Contacts of the strand formed by residues 67 - 71 (chain C) in PDB entry 6H7L


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 67 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38C  ARG*     4.3     1.1    -      -       -      -
     48C  VAL*     3.6    20.0    -      -       +      -
     59C  TYR*     3.4    17.2    -      -       +      -
     63C  VAL*     3.0    43.4    +      -       +      +
     65C  GLY      4.9     3.5    +      -       -      -
     66C  ARG*     1.3   105.6    +      -       +      +
     68C  THR*     1.3    64.4    +      -       -      +
     80C  LEU*     4.0    12.1    -      -       +      -
     81C  GLN      3.4     4.3    -      -       -      +
     82C  MET*     3.6    51.4    -      -       +      -
     83C  ASN      3.9     3.6    -      -       -      -
     85C  LEU*     3.8    17.9    -      -       +      -
     89C  ASP*     3.9    17.9    -      -       -      -
     93C  TYR*     3.8    10.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with THR 68 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     59C  TYR*     3.5    10.6    +      -       -      +
     66C  ARG      4.4     3.6    +      -       -      -
     67C  PHE*     1.3    78.0    +      -       -      +
     69C  ILE*     1.3    69.5    +      -       -      +
     70C  SER*     4.1     7.8    +      -       -      -
     79C  TYR      3.6     1.7    -      -       -      +
     80C  LEU*     3.5     4.1    -      -       -      -
     81C  GLN*     2.8    49.3    +      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 69 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     34C  MET      3.9     4.9    -      -       -      +
     35C  GLY*     4.2     0.2    -      -       -      -
     36C  TRP*     3.9    14.1    -      -       +      -
     49C  ALA*     3.4    37.7    -      -       +      +
     50C  ALA*     3.6    28.7    -      -       -      +
     51C  ILE*     3.9    10.5    -      -       +      +
     57C  THR*     4.0    12.3    -      -       +      +
     59C  TYR*     2.9    32.4    +      -       +      +
     68C  THR*     1.3    76.1    -      -       -      +
     70C  SER*     1.3    67.0    +      -       -      +
     78C  VAL*     3.7    24.0    -      -       +      -
     79C  TYR      3.3    11.0    -      -       -      +
     80C  LEU*     4.1     2.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 70 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19C  ARG*     5.0     2.8    +      -       -      -
     51C  ILE*     4.1     9.0    -      -       -      -
     68C  THR*     4.8     8.7    +      -       -      +
     69C  ILE*     1.3    77.5    -      -       -      +
     71C  ARG*     1.3    63.8    +      -       -      +
     78C  VAL*     3.5     5.3    -      -       -      +
     79C  TYR*     2.8    47.9    +      -       -      +
     81C  GLN*     6.1     0.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 71 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    237A  GLN*     6.1     0.9    -      -       -      +
     32C  ASN*     2.9    30.7    +      -       -      +
     34C  MET*     3.3    35.9    -      -       -      +
     51C  ILE*     3.7    32.6    +      -       +      +
     52C  HIS      3.9    14.1    -      -       -      -
     53C  SER*     3.6    28.2    +      -       -      +
     55C  GLY*     6.0     0.7    -      -       -      -
     70C  SER*     1.3    77.7    -      -       -      +
     72C  ASP*     1.3    74.3    +      -       -      +
     73C  ASN*     3.3     6.0    +      -       -      +
     75C  ALA      5.2     1.2    +      -       -      -
     76C  ASN*     4.0    17.4    +      -       -      +
     77C  THR      3.4    11.8    +      -       -      +
     78C  VAL*     4.3     4.0    -      -       +      -
     79C  TYR*     4.6     4.5    -      -       -      -
----------------------------------------------------------
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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