Contacts of the strand formed by residues 537 - 546 (chain A) in PDB entry 1HKC


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 537 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    534A  GLY      5.2     1.4    +      -       -      -
    535A  GLY*     3.0     9.7    +      -       -      +
    536A  THR*     1.3    90.1    -      -       -      +
    538A  PHE*     1.3    62.5    +      -       -      +
    539A  ARG*     5.3     1.7    -      -       -      +
    559A  ILE*     4.1    17.7    -      -       +      +
    560A  TYR      3.2     6.8    -      -       -      +
    561A  ALA*     3.7    18.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 538 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    531A  LEU*     4.1    29.6    -      -       +      -
    532A  ASP      3.0    19.7    -      -       -      +
    533A  LEU*     3.6    25.6    -      -       +      +
    534A  GLY      5.1     0.2    -      -       -      +
    535A  GLY      4.3     0.7    -      -       -      +
    537A  ASN*     1.3    75.7    -      -       -      +
    539A  ARG*     1.3    66.7    +      -       -      +
    540A  VAL*     4.3     6.5    -      -       +      -
    559A  ILE*     3.6     2.5    -      -       -      +
    560A  TYR*     2.8    53.8    +      -       +      +
    561A  ALA      4.1     1.6    -      -       -      -
    562A  ILE*     3.6    32.3    -      -       +      -
    577A  HIS*     4.4     1.3    -      -       -      -
    578A  ILE*     4.1    18.2    -      -       +      -
    581A  CYS*     3.4    39.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 539 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    531A  LEU*     3.6     4.0    -      -       -      +
    532A  ASP*     2.8    50.0    +      -       +      +
    537A  ASN      5.3     1.3    -      -       -      +
    538A  PHE*     1.3    81.2    -      -       -      +
    540A  VAL*     1.3    68.2    +      -       -      +
    541A  LEU*     3.6    24.5    -      -       +      +
    557A  ASN*     3.9    20.4    +      -       -      +
    558A  LYS      3.2    20.4    -      -       -      +
    559A  ILE*     4.1    17.0    -      -       +      -
    560A  TYR      4.6     0.7    -      -       -      +
    895A  ASP*     2.5    33.1    +      -       -      -
    897A  SER*     3.1    20.4    +      -       -      -
    898A  GLY*     3.7     7.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 540 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    529A  LEU*     4.5     6.7    -      -       +      -
    530A  ALA      3.4    10.8    -      -       -      +
    531A  LEU*     4.0    17.7    -      -       +      +
    538A  PHE*     4.3     5.8    -      -       +      -
    539A  ARG*     1.3    77.9    -      -       -      +
    541A  LEU*     1.3    67.6    +      -       -      +
    557A  ASN*     3.3    19.6    -      -       -      +
    558A  LYS      3.2    13.1    +      -       -      -
    560A  TYR*     3.9    22.4    -      -       +      -
    582A  ILE*     4.2    33.2    -      -       +      +
    585A  PHE*     3.5    33.4    -      -       +      -
    598A  LEU*     6.0     1.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 541 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    529A  LEU*     3.1    12.6    -      -       -      +
    530A  ALA*     2.9    49.9    +      -       +      +
    532A  ASP*     4.3     6.7    -      -       +      -
    539A  ARG*     3.6    45.8    -      -       -      +
    540A  VAL*     1.3    78.6    -      -       -      +
    542A  LEU*     1.3    60.8    +      -       -      +
    543A  VAL*     4.1     6.7    -      -       +      -
    555A  MET*     4.6    10.1    -      -       -      -
    556A  HIS      3.4     8.5    -      -       -      +
    557A  ASN*     3.4    21.5    -      -       +      +
    585A  PHE*     3.6     6.5    -      -       -      -
    895A  ASP*     4.3     5.2    -      -       -      +
    898A  GLY*     3.7    24.9    -      -       -      -
    899A  LYS      4.5     0.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 542 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    527A  ASP*     4.5     7.9    -      -       +      -
    528A  PHE      3.4    14.6    -      -       -      +
    529A  LEU*     4.5     2.0    -      -       +      -
    541A  LEU*     1.3    74.1    -      -       -      +
    543A  VAL*     1.3    62.8    +      -       -      +
    544A  LYS*     3.8    34.3    -      -       +      +
    555A  MET*     3.1     6.9    -      -       -      +
    556A  HIS*     3.0    34.2    +      -       -      +
    585A  PHE*     3.7    16.9    -      -       +      -
    589A  MET*     4.4    19.3    -      -       +      -
    591A  ILE*     3.9    19.5    -      -       +      -
    596A  MET*     3.4    33.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 543 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    526A  GLY      3.6     1.4    -      -       -      +
    527A  ASP*     3.5     1.1    -      -       -      -
    528A  PHE*     2.7    41.7    +      -       +      +
    530A  ALA*     5.2     2.2    -      -       +      -
    541A  LEU*     4.6    13.5    -      -       +      +
    542A  LEU*     1.3    79.5    -      -       -      +
    544A  LYS*     1.3    62.9    +      -       -      +
    545A  ILE*     3.7    13.6    +      -       +      -
    553A  VAL*     3.8    25.6    -      -       +      -
    554A  GLU      3.7     2.7    -      -       -      +
    555A  MET*     3.9    22.0    -      -       +      -
    898A  GLY      4.9     1.1    -      -       -      +
    899A  LYS*     4.8    10.1    -      -       +      +
    902A  ALA*     3.7    31.0    -      -       +      -
    903A  LEU*     6.4     0.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 544 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    526A  GLY      3.5     4.0    -      -       -      -
    527A  ASP*     3.4    29.2    -      -       -      +
    542A  LEU*     3.8    28.9    -      -       +      +
    543A  VAL*     1.3    73.4    -      -       -      +
    545A  ILE*     1.3    61.1    +      -       -      +
    546A  ARG*     4.0    13.1    +      -       +      +
    552A  THR      4.1     0.5    -      -       -      +
    553A  VAL*     3.3     6.8    -      -       -      +
    554A  GLU*     2.8    69.4    +      -       +      +
    556A  HIS*     4.4     8.2    -      -       +      -
    591A  ILE*     6.2     2.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 545 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    524A  GLU*     3.2    27.1    -      -       +      +
    525A  ASN*     3.1     1.2    -      -       -      -
    526A  GLY      2.5    46.9    +      -       -      +
    528A  PHE*     3.9    22.2    -      -       +      -
    543A  VAL*     4.0    19.3    -      -       +      -
    544A  LYS*     1.3    76.4    -      -       -      +
    546A  ARG*     1.3    71.4    +      -       -      +
    552A  THR      4.1     2.7    -      -       -      +
    553A  VAL*     4.5     7.2    -      -       +      -
    667A  TYR*     3.5    22.9    -      -       +      +
    902A  ALA      4.7     4.3    -      -       -      +
    903A  LEU*     3.6    29.2    -      -       +      -
    906A  ALA*     4.1     8.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 546 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    524A  GLU      4.2     1.3    -      -       -      -
    525A  ASN*     3.2    17.6    -      -       -      +
    526A  GLY*     2.8    36.3    +      -       -      +
    527A  ASP*     2.6    28.8    +      -       -      -
    544A  LYS*     3.8    14.6    +      -       +      +
    545A  ILE*     1.3    95.3    +      -       -      +
    547A  SER*     1.3    57.2    -      -       -      +
    548A  GLY*     2.9    14.7    +      -       -      +
    550A  LYS      4.2     0.2    -      -       -      +
    551A  ARG*     4.3     1.9    -      -       -      -
    552A  THR*     3.1    49.3    +      -       +      +
    667A  TYR*     4.6     2.3    +      -       -      -
----------------------------------------------------------
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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