Contacts of the strand formed by residues 71 - 76 (chain B) in PDB entry 5HAN


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 71 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6B  ARG      3.4    26.2    -      -       -      +
      7B  TYR*     3.4     8.5    -      -       -      +
      8B  ALA      4.5     4.0    -      -       -      +
      9B  ASN*     4.6    10.8    -      -       +      +
     12B  LEU*     3.8    30.7    -      -       +      -
     23B  HIS*     5.7     7.2    -      -       +      +
     69B  ASP*     3.8    18.6    -      -       +      +
     70B  ALA*     1.3    82.0    -      -       -      +
     72B  VAL*     1.4    65.3    +      -       -      +
     73B  TYR*     3.2     4.2    +      -       -      -
     84B  ILE*     4.1     4.2    -      -       -      +
     85B  ALA*     2.9    40.6    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 72 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7B  TYR      2.8    19.1    +      -       -      +
      8B  ALA*     3.5     6.8    -      -       +      -
      9B  ASN      2.8    26.7    +      -       -      -
     10B  LEU*     3.8     4.3    -      -       +      +
     40B  ILE*     4.1    10.1    -      -       +      -
     43B  ALA*     3.2    40.4    -      -       +      +
     44B  ALA*     3.9     2.9    -      -       -      +
     47B  ALA*     4.0     8.1    -      -       +      -
     70B  ALA      4.4     0.2    -      -       -      -
     71B  LEU*     1.4    68.9    -      -       -      +
     73B  TYR*     1.3    59.0    +      -       -      +
     74B  GLU      4.1     1.6    -      -       -      +
     75B  VAL*     3.5    32.1    -      -       +      -
     82B  MET*     4.7     2.9    -      -       +      -
     83B  LYS      3.6    11.9    -      -       -      +
     84B  ILE*     4.1     8.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 73 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      9B  ASN      3.4    13.7    -      -       -      +
     10B  LEU*     3.5    25.8    -      -       -      +
     12B  LEU*     3.9    25.6    -      -       +      +
     14B  GLU*     2.9    50.8    +      -       +      -
     17B  LEU*     3.7    12.1    -      -       +      -
     25B  LEU*     3.6    31.2    -      -       +      +
     26B  CYS      5.1     0.9    +      -       -      -
     71B  LEU      3.2     2.1    +      -       -      +
     72B  VAL*     1.3    72.9    -      -       -      +
     74B  GLU*     1.3    70.8    +      -       +      +
     83B  LYS*     3.0    39.5    +      -       +      +
     84B  ILE      3.6    16.8    -      -       -      -
     85B  ALA*     3.6    20.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 74 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10B  LEU*     3.7     4.0    -      -       -      +
     14B  GLU*     3.9    14.0    +      -       -      +
     72B  VAL      3.7     1.2    -      -       -      -
     73B  TYR*     1.3    96.3    -      -       +      +
     75B  VAL*     1.3    75.2    +      -       -      +
     76B  ASP*     6.3     0.2    -      -       +      -
     81B  LEU*     4.5    10.5    -      -       +      +
     82B  MET      3.7     0.2    -      -       -      -
     83B  LYS*     2.8    69.2    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 75 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10B  LEU*     3.9    25.7    -      -       +      +
     39B  PHE*     3.9    26.0    -      -       +      -
     40B  ILE*     4.0    15.0    -      -       +      -
     43B  ALA*     4.6     3.1    -      -       +      -
     72B  VAL*     3.5    23.3    -      -       +      -
     74B  GLU*     1.3    87.0    -      -       -      +
     76B  ASP*     1.3    62.1    +      -       -      +
     77B  GLU*     5.3     1.6    -      -       +      +
     81B  LEU*     3.3     7.6    -      -       -      +
     82B  MET*     4.5     3.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with ASP 76 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     74B  GLU*     6.3     0.2    -      -       +      -
     75B  VAL*     1.3    74.3    -      -       -      +
     77B  GLU*     1.3    63.2    +      -       -      +
     78B  ALA*     3.5    17.8    +      -       -      +
     79B  ASN*     2.9    33.6    +      -       -      +
     80B  SER      3.0     4.5    +      -       -      -
     81B  LEU*     2.9    50.2    +      -       +      +
----------------------------------------------------------
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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