Contacts of the strand formed by residues 97 - 102 (chain B) in PDB entry 3OPY


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 ASN 97 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     95B  GLN      3.1    14.3    -      -       -      +
     96B  SER*     1.3    76.4    -      -       -      +
     98B  ILE*     1.3    75.0    +      -       -      +
     99B  ALA*     4.6     2.9    +      -       -      +
    130B  GLU*     3.6    22.9    +      -       -      +
    137B  LEU*     3.3    31.9    -      -       +      +
    139B  SER*     3.7    12.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 98 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     13B  ILE*     3.8    40.6    -      -       +      -
     97B  ASN*     1.3    84.4    -      -       -      +
     99B  ALA*     1.3    62.9    +      -       -      +
    100B  PHE*     4.0    29.8    -      -       +      -
    137B  LEU      3.8     3.8    +      -       -      +
    138B  GLY*     3.8     4.0    -      -       -      -
    139B  SER*     2.8    28.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 99 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     97B  ASN*     4.4     2.9    -      -       -      +
     98B  ILE*     1.3    77.0    -      -       -      +
    100B  PHE*     1.3    64.3    +      -       -      +
    139B  SER*     3.3    20.2    -      -       -      -
    140B  LEU      4.5     1.1    -      -       -      +
    141B  ILE*     4.7    14.4    -      -       +      +
----------------------------------------------------------
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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
----------------------------------------------------------
     13B  ILE*     5.0    13.7    -      -       +      -
     30B  TYR*     5.6     6.3    -      +       -      -
     34B  LEU*     4.3    22.7    -      -       +      -
     36B  PHE*     4.4    20.4    -      +       -      -
     52B  GLU*     5.4     1.8    -      -       -      -
     58B  VAL*     4.5    18.8    -      -       +      -
     98B  ILE*     4.0    26.2    -      -       +      -
     99B  ALA*     1.3    77.7    -      -       -      +
    101B  LYS*     1.4    63.8    +      -       -      +
    102B  SER*     3.5     1.8    +      -       -      -
    138B  GLY*     5.0     9.2    -      -       -      -
    139B  SER      3.0    28.1    +      -       -      +
    140B  LEU*     3.4    23.7    -      -       +      +
    141B  ILE*     2.7    33.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 101 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    100B  PHE*     1.4    72.6    -      -       -      +
    102B  SER*     1.4    58.5    +      -       -      +
    141B  ILE*     3.4     8.1    -      -       +      +
    143B  PHE      4.3    28.0    -      -       -      +
    145B  GLY      6.0     2.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER 102 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    100B  PHE*     3.5     2.7    +      -       -      -
    101B  LYS*     1.4    74.6    -      -       -      +
    103B  SER*     1.4    67.8    +      -       -      +
    105B  LEU*     3.7    13.5    -      -       -      +
    140B  LEU*     4.1    28.9    -      -       -      +
    141B  ILE      3.1     9.1    +      -       -      +
    142B  GLY*     3.6    22.1    -      -       -      -
    151B  ALA*     5.7     1.6    -      -       -      -
----------------------------------------------------------
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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