Contacts of the strand formed by residues 67 - 72 (chain H) in PDB entry 1RZK


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 VAL 67 (chain H).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     48H  MET*     3.8    17.5    -      -       +      +
     59H  TYR*     3.4    36.5    -      -       +      -
     63H  LEU*     3.5    31.9    -      -       +      +
     64H  GLN*     4.7     0.8    -      -       -      +
     65H  GLY      4.6     5.2    +      -       -      +
     66H  ARG*     1.3    81.8    -      -       -      +
     68H  THR*     1.3    80.1    +      -       -      +
     69H  ILE*     4.6     0.9    -      -       +      -
     80H  LEU*     3.4    28.7    -      -       +      -
     81H  GLU      3.1     7.4    -      -       -      +
     82H  ARG*     3.2    14.1    +      -       +      +
----------------------------------------------------------
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Residues in contact with THR 68 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     59H  TYR*     3.3    13.8    +      -       -      +
     67H  VAL*     1.3    78.6    +      -       -      +
     69H  ILE*     1.3    73.4    +      -       -      +
     70H  THR*     3.5    25.1    -      -       +      -
     79H  TYR      3.8     0.5    -      -       -      +
     80H  LEU*     3.4     2.1    -      -       -      +
     81H  GLU*     2.9    40.4    +      -       +      +
     82H  ARG*     2.9    27.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 69 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     34H  PHE      4.9     0.7    -      -       -      +
     36H  TRP*     3.9    21.3    -      -       +      +
     48H  MET      4.6     1.1    -      -       -      +
     49H  GLY*     3.5    42.4    -      -       -      +
     50H  ARG*     3.7     4.0    -      -       -      +
     51H  ILE*     3.7    37.9    -      -       +      +
     57H  ALA*     3.9    14.2    -      -       +      +
     58H  HIS      4.7     0.2    -      -       -      +
     59H  TYR*     3.3    24.6    +      -       +      -
     68H  THR*     1.3    81.4    -      -       -      +
     70H  THR*     1.3    67.8    +      -       -      +
     78H  VAL*     4.3     2.7    -      -       +      -
     79H  TYR      3.4    10.1    -      -       -      +
     80H  LEU*     3.6    16.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 70 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19H  LYS*     4.7     9.3    +      -       -      +
     51H  ILE*     3.9     7.4    -      -       -      -
     55H  ASP*     5.7     0.7    -      -       -      -
     68H  THR*     3.5    21.5    -      -       +      -
     69H  ILE*     1.3    79.1    -      -       -      +
     71H  ALA*     1.3    59.5    +      -       -      +
     78H  VAL*     3.4     5.2    -      -       -      +
     79H  TYR*     2.7    54.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 71 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29H  PHE*     3.9     8.7    -      -       +      -
     51H  ILE*     3.8    14.2    -      -       +      +
     52H  THR*     3.9    28.3    -      -       +      -
     55H  ASP*     4.3     5.4    +      -       -      +
     70H  THR*     1.3    77.9    -      -       -      +
     72H  ASP*     1.3    60.3    +      -       -      +
     73H  LYS*     3.6    18.9    +      -       -      +
     77H  THR      3.1    11.7    -      -       -      +
     78H  VAL*     4.2     6.3    -      -       +      -
     79H  TYR*     4.7     1.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with ASP 72 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29H  PHE*     4.8     0.9    -      -       -      -
     71H  ALA*     1.3    70.2    -      -       -      +
     73H  LYS*     1.3    52.2    +      -       -      +
     74H  SER*     2.9    32.2    +      -       -      -
     75H  THR*     3.3    29.7    +      -       -      +
     76H  SER*     2.7    30.1    +      -       -      -
     77H  THR      2.7    15.3    +      -       -      +
     79H  TYR*     3.9    23.0    +      -       +      -
----------------------------------------------------------
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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