Contacts of the strand formed by residues 114 - 118 (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 ILE 114 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    112B  LEU*     3.0    16.7    +      -       +      +
    113B  PRO*     1.3    76.8    -      -       -      +
    115B  GLU*     1.3    62.2    +      -       -      +
    116B  ILE*     3.7    25.8    -      -       +      -
    134B  VAL*     3.8    14.1    -      -       +      -
    135B  GLU      3.3    10.5    -      -       -      +
    136B  ASN*     4.5     2.9    -      -       -      -
    137B  THR*     4.0     4.7    -      -       -      -
    144B  LEU*     3.2    42.6    -      -       +      +
    145B  THR      4.9     2.2    -      -       -      +
    148B  ILE*     3.3    28.7    -      -       +      -
    462B  PHE*     3.5    14.1    -      -       +      -
    463B  LYS*     3.3     4.3    -      -       -      -
    464B  ASN*     3.1    22.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 115 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    114B  ILE*     1.3    74.6    -      -       -      +
    116B  ILE*     1.3    63.9    +      -       -      +
    117B  LYS*     3.3    23.5    +      -       +      +
    133B  THR*     3.6     1.2    +      -       -      +
    134B  VAL*     3.5     3.5    -      -       -      -
    135B  GLU*     2.7    53.3    +      -       +      +
    137B  THR*     3.8    16.1    -      -       +      +
    460B  THR*     2.8    34.5    +      -       +      +
    462B  PHE      3.4     8.7    -      -       -      +
    463B  LYS*     4.0    26.2    +      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 116 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     62B  LEU*     4.3    14.4    -      -       +      -
     66B  LEU*     3.8    24.7    -      -       +      -
     70B  LEU*     4.2     8.3    -      -       +      -
    114B  ILE*     3.7    19.7    -      -       +      -
    115B  GLU*     1.3    78.7    -      -       -      +
    117B  LYS*     1.3    63.9    +      -       -      +
    132B  PHE*     4.3    10.1    -      -       +      -
    133B  THR      3.1    10.3    -      -       -      +
    134B  VAL*     4.1     8.7    -      -       +      -
    148B  ILE*     4.8     0.4    -      -       +      -
    152B  LEU*     4.1    23.6    -      -       +      -
    460B  THR*     3.4     3.5    -      -       -      -
    461B  VAL*     2.8    43.2    +      -       +      -
    462B  PHE*     2.9    25.3    +      -       +      +
----------------------------------------------------------
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Residues in contact with LYS 117 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     34B  TYR*     6.5     0.2    -      -       +      -
    115B  GLU*     3.3    31.0    +      -       +      +
    116B  ILE*     1.3    76.1    -      -       -      +
    118B  ALA*     1.3    62.0    +      -       -      +
    132B  PHE*     3.0     6.1    -      -       -      +
    133B  THR*     2.8    47.9    +      -       -      +
    135B  GLU*     4.3    13.1    +      -       -      +
    456B  ASP*     5.0    13.1    +      -       -      +
    458B  LEU*     4.1    17.6    -      -       +      +
    459B  HIS      3.1     7.9    -      -       -      +
    460B  THR*     3.7    18.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 118 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     59B  PHE*     4.0     4.3    -      -       +      -
     62B  LEU*     3.8    21.5    -      -       +      -
    117B  LYS*     1.3    77.8    -      -       -      +
    119B  VAL*     1.3    70.3    +      -       -      +
    120B  PRO*     3.8     1.0    -      -       -      +
    131B  LEU      3.5     6.7    -      -       -      +
    132B  PHE*     3.8    13.5    -      -       +      -
    458B  LEU*     3.8     4.7    -      -       -      +
    459B  HIS*     2.7    37.3    +      -       -      +
    461B  VAL*     3.8    17.2    -      -       +      +
    471B  TYR*     5.2     0.2    +      -       -      -
----------------------------------------------------------
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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