Contacts of the strand formed by residues 308 - 311 (chain B) in PDB entry 3DGR


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 LEU 308 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    266B  VAL*     3.8    15.0    -      -       +      -
    274B  VAL*     3.5     7.0    -      -       +      +
    276B  VAL*     3.5    33.2    -      -       +      -
    291B  TRP*     3.7    37.7    -      -       +      -
    299B  ILE*     3.7    18.8    -      -       +      -
    302B  ARG*     3.8    15.6    -      -       -      +
    306B  ALA      3.7     0.6    +      -       -      -
    307B  PRO*     1.3    72.5    -      -       -      +
    309B  ILE*     1.3    68.4    +      -       -      +
    310B  ILE*     3.9    19.7    -      -       +      +
    347B  TYR      2.9    11.2    +      -       -      +
    348B  LEU*     3.5    12.2    -      -       +      +
    349B  ARG      2.9    25.3    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 309 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    242B  VAL*     4.7    11.4    -      -       +      -
    273B  PRO*     4.1    25.1    -      -       +      -
    274B  VAL      2.8    20.7    +      -       -      +
    275B  SER*     3.3     8.9    +      -       -      +
    276B  VAL*     2.8    28.8    +      -       -      -
    307B  PRO*     4.2     9.6    -      -       +      +
    308B  LEU*     1.3    80.1    -      -       -      +
    310B  ILE*     1.3    60.9    +      -       -      +
    349B  ARG*     3.3    17.0    -      -       +      +
    350B  VAL      3.7     7.4    -      -       -      +
    351B  ILE*     3.6    41.1    -      -       +      +
    379B  ALA*     6.2     0.9    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 310 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    276B  VAL      4.0     3.4    -      -       -      -
    278B  SER*     3.8    15.7    -      -       -      +
    283B  ILE*     4.4     4.7    -      -       +      -
    287B  CYS*     3.8    20.4    -      -       -      -
    291B  TRP*     3.7    27.4    -      -       +      +
    308B  LEU*     3.9    18.8    -      -       +      -
    309B  ILE*     1.3    70.3    -      -       -      +
    311B  ARG*     1.3    63.9    +      -       -      +
    312B  PRO*     3.4     8.6    -      -       +      +
    324B  VAL*     4.7     5.4    -      -       +      -
    328B  LEU*     3.5    37.0    -      -       +      -
    348B  LEU*     3.7    17.7    -      -       +      -
    349B  ARG      2.8    13.5    +      -       -      +
    350B  VAL*     3.3     6.1    -      -       +      -
    351B  ILE      2.9    22.3    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ARG 311 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    245B  ALA      3.5    16.0    +      -       -      -
    246B  GLU*     4.7     3.8    -      -       -      +
    247B  HIS*     5.0     2.6    +      -       -      -
    275B  SER*     3.9    10.8    -      -       -      +
    276B  VAL      3.1    16.7    +      -       -      +
    277B  VAL*     3.4    35.8    -      -       -      +
    278B  SER      2.9    26.1    +      -       -      -
    279B  ASP      4.2     0.3    +      -       -      -
    283B  ILE*     4.7     0.4    -      -       -      -
    309B  ILE      3.6     0.2    +      -       -      -
    310B  ILE*     1.3    76.8    -      -       -      +
    312B  PRO*     1.3    70.7    +      -       -      +
    313B  ASP*     3.3    28.1    +      -       -      -
    351B  ILE*     3.5    21.1    -      -       +      +
    353B  GLY*     4.9     2.1    -      -       -      +
    501B  A12      3.1    78.4    +      -       +      -
----------------------------------------------------------
 Back to top of page


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