Contacts of the strand formed by residues 75 - 79 (chain A) in PDB entry 6HBU


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 LEU 75 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     74A  GLY*     1.3    71.9    -      -       -      -
     76A  ASN*     1.3    61.7    +      -       -      +
     77A  ALA      3.8     2.1    +      -       -      -
    225A  LEU*     4.4    15.0    -      -       +      +
    228A  LEU*     4.0    20.6    -      -       +      +
    229A  LYS*     4.0    16.6    -      -       +      -
    232A  SER*     4.4     4.7    -      -       -      +
    238A  ILE*     3.8    25.6    -      -       +      -
    240A  PHE*     3.6    24.5    -      -       +      -
    252A  LEU*     3.4    38.6    -      -       +      +
    253A  PHE*     3.8     4.9    -      -       +      +
    254A  ASP*     2.8    43.9    +      -       -      +
    255A  SER      3.4     3.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with ASN 76 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     71A  MET*     3.6    29.4    -      -       +      +
     72A  LYS*     3.1    30.0    +      -       -      +
     74A  GLY      4.6     0.6    +      -       -      -
     75A  LEU*     1.3    75.7    +      -       -      +
     77A  ALA*     1.3    61.0    +      -       -      +
     78A  ILE*     5.3     0.4    -      -       -      -
    237A  THR*     3.2    16.8    +      -       -      -
    238A  ILE      2.7    17.8    +      -       -      +
    239A  ILE*     3.4    14.0    -      -       +      +
    240A  PHE*     2.9    29.8    +      -       -      +
    254A  ASP*     4.8     2.1    -      -       -      +
    255A  SER*     3.2    27.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 77 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     75A  LEU      3.8     1.0    +      -       -      -
     76A  ASN*     1.3    74.6    -      -       -      +
     78A  ILE*     1.3    61.5    +      -       -      +
     79A  LEU*     4.1     8.1    -      -       +      -
    240A  PHE*     3.3    16.8    -      -       +      -
    253A  PHE*     3.6    46.4    -      -       +      -
    255A  SER      3.0    11.1    +      -       -      +
    256A  LEU*     4.4     1.8    -      -       +      -
    257A  THR*     3.0    28.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 78 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     71A  MET*     4.4     9.2    -      -       +      -
     77A  ALA*     1.3    78.0    -      -       -      +
     79A  LEU*     1.3    62.5    +      -       -      +
     86A  LYS*     3.7    28.8    -      -       +      +
     89A  LEU*     4.3    18.2    -      -       +      -
     90A  LEU*     4.0    15.5    -      -       +      -
     93A  LEU*     5.5     0.7    -      -       +      -
    239A  ILE*     3.9    25.1    -      -       +      -
    240A  PHE      2.7    18.1    +      -       -      +
    241A  SER*     3.3     7.1    -      -       -      +
    242A  ILE      3.1    24.1    +      -       -      +
    257A  THR*     3.3    15.5    -      -       +      +
    259A  LEU*     3.9    26.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 79 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     77A  ALA*     4.1     1.6    -      -       +      -
     78A  ILE*     1.3    77.6    -      -       -      +
     80A  GLY*     1.3    59.0    +      -       -      +
     86A  LYS*     3.8     6.2    -      -       -      +
    242A  ILE*     3.3    38.4    -      -       +      +
    243A  HIS*     4.9     0.2    -      -       -      -
    244A  GLN      4.9     2.0    -      -       -      +
    245A  PRO*     3.8    25.1    -      -       +      -
    250A  PHE*     5.3     1.8    -      -       +      -
    253A  PHE*     3.9    14.1    -      -       +      -
    256A  LEU*     3.7    23.6    -      -       +      -
    257A  THR      2.7     9.6    +      -       -      +
    258A  LEU*     3.4    21.6    -      -       +      -
    259A  LEU*     3.0    24.4    +      -       -      +
    291A  ALA*     5.0     6.1    -      -       +      +
    294A  PHE*     6.2     1.8    -      -       +      -
    295A  LEU*     3.7    23.8    -      -       +      -
    218B  SER*     6.2     0.2    -      -       -      +
----------------------------------------------------------
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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