Contacts of the strand formed by residues 191 - 196 (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 PHE 191 (chain E).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    166E  LEU*     4.8     4.3    -      -       +      -
    168E  ARG*     5.6     2.0    -      -       -      -
    176E  LEU*     3.5    35.2    -      -       +      -
    177E  ILE*     4.5     9.0    -      -       +      -
    183E  LEU*     3.4    30.3    -      -       +      +
    187E  VAL*     3.5    23.6    -      -       +      -
    188E  PRO*     3.5    21.3    +      -       +      +
    189E  ASP      3.2     8.1    -      -       -      +
    190E  ARG*     1.3    83.7    -      -       +      +
    192E  SER*     1.3    63.9    +      -       -      +
    202E  LEU*     4.9     6.3    -      -       +      -
    203E  THR      3.6     2.0    -      -       -      +
    204E  ILE*     3.6    39.9    -      -       +      -
    211E  ASP*     3.1    33.9    -      -       -      -
    215E  TYR*     4.0     5.6    -      +       -      -
----------------------------------------------------------
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Residues in contact with SER 192 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    177E  ILE*     3.6     7.4    -      -       -      +
    181E  SER      6.0     0.2    -      -       -      -
    183E  LEU*     4.9     2.0    -      -       -      -
    189E  ASP      5.6     0.9    -      -       -      -
    190E  ARG      5.2     0.7    -      -       -      -
    191E  PHE*     1.3    77.1    -      -       -      +
    193E  GLY*     1.3    67.3    +      -       -      +
    202E  LEU*     3.5     5.2    -      -       -      +
    203E  THR*     2.9    45.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 193 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    164E  TRP*     5.6     0.7    -      -       -      -
    177E  ILE*     3.5    10.7    -      -       -      +
    180E  MET      3.2    23.3    -      -       -      -
    181E  SER*     3.6    21.7    +      -       -      +
    192E  SER*     1.3    82.9    +      -       -      +
    194E  SER*     1.3    64.2    +      -       -      -
    201E  THR      3.5     6.3    -      -       -      -
    202E  LEU*     4.9     0.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 194 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    162E  LEU*     5.8     0.3    -      -       -      +
    164E  TRP*     5.7     0.5    +      -       -      -
    180E  MET*     3.8     8.6    +      -       -      +
    181E  SER*     5.4     1.8    -      -       -      -
    192E  SER*     5.9     0.2    -      -       -      -
    193E  GLY*     1.3    75.6    -      -       -      -
    195E  GLY*     1.3    59.6    +      -       -      +
    200E  PHE*     3.7     5.9    -      -       -      +
    201E  THR*     2.8    50.1    +      -       -      +
    203E  THR*     4.8     2.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 195 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    160E  THR*     6.4     0.2    -      -       -      -
    180E  MET*     5.6     2.2    -      -       -      +
    194E  SER*     1.3    79.4    +      -       -      +
    196E  SER*     1.3    63.1    +      -       -      -
    199E  ALA      3.3    13.0    -      -       -      -
    200E  PHE*     4.0     9.2    -      -       -      -
    201E  THR*     4.4     1.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 196 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    154E  LEU*     5.4     0.2    -      -       -      -
    160E  THR*     5.1    10.7    -      -       -      +
    195E  GLY*     1.3    75.9    -      -       -      -
    197E  GLY*     1.3    72.9    +      -       -      +
    199E  ALA*     2.8    24.7    +      -       -      +
    200E  PHE*     3.3    20.3    -      -       -      -
----------------------------------------------------------
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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