Contacts of the strand formed by residues 182 - 187 (chain S) in PDB entry 6NZO


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 182 (chain S).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    180S  ALA*     3.9     3.2    +      -       +      +
    181S  LYS*     1.3    80.6    +      -       -      +
    183S  SER*     1.3    70.2    +      -       -      +
    194S  LEU*     4.0    42.0    -      -       +      -
    195S  ARG      3.0    13.0    -      -       -      +
    196S  ALA*     4.6     0.7    -      -       +      -
    197S  ASP*     3.0     5.6    -      -       -      +
    200S  LEU*     5.6     1.6    -      -       +      -
    206S  ILE*     4.7    17.0    -      -       +      -
    207S  TYR*     5.1    16.6    -      -       +      -
    253S  LEU*     5.1    14.8    -      -       +      +
    292S  LEU*     4.4    16.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 183 (chain S). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     89S  PRO*     4.0    19.0    -      -       -      +
     90S  GLN      5.7     0.2    -      -       -      -
    182S  VAL*     1.3    71.8    +      -       -      +
    184S  VAL*     1.3    67.2    +      -       -      +
    193S  GLY      2.9     3.8    -      -       -      +
    194S  LEU*     3.2     6.0    -      -       -      -
    195S  ARG*     2.9    40.2    +      -       -      +
    197S  ASP*     2.4    32.7    +      -       -      -
    253S  LEU*     6.0     2.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 184 (chain S). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     89S  PRO*     3.3     4.8    -      -       -      +
     90S  GLN*     2.5    62.9    +      -       +      +
     91S  LEU      3.7    13.0    -      -       -      +
    102S  ALA*     5.2     0.7    -      -       -      -
    183S  SER*     1.3    78.7    -      -       -      +
    185S  ILE*     1.3    57.4    +      -       -      +
    186S  LYS      4.0     0.3    +      -       -      -
    192S  TYR*     4.3    17.0    -      -       +      -
    193S  GLY      3.5     3.4    -      -       -      +
    194S  LEU*     4.7     0.7    -      -       +      -
    195S  ARG*     4.8     0.4    -      -       -      -
    253S  LEU*     4.1    13.5    -      -       +      -
    256S  PHE*     3.6    52.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 185 (chain S). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     83S  LEU*     3.6    34.3    -      -       +      +
     84S  PRO      3.3    23.3    -      -       -      +
     88S  PRO      4.3    17.5    -      -       -      +
     89S  PRO*     5.0     0.2    -      -       -      -
    183S  SER      3.6     1.0    +      -       -      -
    184S  VAL*     1.3    75.6    -      -       -      +
    186S  LYS*     1.3    74.4    +      -       -      +
    187S  THR*     3.7     7.3    +      -       +      -
    191S  GLY      3.7     0.2    -      -       -      +
    192S  TYR*     3.3     7.8    -      -       -      +
    193S  GLY*     2.9    53.0    +      -       -      +
    195S  ARG*     3.5    33.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with LYS 186 (chain S). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     88S  PRO      4.9     5.1    +      -       -      +
     90S  GLN*     5.3     0.6    -      -       +      +
    101S  GLU*     3.8    35.0    +      -       +      +
    184S  VAL      4.0     2.0    +      -       -      -
    185S  ILE*     1.3    83.9    -      -       +      +
    187S  THR*     1.3    91.0    +      -       -      +
    188S  GLU*     4.4     8.1    +      -       -      +
    191S  GLY*     3.5    17.1    +      -       -      +
    192S  TYR*     3.6    29.8    +      -       +      -
----------------------------------------------------------
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Residues in contact with THR 187 (chain S). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     83S  LEU*     4.8     6.7    -      -       +      -
    185S  ILE*     3.7    16.3    +      -       +      -
    186S  LYS*     1.3    92.3    +      -       -      +
    188S  GLU*     1.3    66.4    +      -       -      +
    189S  LYS      3.2     0.2    -      -       -      -
    190S  LYS*     3.2    38.6    -      -       -      +
    191S  GLY      2.7    57.5    +      -       -      +
    192S  TYR*     3.9     1.6    +      -       -      -
    193S  GLY      4.7     0.3    +      -       -      -
    291S  GLU*     4.1     9.5    +      -       -      +
----------------------------------------------------------
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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