Contacts of the strand formed by residues 82 - 87 (chain B) in PDB entry 3KDH


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 82 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     72B  LEU*     3.5     5.9    -      -       -      -
     73B  ILE*     2.8    47.3    +      -       +      -
     74B  SER*     2.9    29.4    +      -       -      +
     80B  GLY      3.7     7.9    -      -       -      +
     81B  SER*     1.3    78.1    -      -       -      +
     83B  ARG*     1.3    61.7    +      -       -      +
     97B  THR*     3.8    20.2    -      -       -      -
     98B  GLU      3.3    10.1    -      -       -      +
     99B  ARG*     4.0    19.7    -      -       +      +
    115B  VAL*     4.4     6.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 83 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     54B  ILE      5.6     2.0    +      -       -      -
     56B  ARG      5.0     0.2    +      -       -      -
     57B  PHE*     2.9    63.7    +      -       +      +
     60B  PRO*     4.0    18.2    -      -       -      +
     64B  LYS*     3.5    20.4    -      -       -      +
     70B  CYS*     3.8    19.1    -      -       -      -
     71B  ARG      3.3    10.1    -      -       -      +
     72B  LEU*     4.1     9.4    -      -       +      +
     73B  ILE*     4.8     0.7    -      -       -      -
     82B  VAL*     1.3    77.4    -      -       -      +
     84B  GLU*     1.3    59.0    +      -       -      +
     85B  VAL*     3.9    10.8    +      -       +      +
     96B  SER      3.7     0.5    -      -       -      +
     97B  THR*     3.2     5.6    -      -       -      -
     98B  GLU*     2.8    67.4    +      -       +      +
    110B  LEU*     5.7     0.6    -      -       -      +
    112B  PHE*     3.7    22.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 84 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     69B  ARG*     3.9     0.9    -      -       -      +
     70B  CYS*     3.3     4.3    -      -       -      -
     71B  ARG*     2.8    59.8    +      -       +      +
     73B  ILE*     3.6    29.7    -      -       +      +
     82B  VAL      4.3     0.4    +      -       -      -
     83B  ARG*     1.3    72.1    -      -       -      +
     85B  VAL*     1.3    59.7    +      -       -      +
     86B  THR*     4.0     4.8    +      -       -      +
     95B  THR*     3.1    37.5    +      -       +      +
     96B  SER      3.5     3.6    -      -       -      +
     97B  THR*     4.1    13.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 85 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     60B  PRO*     4.6     5.8    -      -       +      -
     67B  VAL*     4.1    22.2    -      -       +      -
     69B  ARG      3.5     8.7    -      -       -      +
     70B  CYS*     3.9    17.7    -      -       +      -
     83B  ARG*     3.9    11.7    -      -       +      +
     84B  GLU*     1.3    75.6    -      -       -      +
     86B  THR*     1.3    62.8    +      -       -      +
     87B  VAL*     3.7    21.3    +      -       +      +
     95B  THR*     3.4     3.4    -      -       -      -
     96B  SER*     2.8    44.6    +      -       -      +
     98B  GLU*     3.8    27.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with THR 86 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     67B  VAL*     3.6     4.7    -      -       -      +
     68B  LYS*     2.7    55.3    +      -       +      +
     69B  ARG*     2.8    37.1    +      -       +      +
     84B  GLU*     5.1     4.7    +      -       -      +
     85B  VAL*     1.3    71.9    -      -       -      +
     87B  VAL*     1.3    56.9    +      -       -      +
     93B  ALA*     4.1    14.6    -      -       +      -
     94B  SER      3.3    10.5    -      -       -      +
     95B  THR*     3.7    15.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 87 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     66B  PHE*     3.4    15.7    -      -       +      +
     67B  VAL*     5.3     2.2    -      -       +      -
     85B  VAL*     3.9    23.3    -      -       +      +
     86B  THR*     1.3    78.2    -      -       -      +
     88B  ILE*     1.3    79.2    +      -       -      +
     89B  SER*     4.2     5.6    +      -       -      -
     92B  PRO      4.8     0.2    -      -       -      +
     93B  ALA*     3.5     8.3    -      -       -      +
     94B  SER*     2.8    42.3    +      -       -      +
     96B  SER*     5.0     7.0    -      -       -      +
----------------------------------------------------------
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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