Contacts of the strand formed by residues 66 - 71 (chain C) in PDB entry 3DGG


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 PHE 66 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     41C  GLN*     3.8    14.8    -      -       -      -
     51C  LEU*     4.0    18.4    -      -       +      -
     52C  ILE*     4.6     6.3    -      -       +      -
     58C  LEU*     3.4    30.6    -      -       +      +
     62C  VAL*     4.0    15.0    -      -       +      -
     63C  PRO*     3.2    24.8    +      -       +      +
     64C  ALA      3.5     9.6    -      -       -      +
     65C  ARG*     1.3   100.9    -      -       +      +
     67C  SER*     1.3    61.8    +      -       -      +
     77C  LEU*     4.6     7.6    -      -       +      -
     78C  ASN      3.5     2.9    -      -       -      -
     79C  ILE*     3.7    29.6    -      -       +      -
     86C  ASP*     3.4    20.4    -      -       -      -
     90C  TYR*     3.7    22.0    -      +       -      -
----------------------------------------------------------
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Residues in contact with SER 67 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     52C  ILE*     4.1     9.0    -      -       -      -
     56C  SER      5.9     0.4    -      -       -      -
     58C  LEU*     5.2     0.9    -      -       -      -
     64C  ALA      5.1     2.7    -      -       -      -
     65C  ARG      3.9     1.3    +      -       -      -
     66C  PHE*     1.3    76.7    -      -       -      +
     68C  GLY*     1.3    59.1    +      -       -      +
     77C  LEU*     3.7     3.8    -      -       -      +
     78C  ASN*     2.8    55.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 68 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     54B  TYR*     4.5     6.9    +      -       -      -
     39C  TRP*     5.2     1.3    -      -       -      -
     52C  ILE*     3.9    14.8    -      -       -      +
     55C  ALA      3.1    22.8    -      -       -      +
     56C  SER*     3.4    19.6    +      -       -      +
     67C  SER*     1.3    77.5    -      -       -      +
     69C  SER*     1.3    62.7    +      -       -      -
     76C  THR      3.3     8.5    -      -       -      -
     77C  LEU*     4.6     1.3    -      -       -      -
     78C  ASN*     6.1     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 69 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     54B  TYR*     5.8     4.7    -      -       -      -
     39C  TRP*     5.4     0.3    +      -       -      -
     55C  ALA*     3.5     6.7    +      -       -      +
     56C  SER*     5.1     2.9    -      -       -      -
     68C  GLY*     1.3    74.8    -      -       -      -
     70C  GLY*     1.3    63.0    +      -       -      +
     75C  PHE*     3.4    10.6    -      -       -      +
     76C  THR*     2.6    50.9    +      -       -      +
     78C  ASN*     4.7     4.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 70 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     55B  ASN*     3.8    12.5    +      -       -      +
     35C  SER*     4.2     1.7    +      -       -      -
     55C  ALA*     4.1     6.9    -      -       -      +
     69C  SER*     1.3    80.4    -      -       -      +
     71C  SER*     1.3    65.1    +      -       -      -
     74C  ASP      3.2    15.0    -      -       -      -
     75C  PHE*     3.4    15.5    -      -       -      -
     76C  THR      4.9     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 71 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     52B  ASN*     6.1     0.4    -      -       -      -
     55B  ASN*     3.8    15.3    +      -       -      -
     57B  ASP*     3.6    31.7    +      -       -      +
     30C  SER*     3.9     1.1    -      -       -      -
     35C  SER*     4.0     7.9    -      -       -      -
     70C  GLY*     1.3    75.7    -      -       -      -
     72C  GLY*     1.3    62.9    +      -       -      +
     73C  THR      3.1     7.6    +      -       -      -
     74C  ASP*     3.3    12.9    +      -       -      +
     75C  PHE*     3.6    12.1    -      -       -      -
----------------------------------------------------------
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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