Contacts of the strand formed by residues 71 - 75 (chain D) in PDB entry 5HP1


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 TRP 71 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29D  GLU*     3.6    55.1    +      -       +      +
     30D  LYS*     4.3    13.5    -      -       +      -
     33D  ALA*     3.3    30.4    -      -       +      +
     37D  ILE*     3.8    17.7    -      -       +      +
     62D  ALA*     3.9    23.6    -      -       +      -
     63D  ILE*     3.5    33.4    -      -       -      -
     64D  LYS*     3.3    38.0    -      -       +      +
     69D  THR      5.0     1.8    -      -       -      -
     70D  LYS*     1.3    81.1    +      -       -      +
     72D  ARG*     1.3    59.9    +      -       -      +
    226D  PRO*     3.9     8.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 72 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37D  ILE*     4.6     1.1    -      -       -      -
     62D  ALA*     3.4     4.3    -      -       -      -
     63D  ILE*     2.7    51.0    +      -       +      +
     64D  LYS*     5.4     0.2    -      -       -      -
     65D  LYS*     4.9     7.6    -      -       +      +
     70D  LYS      4.6     0.4    -      -       -      +
     71D  TRP*     1.3    76.7    -      -       -      +
     73D  LYS*     1.3    92.9    +      -       -      +
     74D  LEU*     4.4    10.1    -      -       -      +
    110D  ASP*     3.2    31.3    +      -       -      -
    151D  GLN*     3.3    37.9    +      -       -      +
    185D  ASP*     3.7    12.9    +      -       -      +
    226D  PRO*     3.4    38.1    -      -       +      +
    409D  THR*     3.4    33.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 73 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     34D  LEU*     3.7    28.7    -      -       +      -
     37D  ILE*     4.2    29.2    -      -       +      +
     38D  CYS*     4.3     7.2    -      -       -      -
     41D  MET*     4.2    13.5    -      -       -      -
     60D  VAL*     3.3    22.5    -      -       +      +
     61D  PHE      3.8     4.7    -      -       -      -
     72D  ARG*     1.3    98.3    +      -       -      +
     74D  LEU*     1.3    63.3    +      -       -      +
     75D  VAL*     3.4    11.0    -      -       +      +
    130D  PHE*     3.4    28.9    -      -       -      -
    146D  TYR*     3.0    29.6    +      -       -      -
    151D  GLN*     4.1     9.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 74 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     60D  VAL*     3.6     1.6    -      -       -      +
     61D  PHE*     3.1    61.7    +      -       +      +
     63D  ILE*     4.6    12.8    -      -       +      -
     72D  ARG*     3.6    12.1    +      -       -      +
     73D  LYS*     1.3    76.2    -      -       -      +
     75D  VAL*     1.3    80.9    +      -       -      +
    151D  GLN      5.9     0.7    -      -       -      +
    152D  GLY*     5.4     4.0    -      -       -      -
    406D  TRP*     3.7    20.0    -      -       +      +
    408D  ALA      3.1    25.6    -      -       -      +
    409D  THR*     3.2    28.9    -      -       -      +
    411D  ILE*     4.4     9.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 75 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     58D  THR*     3.5    23.1    -      -       +      +
     59D  PRO      3.7     7.0    -      -       -      +
     60D  VAL*     4.0     4.9    -      -       +      -
     73D  LYS*     3.4    31.4    -      -       +      +
     74D  LEU*     1.3    89.7    -      -       -      +
     76D  ASP*     1.3    62.8    +      -       -      +
     77D  PHE*     3.0    50.9    +      -       +      +
    130D  PHE*     5.2     4.9    -      -       +      -
    146D  TYR*     3.9    13.2    -      -       +      +
    151D  GLN      4.5     6.2    +      -       -      +
    152D  GLY*     4.8     4.9    -      -       -      +
    411D  ILE*     4.6     1.7    -      -       -      +
----------------------------------------------------------
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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