Contacts of the strand formed by residues 113 - 117 (chain B) 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 THR 113 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6B  GLN*     3.3    21.1    +      -       -      +
      7B  SER*     2.9    23.1    +      -       -      +
      8B  GLY      3.2    27.1    -      -       -      +
      9B  PRO*     4.5     0.2    -      -       +      -
     10B  GLU*     4.9     5.2    -      -       +      +
     20B  MET*     4.0    30.3    -      -       +      +
     92B  ALA      3.7     0.9    -      -       -      +
     93B  VAL*     3.4     1.7    -      -       -      -
     94B  TYR*     2.7    42.6    +      -       -      +
    112B  GLY*     1.3    70.9    -      -       -      -
    114B  THR*     1.3    69.7    +      -       -      +
    115B  LEU*     3.8     1.6    +      -       +      +
----------------------------------------------------------
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Residues in contact with THR 114 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      9B  PRO*     3.4    18.5    -      -       +      +
     10B  GLU      3.1    23.6    +      -       -      +
     92B  ALA      3.5    10.3    -      -       -      +
     93B  VAL*     3.6    22.3    -      -       +      +
    112B  GLY      4.2     1.5    +      -       -      -
    113B  THR*     1.3    72.6    -      -       -      +
    115B  LEU*     1.3    67.8    +      -       -      +
    116B  THR*     4.8     7.5    +      -       -      +
    154B  GLU*     5.8     9.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 115 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10B  GLU*     3.5    30.3    -      -       +      +
     12B  VAL*     4.1    15.3    -      -       +      -
     18B  VAL*     4.1    14.6    -      -       +      -
     20B  MET*     5.0     6.5    -      -       +      -
     83B  LEU*     4.1    17.3    -      -       +      -
     86B  LEU*     4.0    18.4    -      -       +      -
     90B  ASP      3.8    15.7    -      -       -      +
     91B  SER*     3.3     6.1    -      -       -      -
     92B  ALA      2.8    26.8    +      -       -      +
     94B  TYR*     3.9    15.9    -      -       +      -
    113B  THR*     3.8     1.9    +      -       +      +
    114B  THR*     1.3    77.1    -      -       -      +
    116B  THR*     1.3    67.2    +      -       -      +
    117B  VAL*     3.8    19.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 116 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10B  GLU      2.8    13.5    +      -       -      +
     11B  LEU*     3.2    25.5    -      -       +      +
     12B  VAL*     2.9    26.3    +      -       -      +
     91B  SER*     3.7     6.5    -      -       -      +
    114B  THR*     4.1     8.5    +      -       -      +
    115B  LEU*     1.3    73.9    +      -       -      +
    117B  VAL*     1.3    63.5    +      -       -      +
    118B  SER*     3.7    12.8    -      -       -      -
    152B  PHE*     4.1    13.0    -      -       +      -
    153B  PRO*     4.5    11.4    -      -       +      +
    154B  GLU*     5.0     9.5    +      -       -      +
    181B  TYR*     5.0     9.6    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 117 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12B  VAL*     3.3    15.5    -      -       +      +
     13B  LYS      4.2     0.7    -      -       -      -
     14B  PRO*     3.8    23.7    -      -       +      +
     86B  LEU*     3.9    13.7    -      -       +      -
     87B  THR*     3.3    44.0    -      -       -      +
     88B  SER*     3.8    17.9    -      -       -      +
     90B  ASP*     4.3     2.9    -      -       +      -
     91B  SER*     3.0    14.9    +      -       -      +
    115B  LEU*     3.8    26.2    -      -       +      -
    116B  THR*     1.3    74.4    -      -       -      +
    118B  SER*     1.3    61.3    +      -       -      +
----------------------------------------------------------
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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