Contacts of the strand formed by residues 65 - 68 (chain B) in PDB entry 1H1B


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 ARG 65 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     32B  SER      3.6     1.9    -      -       -      +
     33B  LEU*     3.5     4.7    -      -       -      -
     34B  GLN*     2.9    48.8    +      -       -      +
     36B  ARG      4.2    19.0    +      -       -      +
     38B  GLY*     5.6     2.2    -      -       -      -
     64B  ALA      3.4     5.6    -      -       -      +
     65B  VAL*     1.3    75.3    +      -       -      +
     66B  VAL*     1.3    62.5    +      -       -      +
     67B  VAL*     3.6     7.1    +      -       -      +
     82B  VAL*     4.1    21.7    -      -       -      +
     83B  PHE      3.5     3.1    +      -       -      +
      2F  FUC      3.6    46.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 66 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     31B  VAL*     3.5    24.2    -      -       +      -
     32B  SER      4.0     2.0    -      -       -      -
     33B  LEU*     3.9    17.7    -      -       +      -
     52B  VAL*     4.3    10.8    -      -       +      -
     65B  ARG*     1.3    78.8    +      -       +      +
     67B  VAL*     1.3    57.9    +      -       -      +
     68B  LEU*     3.8    10.9    +      -       +      -
     81B  GLN      3.7     1.7    -      -       -      +
     82B  VAL*     3.5     2.3    -      -       -      -
     83B  PHE*     2.8    48.3    +      -       +      +
     84B  ALA      4.6     0.4    -      -       -      -
     85B  VAL*     4.2    22.2    -      -       +      -
    106B  LEU*     5.5     0.2    -      -       +      -
    108B  LEU*     4.1    29.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 67 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     30B  MET      4.6     0.3    -      -       -      +
     31B  VAL*     3.4     5.0    -      -       -      +
     32B  SER*     2.9    41.0    +      -       -      +
     34B  GLN*     3.7    33.7    -      -       +      +
     65B  ARG*     4.2     5.2    -      -       -      +
     66B  VAL*     1.3    74.2    -      -       -      +
     68B  LEU*     1.3    63.9    +      -       -      +
     70B  ALA*     4.0    13.1    -      -       +      +
     80B  ARG*     3.7    39.7    -      -       +      +
     81B  GLN      3.8     2.5    -      -       -      -
     82B  VAL*     4.3    19.3    -      -       +      +
    141B  TRP*     5.7     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 68 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     28B  PRO      6.2     0.2    -      -       -      +
     30B  MET      4.7     4.7    -      -       -      -
     31B  VAL*     3.7    28.9    -      -       +      -
     46B  LEU*     4.4    16.4    -      -       +      -
     52B  VAL*     4.9     0.7    -      -       +      -
     66B  VAL*     4.2    12.6    -      -       +      +
     67B  VAL*     1.3    75.4    -      -       -      +
     69B  GLY*     1.3    67.0    +      -       -      +
     70B  ALA      3.2     4.5    +      -       -      -
     80B  ARG*     3.3     7.3    -      -       -      +
     81B  GLN*     2.8    36.9    +      -       +      +
     83B  PHE*     3.4    37.7    -      -       +      -
    108B  LEU*     5.0     2.2    -      -       +      -
    112B  ALA*     3.7    22.0    -      -       +      -
    118B  VAL*     4.1    16.2    -      -       +      -
----------------------------------------------------------
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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