Contacts of the strand formed by residues 98 - 102 (chain B) in PDB entry 2O2C


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 PHE 98 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     88B  LYS*     3.5    35.2    -      -       +      -
     89B  VAL      3.3    15.5    -      -       -      +
     90B  SER*     4.3     2.9    -      -       -      -
     91B  LEU*     3.9    10.0    -      -       -      +
     96B  GLU      3.6    15.3    -      -       -      +
     97B  ASN*     1.3    80.4    +      -       -      +
     99B  LEU*     1.3    62.6    +      -       -      +
    100B  PHE*     3.9     7.0    -      -       +      -
    463B  ILE*     3.8    15.0    -      -       +      -
    530B  LEU      3.7    18.8    -      -       -      -
    531B  ILE*     3.3    28.0    -      -       -      +
    532B  LYS*     4.1    16.6    -      -       +      -
    600C  MET*     3.7    25.1    -      -       -      -
    604C  LEU*     3.5    33.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 99 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     87B  VAL      3.8     2.3    -      -       -      +
     88B  LYS*     3.7     0.5    -      -       -      -
     89B  VAL*     2.9    41.7    +      -       +      +
     91B  LEU*     4.5     9.4    -      -       +      -
     98B  PHE*     1.3    74.5    -      -       -      +
    100B  PHE*     1.3    60.0    +      -       -      +
    101B  LEU      4.1     0.3    +      -       -      -
    356B  ILE*     4.1    12.3    -      -       +      -
    369B  VAL*     5.2     7.0    -      -       +      +
    529B  LEU*     4.0    27.4    -      -       +      -
    530B  LEU      3.9     1.8    -      -       -      +
    531B  ILE*     3.7    21.1    -      -       +      -
    541B  ALA*     3.9    36.1    -      -       +      +
    542B  ILE*     4.2    11.2    -      -       +      +
    545B  MET*     4.0    21.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 100 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     82B  GLY      5.0     0.9    -      -       -      -
     86B  SER*     3.5    35.9    -      -       -      -
     87B  VAL      3.4    20.4    -      -       -      -
     88B  LYS*     3.9    13.0    -      -       +      +
     98B  PHE*     3.9    15.7    -      -       +      -
     99B  LEU*     1.3    73.7    -      -       -      +
    101B  LEU*     1.3    59.2    +      -       -      +
    102B  ASP*     4.1    12.6    -      -       +      -
    528B  THR      3.4     2.5    -      -       -      +
    529B  LEU*     3.3     8.4    -      -       -      -
    530B  LEU*     2.8    48.0    +      -       +      +
    596C  GLY      5.8     2.5    -      -       -      -
    597C  LEU*     3.7    31.9    -      -       +      -
    600C  MET*     3.7    32.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 101 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     86B  SER*     3.1     6.5    -      -       -      -
     87B  VAL*     2.9    36.4    +      -       +      +
     99B  LEU*     4.1     1.2    -      -       +      -
    100B  PHE*     1.3    72.8    -      -       -      +
    102B  ASP*     1.3    66.8    +      -       -      +
    103B  TYR*     4.0    25.5    -      -       +      +
    369B  VAL*     3.8    45.1    -      -       +      +
    372B  LEU*     4.5     2.7    -      -       +      -
    373B  LEU*     3.9    31.4    -      -       +      +
    527B  ASN*     4.2    12.8    -      -       +      -
    528B  THR      3.5     4.7    -      -       -      +
    529B  LEU*     3.8    26.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 102 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     82B  GLY      4.6     4.0    -      -       -      +
     85B  TYR      3.8     5.0    -      -       -      +
     86B  SER*     4.0     7.0    -      -       -      -
    100B  PHE*     4.1    17.1    -      -       +      -
    101B  LEU*     1.3    73.6    -      -       -      +
    103B  TYR*     1.3    59.4    +      -       -      +
    104B  SER*     2.6    30.6    +      -       -      -
    105B  LYS*     4.5     1.8    +      -       -      +
    526B  SER      4.3     1.0    -      -       -      +
    527B  ASN*     3.4     4.7    -      -       -      +
    528B  THR*     2.8    47.6    +      -       -      +
    593C  SER*     2.7    29.5    +      -       -      +
    597C  LEU*     3.8    14.9    -      -       +      +
----------------------------------------------------------
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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