Contacts of the strand formed by residues 180 - 183 (chain C) in PDB entry 4B2B


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 MET 180 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     98C  THR      3.2    27.4    -      -       -      +
     99C  TYR      3.6    21.3    -      -       -      +
    100C  ASN*     3.7     8.5    -      -       -      +
    101C  ASN      6.1     0.2    -      -       -      +
    165C  ASP*     4.7     5.5    -      -       -      +
    175C  ILE      4.5     3.6    -      -       -      +
    176C  ILE*     4.2    15.5    -      -       +      +
    177C  THR*     3.1    42.8    +      -       +      +
    178C  SER*     3.2     1.1    +      -       -      -
    179C  ASN*     1.3    85.1    -      -       +      +
    181C  PHE*     1.3    63.6    +      -       -      +
    214C  SER*     6.5     0.2    -      -       -      -
    215C  TRP*     3.5    35.9    -      -       +      +
    227C  PHE*     4.5     6.5    -      -       +      -
    228C  TYR      3.2    12.3    -      -       -      +
    229C  THR*     5.4     1.1    -      -       -      -
    230C  LYS*     3.6    15.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 181 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    162C  ILE*     3.9    40.2    -      -       +      -
    163C  LEU      5.5     1.1    -      -       -      +
    165C  ASP*     4.9    10.5    -      -       -      +
    168C  CYS*     5.1     0.7    -      -       -      -
    176C  ILE*     5.7     1.6    -      -       -      -
    180C  MET*     1.3    74.6    -      -       -      +
    182C  CYS*     1.3    72.6    +      -       -      +
    183C  ALA*     4.1     5.8    -      -       +      -
    199C  VAL*     4.2    13.7    -      -       +      -
    210C  GLN*     3.3    25.1    -      -       +      -
    211C  GLY*     3.7    18.2    -      -       -      -
    227C  PHE*     3.4     8.7    -      -       -      -
    228C  TYR*     2.9    57.5    +      +       +      +
    229C  THR      3.8     6.5    -      -       -      -
    230C  LYS*     4.0    26.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with CYS 182 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    162C  ILE*     3.8     0.2    -      -       -      +
    163C  LEU*     2.9    33.9    +      -       -      +
    168C  CYS*     1.9    63.3    -      -       +      -
    181C  PHE*     1.3    81.4    -      -       -      +
    183C  ALA*     1.3    61.8    +      -       -      +
    225C  PRO*     3.5    22.2    -      -       +      -
    226C  GLY      3.1    17.9    -      -       -      +
    227C  PHE*     3.8    14.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 183 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    136C  CYS*     6.2     0.4    -      -       +      -
    138C  ILE*     4.7    10.7    -      -       +      +
    160C  ALA*     4.7     3.8    -      -       +      +
    161C  PRO      3.2    17.7    -      -       -      +
    162C  ILE*     3.9     8.3    -      -       +      -
    163C  LEU*     4.0     3.8    -      -       -      +
    181C  PHE*     4.1     9.0    -      -       +      -
    182C  CYS*     1.3    76.5    -      -       -      +
    184C  GLY*     1.3    59.2    +      -       -      +
    189C  ASP*     4.8     1.7    -      -       -      +
    199C  VAL*     5.6     2.7    -      -       +      -
    225C  PRO*     3.7     5.0    -      -       -      +
    226C  GLY      3.2    24.3    +      -       -      +
    228C  TYR*     3.7    25.6    +      -       +      -
----------------------------------------------------------
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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