Contacts of the strand formed by residues 214 - 219 (chain E) in PDB entry 6DDE


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 VAL 214 (chain E).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    165E  PHE      4.0     0.5    -      -       -      +
    166E  LEU*     3.6     2.4    -      -       -      -
    167E  GLN*     2.8    44.7    +      -       +      +
    169E  PRO*     6.4     0.9    -      -       +      -
    213E  GLY*     1.3    78.3    -      -       -      +
    215E  TYR*     1.3    63.4    +      -       -      +
    216E  TYR*     3.5    36.8    -      -       +      +
    229E  ALA      5.2     0.2    -      -       -      +
    230E  GLY*     3.9    17.3    -      -       -      -
    231E  THR      3.3     9.9    -      -       -      +
    232E  LYS*     4.6    18.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 215 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    130E  GLN*     5.8     0.3    -      -       -      +
    145E  ILE*     3.5    26.5    -      -       +      -
    164E  TRP*     4.6    14.3    -      -       +      -
    165E  PHE      3.4     5.6    -      -       -      +
    166E  LEU*     3.4    36.8    -      -       +      -
    176E  LEU*     4.6     6.1    -      -       +      -
    191E  PHE*     4.0     5.1    -      +       -      -
    202E  LEU*     3.9    17.3    -      -       +      -
    204E  ILE*     3.3    26.2    -      -       +      +
    211E  ASP*     2.4    34.7    +      -       -      -
    213E  GLY      4.9     1.6    -      -       -      -
    214E  VAL*     1.3    79.2    -      -       -      +
    216E  TYR*     1.3    61.5    +      -       -      +
    217E  CYS      4.2     0.5    +      -       -      -
    230E  GLY*     3.3     4.3    -      -       -      -
    231E  THR*     2.8    42.1    +      -       -      +
    233E  LEU*     3.5    18.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 216 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     39E  GLN*     2.7    26.8    +      -       -      -
     43E  LYS      3.9     5.7    +      -       -      -
     44E  GLY*     3.7    21.5    -      -       -      -
     45E  LEU*     3.7    34.8    -      -       +      -
    164E  TRP*     3.3    11.5    -      -       -      -
    165E  PHE*     2.9    44.2    +      -       +      +
    167E  GLN*     3.2    26.7    +      -       +      -
    173E  PRO*     5.4     0.4    -      -       +      -
    214E  VAL*     3.5    35.7    -      -       +      +
    215E  TYR*     1.3    75.0    -      -       -      +
    217E  CYS*     1.3    66.0    +      -       -      +
    227E  PHE*     4.4     5.2    -      -       +      -
    228E  GLY      3.7    17.0    -      -       -      -
    229E  ALA      4.4     1.1    -      -       -      -
    230E  GLY*     4.0    11.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with CYS 217 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    128E  MET*     3.5     8.1    -      -       +      -
    130E  GLN*     4.9     2.0    -      -       -      +
    147E  CYS*     2.7    44.0    -      -       +      -
    162E  LEU*     3.1    40.2    -      -       -      -
    163E  TYR      3.5     3.8    -      -       -      -
    164E  TRP*     4.2    10.6    -      -       +      -
    215E  TYR      4.2     1.0    +      -       -      -
    216E  TYR*     1.3    75.1    -      -       -      +
    218E  MET*     1.3    67.6    +      -       -      +
    227E  PHE*     3.3     8.1    -      -       -      +
    228E  GLY*     3.0    31.3    +      -       -      +
    230E  GLY      5.7     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with MET 218 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    108E  PHE*     4.2    15.5    -      -       +      -
    128E  MET*     4.6     1.8    -      -       -      -
    162E  LEU*     3.5     8.0    -      -       -      +
    163E  TYR*     2.9    72.0    +      -       +      +
    165E  PHE*     4.0    12.8    -      -       +      -
    217E  CYS*     1.3    82.1    -      -       -      +
    219E  GLN*     1.3    80.2    +      -       -      +
    220E  HIS*     3.7    19.1    -      -       +      -
    225E  LEU*     4.2     8.3    -      -       +      -
    226E  THR      3.3    14.8    -      -       -      +
    227E  PHE*     3.5    39.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLN 219 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    126E  ILE*     3.4    29.2    -      -       +      +
    128E  MET*     3.7    21.4    -      -       -      +
    153E  LEU*     3.7    26.2    -      -       +      -
    161E  TYR      3.8     3.8    -      -       -      -
    218E  MET*     1.3    81.1    -      -       -      +
    220E  HIS*     1.3    62.0    +      -       -      +
    221E  LEU*     2.6    26.5    +      -       +      +
    222E  GLU      2.6    21.8    +      -       -      +
    224E  PRO      3.7    14.3    +      -       -      -
    225E  LEU*     3.4    19.2    -      -       -      +
    226E  THR*     2.9    29.0    +      -       -      +
----------------------------------------------------------
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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