Contacts of the strand formed by residues 12 - 20 (chain B) in PDB entry 5HKE


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 ASN 12 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7B  LEU      3.6     2.9    -      -       -      -
      8B  ASN*     2.7    32.9    +      -       -      +
      9B  GLY      4.5     1.4    +      -       -      +
     11B  SER*     1.3    84.3    +      -       -      +
     13B  TYR*     1.3    56.8    +      -       -      +
    146B  ARG*     3.3    51.2    +      -       +      +
    279B  ASP*     3.7     4.0    -      -       -      +
    280B  LEU*     2.8    36.5    +      -       +      +
    281B  ASP*     3.2    23.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 13 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6B  THR*     3.2     8.5    -      -       -      +
      7B  LEU*     2.8    53.3    +      -       +      +
      8B  ASN*     5.5     0.3    +      -       -      -
      9B  GLY*     4.2     3.1    -      -       -      -
     11B  SER*     3.1    43.0    +      -       -      -
     12B  ASN*     1.3    76.8    -      -       -      +
     14B  PHE*     1.3    64.4    +      -       -      +
    241B  VAL*     3.6    11.4    -      -       +      +
    244B  ASP*     2.7    43.3    +      -       +      +
    245B  ILE*     4.1    17.3    -      -       +      -
    248B  PHE*     3.7    20.6    -      +       +      -
    277B  CYS*     3.9    14.8    -      -       -      -
    278B  TYR      3.1     7.0    -      -       -      +
    279B  ASP*     3.9    22.0    -      -       +      -
    280B  LEU*     4.4     4.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 14 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4B  ALA*     5.2     0.4    -      -       +      -
      5B  ILE      3.5    12.6    -      -       -      -
      6B  THR*     4.3     0.9    -      -       +      -
     13B  TYR*     1.3    78.4    -      -       -      +
     15B  GLY*     1.3    64.5    +      -       -      +
     66B  ASP*     4.9     2.0    -      -       +      -
     67B  ALA      3.9     8.1    -      -       -      -
     68B  ILE*     4.0     9.6    -      -       +      -
     74B  GLY*     3.8     6.1    -      -       -      -
     75B  MET      3.6    40.2    -      -       -      -
     76B  ALA*     3.7    13.2    -      -       +      -
    142B  LEU*     4.1    30.1    -      -       +      -
    144B  ALA*     3.8    24.0    -      -       +      -
    248B  PHE*     3.7     4.0    -      -       -      -
    278B  TYR*     2.7    60.3    +      +       -      -
    280B  LEU*     4.0    19.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 15 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4B  ALA*     3.3     3.5    -      -       -      +
      5B  ILE*     2.9    32.8    +      -       -      +
     14B  PHE*     1.3    84.2    -      -       -      +
     16B  ARG*     1.3    65.7    +      -       -      +
    248B  PHE*     3.5     8.2    -      -       -      -
    252B  LEU*     4.7     0.4    -      -       -      -
    276B  ASN*     3.3    22.2    -      -       -      -
    278B  TYR*     4.4     2.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 16 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      2B  OCS      3.1    28.7    +      -       -      +
      3B  THR      3.1    14.4    -      -       -      +
      4B  ALA*     3.9    11.9    -      -       +      -
     14B  PHE*     6.2     0.4    -      -       +      -
     15B  GLY*     1.3    75.7    -      -       -      +
     17B  ASN*     1.3    79.3    +      -       -      +
     18B  LEU*     3.5    16.3    -      -       -      +
     65B  PHE*     3.0    25.7    +      -       -      +
     66B  ASP*     2.9    41.3    +      -       +      +
     76B  ALA*     4.1     6.3    -      -       +      +
     77B  GLY      2.8    22.0    +      -       -      -
     78B  LEU*     3.7    10.6    -      -       -      +
    252B  LEU*     3.9     9.6    -      -       -      +
    274B  TYR*     3.8    10.2    -      -       -      +
    275B  SER*     3.3     2.8    -      -       -      -
    276B  ASN*     2.8    43.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASN 17 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      2B  OCS      3.5     4.2    +      -       -      -
      3B  THR*     2.8    31.0    +      -       -      +
     16B  ARG*     1.3    82.4    +      -       -      +
     18B  LEU*     1.3    59.7    +      -       -      +
     19B  ASP*     3.6    15.5    +      -       -      +
    252B  LEU*     3.0    39.3    +      -       -      +
    255B  VAL*     3.8    25.1    +      -       -      +
    256B  GLU*     4.0     5.8    -      -       -      +
    272B  THR*     3.8     6.9    +      -       +      -
    274B  TYR      3.4     3.4    -      -       -      -
    275B  SER*     2.7    31.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 18 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      2B  OCS      3.3    17.3    -      -       -      +
     16B  ARG*     3.5    21.4    -      -       -      +
     17B  ASN*     1.3    72.6    -      -       -      +
     19B  ASP*     1.3    55.5    +      -       -      +
     20B  LEU*     3.9    32.8    -      -       +      -
     26B  GLU*     4.8     2.0    -      -       -      +
     65B  PHE*     4.1    31.0    -      -       +      -
     77B  GLY      5.5     0.4    -      -       -      +
    272B  THR*     3.5     1.2    -      -       -      -
    273B  VAL*     2.8    42.9    +      -       +      +
    274B  TYR*     2.9    51.3    +      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 19 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      2B  OCS      2.8    48.5    +      -       -      +
      3B  THR*     4.3     0.9    +      -       -      -
     17B  ASN*     3.6     9.0    -      -       -      +
     18B  LEU*     1.3    73.1    -      -       -      +
     20B  LEU*     1.3    71.6    +      -       -      +
     79B  ASN*     4.3     2.3    +      -       -      -
    224B  ARG*     4.0     5.7    +      -       -      -
    255B  VAL      4.6     2.3    -      -       -      +
    257B  GLN*     3.0    36.9    +      -       -      +
    270B  GLU*     3.7    12.6    -      -       +      +
    271B  TYR      3.3     6.1    -      -       -      +
    272B  THR*     2.6    32.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 20 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     18B  LEU*     3.9    36.0    +      -       +      -
     19B  ASP*     1.3    81.1    -      -       -      +
     21B  ASP*     1.3    61.8    +      -       -      +
     22B  PHE*     3.3    46.8    +      -       +      +
     23B  SER*     5.5     1.8    -      -       -      -
     26B  GLU*     6.0     0.7    -      -       -      +
     65B  PHE*     5.1    10.1    -      -       +      -
     79B  ASN*     3.9    19.7    -      -       -      +
    270B  GLU*     4.0     8.9    -      -       -      +
    271B  TYR*     2.9    35.3    +      -       -      +
    273B  VAL*     4.1     5.4    -      -       +      +
----------------------------------------------------------
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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