Contacts of the strand formed by residues 183 - 188 (chain A) in PDB entry 1NOY


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 183 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    143A  PHE*     3.7     8.7    -      -       +      -
    145A  VAL*     3.4    28.0    -      -       +      -
    159A  TRP*     4.0    22.9    -      -       +      -
    179A  ILE      3.4    16.6    -      -       -      +
    180A  LEU*     3.1    24.1    +      -       +      +
    181A  ASP      4.5     3.3    -      -       -      +
    182A  ARG*     1.3    81.1    -      -       -      +
    184A  ILE*     1.3    68.4    +      -       -      +
    185A  TYR*     3.8     8.7    +      -       +      +
    322A  ILE*     3.5    28.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 184 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    142A  ARG*     3.8    31.4    -      -       +      +
    143A  PHE      2.9    15.7    +      -       -      +
    144A  TYR*     3.8    30.2    -      -       +      +
    145A  VAL      3.2    18.7    +      -       -      -
    182A  ARG      4.3     4.7    -      -       -      +
    183A  VAL*     1.3    79.6    -      -       -      +
    185A  TYR*     1.3    62.1    +      -       -      +
    186A  MET*     3.7    17.7    +      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 185 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    145A  VAL*     4.0    18.6    -      -       +      -
    147A  ASP*     3.0    30.5    +      -       +      -
    149A  LEU*     4.0     1.0    -      -       -      +
    158A  LYS*     3.4    41.9    -      -       -      -
    159A  TRP*     2.9    65.6    +      +       +      -
    183A  VAL*     3.8     3.2    +      -       -      +
    184A  ILE*     1.3    75.5    -      -       -      +
    186A  MET*     1.3    67.7    +      -       -      +
    187A  PRO*     3.4    37.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with MET 186 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    144A  TYR*     4.4    14.4    -      -       -      -
    145A  VAL      2.9    14.3    +      -       -      +
    146A  PHE*     3.6    25.6    -      -       +      -
    147A  ASP      3.0    21.5    +      -       -      -
    184A  ILE*     3.8    24.2    -      -       +      +
    185A  TYR*     1.3    85.6    -      -       -      +
    187A  PRO*     1.3    64.9    -      -       -      +
    188A  PHE*     3.1    37.8    -      -       +      -
    197A  GLU*     4.0    11.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with PRO 187 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    147A  ASP*     3.3     7.4    -      -       +      +
    149A  LEU*     3.5    20.6    -      -       +      -
    158A  LYS*     4.2    11.4    -      -       +      -
    185A  TYR*     3.4    42.6    -      -       +      +
    186A  MET*     1.3    87.0    -      -       -      +
    188A  PHE*     1.3    65.9    +      -       -      +
    189A  ASP*     4.9     3.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 188 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    146A  PHE*     3.8    16.2    -      +       -      -
    147A  ASP      2.7    15.1    +      -       -      +
    148A  LEU*     3.8     2.3    -      -       +      +
    149A  LEU*     2.9    31.9    +      -       -      +
    186A  MET*     3.1    61.2    -      -       +      -
    187A  PRO*     1.3    76.3    -      -       -      +
    189A  ASP*     1.3    65.2    +      -       -      +
    190A  ASN      3.5    15.2    +      -       -      +
    193A  ASP*     3.9    13.0    -      -       +      -
    194A  MET*     3.7    32.5    -      -       +      -
    197A  GLU*     3.7    29.4    -      -       +      -
----------------------------------------------------------
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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