Contacts of the strand formed by residues 65 - 70 (chain B) in PDB entry 1H8O


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 PHE 65 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     40B  GLN*     4.1    10.5    -      -       -      -
     50B  LEU*     3.5    26.9    -      -       +      -
     51B  ILE*     4.4     9.9    -      -       +      +
     57B  ARG*     2.7    34.0    +      -       -      -
     61B  VAL*     3.6    31.6    -      -       +      -
     62B  PRO*     3.6    27.3    +      -       +      -
     63B  ASP      3.4     1.1    -      -       -      +
     64B  ARG*     1.3    88.6    -      -       +      +
     66B  THR*     1.3    51.8    +      -       -      +
     76B  LEU*     4.2     9.6    -      -       +      -
     77B  THR      3.5     4.3    -      -       -      -
     78B  ILE*     3.4    33.7    -      -       +      +
     85B  ASP*     4.1    17.3    -      -       -      -
     89B  TYR*     3.5    17.7    -      +       -      -
----------------------------------------------------------
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Residues in contact with THR 66 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     51B  ILE*     3.9     2.7    -      -       -      +
     57B  ARG*     4.2     8.4    +      -       -      +
     63B  ASP      3.9     6.8    +      -       -      -
     64B  ARG      3.4     9.4    +      -       -      -
     65B  PHE*     1.3    75.4    +      -       -      +
     67B  GLY*     1.3    69.6    +      -       -      +
     68B  SER*     3.8     4.9    +      -       -      -
     75B  THR      3.4     2.4    -      -       -      +
     76B  LEU*     4.5     0.6    -      -       -      +
     77B  THR*     2.8    46.5    +      -       -      +
     79B  SER*     5.2     2.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 67 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38B  TRP*     5.0     3.1    -      -       -      -
     51B  ILE*     3.2    20.0    -      -       -      +
     54B  ALA      3.1    20.9    -      -       -      -
     55B  SER*     3.3    25.9    +      -       -      -
     66B  THR*     1.3    78.9    -      -       -      +
     68B  SER*     1.3    61.1    +      -       -      -
     75B  THR      3.5     5.2    -      -       -      -
     76B  LEU*     4.6     3.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 68 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38B  TRP*     5.2     1.6    +      -       -      +
     54B  ALA*     3.6     7.7    +      -       -      +
     55B  SER*     5.2     2.0    -      -       -      -
     66B  THR*     5.0     6.2    +      -       -      -
     67B  GLY*     1.3    75.1    -      -       -      -
     69B  GLY*     1.3    65.8    +      -       -      +
     74B  PHE*     3.5     9.0    -      -       -      +
     75B  THR*     2.8    47.7    +      -       -      +
     77B  THR*     5.3     1.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 69 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     34B  THR*     4.8     0.9    -      -       -      +
     54B  ALA*     3.6    14.4    -      -       -      +
     68B  SER*     1.3    82.3    +      -       -      +
     70B  SER*     1.3    65.9    +      -       -      -
     73B  ASP      3.4    16.4    -      -       -      -
     74B  PHE*     4.0     5.2    -      -       -      -
     75B  THR*     4.6     1.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 70 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33B  GLY      3.4    12.3    -      -       -      -
     34B  THR*     3.9    14.6    -      -       -      -
     69B  GLY*     1.3    77.2    -      -       -      -
     71B  GLY*     1.3    62.0    +      -       -      +
     72B  THR      2.8     9.9    +      -       -      -
     73B  ASP      3.7     9.7    +      -       -      +
     74B  PHE*     3.6     9.0    -      -       -      -
----------------------------------------------------------
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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