Contacts of the strand formed by residues 90 - 94 (chain C) in PDB entry 7CN9


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 90 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     86C  PHE*     3.7    31.0    -      -       +      +
     89C  GLY*     1.3    80.0    -      -       -      +
     91C  TYR*     1.3    63.6    +      -       -      +
     92C  PHE*     3.9    17.3    -      -       +      -
    106C  PHE*     6.3     1.1    -      -       +      -
    193C  VAL*     3.3     4.5    -      -       -      +
    194C  PHE*     2.9    49.3    +      -       +      +
    238C  PHE*     3.5    45.1    -      -       +      -
    267C  VAL*     3.8    13.5    -      -       +      -
    268C  GLY      4.4     1.3    -      -       -      -
    269C  TYR*     4.8     1.8    -      -       +      -
    270C  LEU*     3.8     3.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 91 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     34C  ARG*     3.4    27.5    -      -       +      -
     35C  GLY*     5.0     7.2    -      -       -      -
     56C  LEU*     5.1    15.0    -      -       +      -
     62C  VAL*     5.3     9.6    -      -       +      -
     90C  VAL*     1.3    76.1    -      -       -      +
     92C  PHE*     1.3    53.4    +      -       -      +
     93C  ALA*     4.0    12.2    +      -       +      +
    191C  GLU*     2.4    56.2    +      -       +      +
    192C  PHE      5.2     0.2    -      -       -      -
    193C  VAL*     4.0    24.7    -      -       +      -
    216C  LEU*     5.4    11.8    -      -       +      +
    217C  PRO*     5.9     0.2    -      -       -      +
    223C  LEU*     6.2     0.4    -      -       +      -
    266C  TYR*     2.7    27.7    -      -       +      +
    267C  VAL*     3.4     3.0    -      -       -      -
    268C  GLY*     3.9    26.3    +      -       -      +
    270C  LEU*     4.6     4.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 92 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     90C  VAL*     3.9    11.4    +      -       +      -
     91C  TYR*     1.3    72.1    -      -       -      +
     93C  ALA*     1.3    69.5    +      -       -      +
     94C  SER*     6.1     0.7    -      -       -      -
    101C  ILE*     3.6    18.6    -      -       +      -
    104C  TRP*     3.0    54.5    -      +       +      +
    192C  PHE*     3.3    28.3    +      -       -      +
    194C  PHE*     4.6     8.7    -      -       +      -
    238C  PHE*     4.2    19.1    -      +       -      -
    239C  GLN*     5.4     0.7    -      -       -      -
    240C  THR*     3.7    27.4    -      -       +      -
    265C  TYR*     3.4    47.3    -      +       +      -
    266C  TYR      3.1     7.9    -      -       -      +
    267C  VAL*     5.6     0.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 93 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     91C  TYR*     4.0    12.9    +      -       +      +
     92C  PHE*     1.3    83.9    -      -       -      +
     94C  SER*     1.3    62.9    +      -       -      +
    190C  ARG      3.1    20.0    -      -       -      +
    191C  GLU*     3.8    19.7    -      -       +      -
    192C  PHE*     5.1     4.3    -      -       -      +
    264C  ALA      3.7     2.8    -      -       -      +
    265C  TYR*     3.7     2.2    -      -       -      -
    266C  TYR*     3.3    38.4    +      -       +      +
----------------------------------------------------------
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Residues in contact with SER 94 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     92C  PHE*     6.1     0.7    -      -       -      -
     93C  ALA*     1.3    77.2    -      -       -      +
     95C  THR*     1.3    90.6    +      -       -      +
     97C  LYS*     4.2     9.0    +      -       -      +
    101C  ILE*     4.6    24.9    -      -       -      +
    189C  LEU*     3.2    19.0    -      -       -      +
    190C  ARG      3.6    12.2    +      -       -      +
    192C  PHE*     5.7     2.3    -      -       -      -
    263C  ALA*     5.4     3.1    -      -       -      +
    264C  ALA      3.7    19.0    +      -       -      -
    265C  TYR*     5.5     0.4    -      -       -      -
    266C  TYR*     4.7     0.9    -      -       -      -
----------------------------------------------------------
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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