Contacts of the strand formed by residues 66 - 74 (chain C) in PDB entry 6RI7


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 SER 66 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     60C  GLN*     4.0     1.0    -      -       -      +
     61C  SER*     2.9    30.7    +      -       -      -
     64C  GLY      3.0    11.7    +      -       -      -
     65C  ASN*     1.3    86.8    +      -       -      +
     67C  GLU*     1.3    64.9    +      -       -      +
    102C  LEU*     6.2     0.4    -      -       -      -
    103C  VAL      3.5    10.3    -      -       -      -
    104C  ILE*     3.5    21.4    -      -       -      +
    105C  TYR*     3.4     8.4    -      -       -      -
    107C  ARG*     5.0     4.2    +      -       -      -
    479C  LEU*     4.2    22.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 67 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     58C  PRO*     3.2    25.9    -      -       +      +
     59C  ILE      3.4    15.0    -      -       -      +
     60C  GLN*     4.1    15.4    -      -       +      +
     61C  SER      4.7     0.2    -      -       -      +
     66C  SER*     1.3    77.7    -      -       -      +
     68C  LEU*     1.3    76.5    +      -       -      +
     69C  GLN*     4.8     7.2    -      -       +      +
    102C  LEU*     3.2     7.9    -      -       -      +
    103C  VAL*     2.9    47.8    +      -       +      +
    105C  TYR*     2.4    34.8    +      -       +      -
    479C  LEU*     4.7     5.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 68 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     57C  PHE*     4.9     9.7    -      -       +      +
     58C  PRO*     3.2     5.5    -      -       -      +
     59C  ILE*     2.9    42.1    +      -       +      +
     67C  GLU*     1.3    75.3    -      -       -      +
     69C  GLN*     1.3    63.4    +      -       -      +
    100C  LEU*     3.7    36.8    -      -       +      -
    101C  ARG      3.2    26.9    -      -       -      +
    102C  LEU*     3.6    23.8    -      -       +      -
    475C  VAL*     4.8    19.1    -      -       +      -
    479C  LEU*     6.0     3.4    -      -       +      -
    489C  PRO*     4.8    10.1    -      -       +      -
    492C  MET*     5.6     5.8    -      -       +      +
    493C  ILE*     5.9     3.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 69 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     57C  PHE*     4.2     2.5    -      -       -      -
     58C  PRO*     3.7    29.7    -      -       +      +
     67C  GLU*     4.8     7.5    -      -       +      +
     68C  LEU*     1.3    77.2    -      -       -      +
     70C  TYR*     1.3    66.1    +      -       -      +
     71C  VAL*     5.6     0.2    -      -       -      +
    100C  LEU*     3.2    12.3    -      -       -      +
    101C  ARG*     2.9    81.3    +      -       +      +
    103C  VAL*     4.8     9.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 70 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     41C  GLN*     4.4     1.4    +      -       -      -
     50C  GLU*     3.0    35.5    +      -       -      -
     53C  PHE*     3.3    45.3    -      +       +      -
     54C  ARG*     5.2    14.8    -      -       +      -
     57C  PHE*     3.6    25.7    -      +       +      +
     69C  GLN*     1.3    83.4    -      -       -      +
     71C  VAL*     1.3    80.9    +      -       -      +
     72C  SER*     3.0    39.7    -      -       -      -
     73C  TYR*     3.0    11.9    +      +       -      -
     98C  VAL*     4.6     5.2    -      -       +      -
     99C  LYS      4.2     2.7    -      -       -      -
    100C  LEU*     3.6     7.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 71 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     69C  GLN*     5.2     0.4    -      -       +      +
     70C  TYR*     1.3    97.5    +      -       -      +
     72C  SER*     1.3    71.3    +      -       -      +
     99C  LYS*     2.9    25.8    +      -       +      +
    100C  LEU      4.4     0.7    -      -       -      -
    101C  ARG*     3.7    47.1    -      -       +      +
    118C  LYS*     4.1    16.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with SER 72 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     41C  GLN*     4.4     4.9    +      -       -      -
     70C  TYR*     3.0    19.3    -      -       -      -
     71C  VAL*     1.3    84.0    -      -       -      +
     73C  TYR*     1.3    78.1    +      -       -      +
     98C  VAL*     3.8     0.3    -      -       -      -
     99C  LYS*     2.9    44.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 73 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38C  PHE      5.2     0.2    +      -       -      -
     39C  ILE*     5.1     1.5    -      -       +      -
     40C  GLU      3.3    27.4    +      -       -      -
     41C  GLN*     2.4    51.3    +      -       -      +
     49C  LEU*     3.7    39.4    +      -       +      +
     50C  GLU*     3.7    23.9    +      -       +      -
     53C  PHE*     4.4     7.6    -      +       +      -
     70C  TYR*     3.0    26.4    +      +       +      -
     72C  SER*     1.3    86.0    +      -       -      +
     74C  ARG*     1.3    61.2    +      -       -      +
     75C  LEU*     3.5    25.6    -      -       +      -
     96C  LEU*     4.1     9.2    -      -       +      -
     97C  ARG      3.1    16.4    -      -       -      +
     98C  VAL*     4.0    11.9    -      -       +      +
     99C  LYS*     4.6     1.8    -      -       -      +
    121C  GLU*     6.3     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 74 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     41C  GLN*     4.1     5.2    -      -       -      +
     73C  TYR*     1.3    75.7    -      -       -      +
     75C  LEU*     1.3    83.8    +      -       -      +
     76C  GLY*     3.5    28.8    -      -       -      +
     97C  ARG*     3.1    49.1    +      -       -      +
    121C  GLU*     2.5    45.9    +      -       -      +
----------------------------------------------------------
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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