.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 83 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     40D  THR*     3.3     3.6    -      -       -      +
     53D  TYR*     4.1    10.5    -      -       +      +
     54D  GLY*     3.2    20.8    -      -       -      -
     55D  ILE*     4.5     0.9    +      -       -      +
     58D  ILE*     3.6    39.9    -      -       +      +
     64D  CYS*     3.8    24.5    -      -       +      -
     78D  ILE*     4.1    19.7    -      -       +      -
     79D  PRO      4.4     3.4    -      -       -      +
     80D  CYS      2.9    10.8    +      -       -      +
     82D  ALA*     1.3    76.1    -      -       -      +
     84D  LEU*     1.3    57.4    +      -       -      +
     85D  SER      3.3     4.3    +      -       -      +
     90D  ALA*     3.9    33.4    -      -       +      +
     91D  SER*     3.7    25.5    +      -       -      +
     94D  CYS*     4.6     3.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 84 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     40D  THR*     3.1    30.9    +      -       -      +
     41D  GLN*     3.7    27.5    +      -       +      +
     42D  ALA      3.7    20.2    -      -       -      +
     43D  THR*     4.0    10.8    -      -       -      +
     53D  TYR*     4.1    19.1    -      -       +      -
     54D  GLY      3.9     7.2    -      -       -      +
     80D  CYS      4.0     7.4    -      -       -      +
     81D  SER*     3.2    21.1    +      -       -      +
     82D  ALA      3.2     1.6    -      -       -      -
     83D  LEU*     1.3    77.5    -      -       -      +
     85D  SER*     1.3    64.5    +      -       -      +
     86D  SER      3.9     0.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with SER 85 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     40D  THR*     3.1    20.1    -      -       -      +
     81D  SER      3.8     3.0    +      -       -      -
     82D  ALA*     3.3    23.7    +      -       -      -
     83D  LEU      3.3     2.7    -      -       -      +
     84D  LEU*     1.3    79.0    -      -       -      +
     86D  SER*     1.3    65.8    +      -       -      +
     87D  ASP*     3.0    28.6    +      -       -      +
     88D  ILE*     5.1     0.7    -      -       -      +
----------------------------------------------------------
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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