Contacts of the strand formed by residues 61 - 69 (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 TYR 61 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     35B  TYR*     3.8     7.6    -      -       -      -
     37B  PHE*     4.4    12.1    -      +       -      -
     38B  LYS*     3.8    24.8    +      -       +      -
     39B  PHE*     5.0     1.2    -      -       -      -
     57B  VAL*     3.3     6.7    -      -       -      +
     58B  ALA      2.9    32.1    +      -       -      +
     59B  ASN      4.2     3.6    -      -       -      +
     60B  ASP*     1.3    78.8    -      -       -      +
     62B  PRO*     1.3    87.3    -      -       +      +
     63B  LEU*     3.3    18.0    +      -       +      +
    100B  PHE*     3.8    27.8    -      +       -      -
    101B  GLU*     3.6    21.1    -      -       +      +
    104B  PRO*     3.5    25.5    -      -       +      +
    130B  PHE*     3.7    18.2    -      +       +      -
    309B  LEU*     4.3     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with PRO 62 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29B  ILE*     3.9    24.2    -      -       +      -
     31B  THR*     3.8    13.9    -      -       -      +
     35B  TYR*     3.4    19.7    -      -       +      +
     37B  PHE*     3.9    17.7    -      -       +      -
     56B  ILE      3.9     3.8    -      -       -      +
     57B  VAL*     4.5     0.7    -      -       +      -
     61B  TYR*     1.3   105.0    -      -       +      +
     63B  LEU*     1.3    59.0    +      -       -      +
     64B  TYR*     3.3    29.0    +      -       +      -
    100B  PHE      4.9     0.9    -      -       -      +
    104B  PRO*     4.6     4.2    -      -       +      +
    309B  LEU*     4.1     9.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 63 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29B  ILE*     4.6     0.4    -      -       -      +
     55B  GLY*     3.3     2.8    -      -       -      -
     56B  ILE*     2.8    49.4    +      -       +      +
     58B  ALA*     3.9    17.5    -      -       +      -
     61B  TYR*     3.7    25.8    -      -       +      +
     62B  PRO*     1.3    69.8    -      -       -      +
     64B  TYR*     1.3    64.6    +      -       -      +
     65B  PHE*     3.6     4.2    +      -       -      -
    100B  PHE*     3.8    29.4    -      -       +      +
    130B  PHE*     3.8    18.4    -      -       +      -
    134B  LEU*     3.8    29.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 64 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29B  ILE*     2.8    43.5    +      -       +      +
     31B  THR*     2.8    34.5    +      -       -      -
     51B  LEU*     3.7    32.7    -      -       +      +
     53B  GLY*     3.5    15.5    -      -       -      -
     54B  VAL      3.6    11.0    -      -       -      -
     55B  GLY      4.6     0.2    -      -       -      -
     62B  PRO*     3.3    22.1    +      -       +      -
     63B  LEU*     1.3    74.1    -      -       -      +
     65B  PHE*     1.3    62.5    +      -       -      +
     66B  ASP      3.4    20.2    -      -       -      +
     67B  ALA*     3.8     4.0    -      -       +      -
     77B  GLY*     6.0     0.2    -      -       -      -
    100B  PHE      5.5     2.0    +      -       -      -
    103B  ILE*     3.5    34.2    -      -       +      +
    104B  PRO*     4.9     6.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 65 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16B  ARG*     3.0    17.1    +      -       -      +
     18B  LEU*     4.1    29.2    -      -       +      -
     20B  LEU*     5.1     9.4    -      -       +      -
     25B  GLY      5.7     0.2    -      -       -      -
     26B  GLU*     3.9    20.4    -      -       +      -
     54B  VAL      2.8     6.8    +      -       -      +
     55B  GLY*     3.6    30.1    -      -       -      -
     56B  ILE*     4.5    15.9    -      -       +      -
     63B  LEU      3.6     3.5    +      -       -      -
     64B  TYR*     1.3    75.2    -      -       -      +
     66B  ASP*     1.3    59.9    +      -       -      +
     77B  GLY*     3.0    31.1    +      -       -      +
    103B  ILE*     4.2     1.6    -      -       -      -
    274B  TYR*     3.4    26.9    -      +       -      +
----------------------------------------------------------
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Residues in contact with ASP 66 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     14B  PHE*     4.9     2.2    -      -       +      -
     16B  ARG*     2.9    26.3    +      -       +      -
     53B  GLY*     3.3     0.2    -      -       -      -
     54B  VAL*     3.0    30.1    +      -       -      +
     64B  TYR*     3.4     4.9    -      -       -      -
     65B  PHE*     1.3    76.8    -      -       -      +
     67B  ALA*     1.3    65.5    +      -       -      +
     75B  MET      3.2    13.0    -      -       -      +
     76B  ALA*     3.8    14.4    -      -       +      +
    103B  ILE*     4.3     2.2    -      -       -      -
    274B  TYR*     2.7    24.9    +      -       -      -
    276B  ASN*     2.9    17.5    +      -       -      -
    278B  TYR*     2.6    31.0    +      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 67 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     14B  PHE*     3.9     1.6    -      -       -      -
     51B  LEU*     4.7     2.5    -      -       +      -
     52B  ILE      3.4    14.1    -      -       -      +
     53B  GLY*     3.9     0.2    -      -       -      -
     64B  TYR*     3.8    26.2    -      -       +      -
     66B  ASP*     1.3    78.1    -      -       -      +
     68B  ILE*     1.3    68.1    +      -       -      +
     74B  GLY*     3.4     2.6    -      -       -      -
     75B  MET      3.0    30.9    +      -       -      +
    103B  ILE*     4.2     5.1    -      -       +      +
    107B  LEU*     3.4    18.0    -      -       +      +
    278B  TYR*     3.6     6.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 68 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     14B  PHE*     4.0     3.8    -      -       +      -
     51B  LEU*     3.2     5.9    -      -       -      +
     52B  ILE*     2.8    51.9    +      -       +      +
     67B  ALA*     1.3    78.2    -      -       -      +
     69B  ASN*     1.3    69.9    +      -       -      +
     72B  GLY*     5.0     0.4    -      -       -      -
     73B  LEU      3.1    10.8    -      -       -      +
     74B  GLY*     3.8     7.6    -      -       -      -
    107B  LEU*     4.0     4.5    -      -       -      -
    278B  TYR*     3.5    38.6    -      -       +      -
    279B  ASP      4.4     3.4    -      -       -      +
    280B  LEU*     3.6    25.4    -      -       +      -
    283B  LYS*     3.8    34.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 69 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     49B  LYS*     3.7     9.9    -      -       +      +
     50B  SER      3.1    13.7    -      -       -      +
     51B  LEU*     3.6     6.1    -      -       +      -
     68B  ILE*     1.3    83.6    -      -       -      +
     70B  GLU*     1.3    61.1    +      -       -      +
     71B  ASP*     2.9    17.4    +      -       -      +
     72B  GLY*     3.0    18.2    +      -       -      -
     73B  LEU*     2.9    36.2    +      -       -      +
    107B  LEU*     2.8    29.2    +      -       +      +
    110B  CYS      2.8    28.9    +      -       -      -
    283B  LYS*     4.1     2.3    -      -       -      +
    300B  LEU*     4.1     4.1    -      -       -      +
----------------------------------------------------------
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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