Contacts of the strand formed by residues 258 - 266 (chain B) in PDB entry 5DK3


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 GLU 258 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    244B  PRO      3.9     2.4    -      -       -      +
    245B  PRO*     3.3    23.8    -      -       -      +
    246B  LYS      4.8     0.5    +      -       -      +
    256B  THR*     3.4    30.4    +      -       -      +
    257B  PRO*     1.3    80.5    -      -       -      +
    259B  VAL*     1.3    66.4    +      -       -      +
    260B  THR*     3.9     7.6    +      -       -      +
    305B  VAL*     3.4    36.3    -      -       +      +
    306B  LEU      3.3     5.2    -      -       -      +
    307B  THR*     3.8    19.6    +      -       -      +
    308B  VAL*     4.3     1.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 259 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    242B  LEU*     3.9     6.7    -      -       +      -
    243B  PHE      3.6    13.2    -      -       -      +
    245B  PRO*     4.3    11.0    -      -       +      -
    258B  GLU*     1.3    75.7    -      -       -      +
    260B  THR*     1.3    60.5    +      -       -      +
    277B  TRP*     3.7    26.1    -      -       +      -
    305B  VAL*     3.6     1.7    -      -       -      -
    306B  LEU      2.7    37.1    +      -       -      +
    308B  VAL*     4.1    12.1    -      -       +      -
    313B  TRP*     4.3     7.2    -      -       +      -
    319B  TYR*     3.8    42.0    -      -       +      -
    336B  ILE*     3.8    14.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 260 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    241B  PHE      3.7     1.6    -      -       -      +
    242B  LEU*     3.4     4.9    -      -       -      +
    243B  PHE*     2.7    52.2    +      -       +      +
    244B  PRO      5.5     0.9    +      -       -      -
    258B  GLU*     3.9     8.9    +      -       -      +
    259B  VAL*     1.3    74.1    -      -       -      +
    261B  CYS*     1.3    59.8    +      -       -      +
    262B  VAL*     3.8    22.4    -      -       +      -
    303B  VAL*     3.8    18.2    -      -       +      -
    304B  SER      3.5     3.8    -      -       -      +
    305B  VAL*     3.7    16.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with CYS 261 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    240B  VAL*     3.6    24.9    -      -       -      -
    241B  PHE      3.7     2.5    -      -       -      -
    242B  LEU*     3.9     5.8    -      -       +      -
    260B  THR*     1.3    70.9    -      -       -      +
    262B  VAL*     1.3    61.0    +      -       -      +
    275B  PHE*     3.9    13.2    -      -       +      -
    277B  TRP*     3.5    18.5    -      -       +      -
    302B  VAL      4.1     0.9    -      -       -      +
    303B  VAL*     3.5     2.9    -      -       -      +
    304B  SER*     2.7    36.3    +      -       -      +
    321B  CYS*     2.0    49.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 262 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    239B  SER      3.9     0.5    -      -       -      +
    240B  VAL*     3.5     1.4    -      -       -      +
    241B  PHE*     2.7    50.0    +      -       +      +
    243B  PHE*     3.9    20.9    -      -       +      -
    260B  THR*     3.8    20.6    -      -       +      -
    261B  CYS*     1.3    78.8    -      -       -      +
    263B  VAL*     1.3    67.6    +      -       -      +
    264B  VAL*     4.3     5.2    -      -       +      -
    301B  ARG*     3.4    42.2    -      -       +      +
    302B  VAL      3.7     2.2    -      -       -      -
    303B  VAL*     3.8    16.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 263 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    238B  PRO*     4.1    10.1    -      -       +      -
    239B  SER      3.3    10.5    -      -       -      +
    240B  VAL*     4.0    12.8    -      -       +      -
    262B  VAL*     1.3    79.8    -      -       -      +
    264B  VAL*     1.3    68.8    +      -       -      +
    266B  VAL*     3.7    23.1    -      -       +      +
    273B  VAL*     5.4     1.1    -      -       +      -
    275B  PHE*     3.5    31.9    -      -       +      -
    300B  TYR      3.9     0.9    -      -       -      +
    301B  ARG*     3.5     6.9    -      -       -      +
    302B  VAL*     3.1    32.1    +      -       +      +
    323B  VAL*     3.5    27.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 264 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    238B  PRO*     3.3     5.7    -      -       -      +
    239B  SER*     2.8    46.6    +      -       -      +
    241B  PHE*     4.0    24.0    -      -       +      -
    262B  VAL*     4.6     7.2    -      -       +      -
    263B  VAL*     1.3    77.8    -      -       -      +
    265B  ASP*     1.4    70.9    +      -       -      +
    266B  VAL*     3.3     2.5    -      -       -      -
    299B  THR*     5.3     1.8    -      -       -      +
    300B  TYR      3.8     6.1    -      -       -      +
    301B  ARG*     4.0    25.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with ASP 265 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    235B  LEU*     4.0    32.7    -      -       +      +
    237B  GLY      4.1     8.3    -      -       -      +
    238B  PRO*     3.3    25.8    -      -       +      +
    239B  SER*     4.2    13.9    +      -       -      +
    264B  VAL*     1.4    82.9    -      -       -      +
    266B  VAL*     1.4    58.3    +      -       -      +
    267B  SER*     3.9     2.1    +      -       -      -
    299B  THR*     3.8    26.2    +      -       -      +
    300B  TYR      3.9     3.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 266 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    238B  PRO*     3.8    15.0    -      -       +      -
    263B  VAL*     3.7    33.2    -      -       +      +
    264B  VAL      4.0     3.1    -      -       -      +
    265B  ASP*     1.4    75.5    -      -       -      +
    267B  SER*     1.3    63.6    +      -       -      +
    270B  ASP      3.5    21.1    -      -       -      +
    271B  PRO      3.8     7.4    -      -       -      +
    273B  VAL*     3.8    28.5    -      -       +      -
    299B  THR*     3.4     5.2    -      -       -      -
    300B  TYR*     2.8    47.2    +      -       +      +
    302B  VAL*     5.0     3.8    -      -       +      -
    325B  ASN*     4.1     3.4    -      -       -      +
----------------------------------------------------------
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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