Contacts of the strand formed by residues 311 - 318 (chain A) in PDB entry 1HK8


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 311 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     77A  THR*     3.8     5.4    -      -       -      -
     78A  ASN*     2.9    48.4    +      -       -      +
     79A  CYS*     3.2    25.6    +      -       -      +
    288A  MET*     4.0     3.8    -      -       +      -
    292A  SER*     3.9     4.8    +      -       -      -
    310A  ASN*     1.3    75.1    -      -       -      +
    312A  LEU*     1.3    61.6    +      -       -      +
    313A  GLY      2.9    33.9    +      -       -      +
    396A  SER*     2.9    31.8    +      -       -      +
    397A  VAL*     3.6     1.4    +      -       -      -
    398A  SER*     3.0    22.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 312 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     76A  PHE      4.9     2.6    -      -       -      +
     77A  THR*     4.6     9.5    -      -       +      -
     78A  ASN*     4.4     2.7    -      -       -      +
    124A  TYR*     3.6    10.5    +      -       -      -
    310A  ASN*     4.0     6.3    -      -       -      +
    311A  ASN*     1.3    76.3    -      -       -      +
    313A  GLY*     1.3    56.2    +      -       -      +
    355A  ARG*     5.1    10.0    -      -       -      +
    356A  ILE*     4.2    19.0    -      -       +      +
    359A  LEU*     4.2    17.7    -      -       +      +
    390A  PHE*     3.7    28.5    -      -       +      -
    395A  SER*     3.3    29.4    -      -       -      +
    396A  SER      3.0    10.6    +      -       -      +
    397A  VAL*     3.9    26.2    -      -       +      -
    436A  PHE*     4.0    23.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 313 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     78A  ASN*     4.2     2.7    -      -       -      -
    124A  TYR*     3.5    16.2    -      -       -      -
    311A  ASN*     2.9    11.3    +      -       -      +
    312A  LEU*     1.3    82.4    -      -       -      +
    314A  VAL*     1.3    64.6    +      -       -      -
    352A  LEU*     4.1     8.9    -      -       -      +
    355A  ARG*     4.4     5.4    -      -       -      -
    396A  SER      4.9     0.2    +      -       -      -
    397A  VAL*     4.0     0.9    -      -       -      -
    398A  SER*     3.0    29.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 314 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     66A  HIS*     3.2    57.3    +      -       +      +
     67A  ASP*     5.3     1.9    +      -       -      +
     78A  ASN*     3.8    20.6    -      -       -      +
    124A  TYR*     4.7     0.4    +      -       -      -
    313A  GLY*     1.3    79.8    -      -       -      +
    315A  VAL*     1.3    70.1    +      -       -      +
    316A  THR*     3.7     9.4    -      -       -      +
    352A  LEU*     4.1     0.2    -      -       -      -
    355A  ARG*     3.6     8.7    +      -       -      +
    398A  SER*     3.5    16.4    -      -       -      +
    400A  GLY      4.3     1.3    -      -       -      +
    441A  TYR*     3.7    33.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 315 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     63A  ILE*     4.3    13.0    -      -       +      -
     64A  HIS      3.4    10.8    -      -       -      +
     65A  VAL*     4.3    15.9    -      -       +      -
    314A  VAL*     1.3    78.8    -      -       -      +
    316A  THR*     1.3    59.5    +      -       -      +
    348A  CYS*     4.1    25.4    -      -       +      -
    351A  ALA*     4.0    27.1    -      -       +      -
    352A  LEU*     3.5    32.3    -      -       +      +
    355A  ARG*     4.5     3.4    -      -       -      -
    398A  SER      3.1     5.3    +      -       -      -
    399A  LEU*     3.5     9.9    -      -       -      +
    400A  GLY      2.8    25.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with THR 316 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     63A  ILE*     3.2     6.6    -      -       -      +
     64A  HIS*     2.9    36.9    +      -       -      -
     66A  HIS*     2.7    26.6    +      -       -      -
    314A  VAL*     3.7     1.2    -      -       -      +
    315A  VAL*     1.3    74.4    -      -       -      +
    317A  LEU*     1.3    62.8    +      -       -      +
    318A  ASN      3.7     0.3    +      -       -      -
    348A  CYS*     5.0     0.9    -      -       -      -
    400A  GLY*     3.5     5.8    -      -       -      -
    401A  TYR*     3.8    16.2    -      -       -      +
    402A  ILE*     4.3     1.6    -      -       +      -
    443A  THR*     2.6    30.6    +      -       -      +
    448A  LEU*     3.7    21.8    -      -       +      -
    452A  PHE*     3.8    11.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 317 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     62A  ILE      3.7    11.9    -      -       -      +
     63A  ILE*     4.3     2.5    -      -       +      -
    315A  VAL      4.3     0.2    +      -       -      -
    316A  THR*     1.3    72.7    -      -       -      +
    318A  ASN*     1.3    64.3    -      -       -      +
    319A  LEU*     3.1    34.1    +      -       +      +
    322A  ILE*     3.6    25.8    -      -       +      -
    341A  PHE*     4.9     2.9    -      -       +      -
    344A  ARG*     4.1    20.6    -      -       +      +
    345A  MET*     4.1    14.6    -      -       -      -
    348A  CYS*     3.8    24.0    -      -       -      -
    399A  LEU*     4.6     0.7    -      -       +      -
    400A  GLY      2.9    16.4    +      -       -      +
    401A  TYR*     3.5    16.8    -      -       -      -
    402A  ILE*     3.6     5.7    +      -       -      +
    423A  MET*     4.0    17.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 318 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     61A  GLY      2.7    29.8    +      -       -      +
     62A  ILE      3.2    16.1    +      -       -      +
    316A  THR      3.7     2.8    +      -       -      -
    317A  LEU*     1.3    68.0    -      -       -      +
    319A  LEU*     1.3    64.4    +      -       -      +
    320A  PRO*     3.5     2.8    -      -       -      +
    321A  ARG*     3.3    21.1    +      -       +      +
    322A  ILE*     3.3    21.3    +      -       -      +
    344A  ARG*     5.1     0.2    +      -       -      -
    402A  ILE*     4.4     1.5    -      -       -      +
    452A  PHE*     3.5    33.7    -      -       +      -
    456A  ASP*     3.0    27.7    +      -       -      -
    472A  TYR*     3.4    16.3    -      -       -      -
----------------------------------------------------------
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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