Contacts of the strand formed by residues 105 - 109 (chain A) in PDB entry 2P2F


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 SER 105 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     97A  TRP*     3.0    20.7    -      -       -      -
     98A  GLU*     4.0    14.6    -      -       -      -
    102A  THR      5.1     0.3    +      -       -      -
    103A  SER      3.9     3.6    +      -       -      -
    104A  GLN*     1.3    74.4    -      -       -      +
    106A  LYS*     1.3    73.4    +      -       -      +
    107A  HIS*     5.2     5.7    -      -       -      -
    348A  LYS*     4.1    12.9    +      -       -      -
    349A  HIS*     4.7     8.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 106 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     95A  ILE      3.8     0.3    -      -       -      +
     96A  ILE*     3.4     5.9    -      -       -      +
     97A  TRP*     2.8    56.4    +      -       +      +
    105A  SER*     1.3    80.7    -      -       -      +
    107A  HIS*     1.3    69.5    +      -       -      +
    108A  ILE*     3.9    24.7    -      -       +      -
    143A  PRO*     4.8     7.3    -      -       +      +
    144A  GLU*     4.6    13.1    +      -       -      -
----------------------------------------------------------
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Residues in contact with HIS 107 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     93A  THR*     3.6    24.5    -      -       -      +
     95A  ILE      3.7     2.9    -      -       -      -
     96A  ILE*     3.8    30.5    -      -       +      +
    105A  SER*     5.2     6.2    +      -       -      -
    106A  LYS*     1.3    78.7    -      -       -      +
    108A  ILE*     1.3    63.4    +      -       -      +
    109A  SER      3.8     0.9    -      -       -      +
    112A  GLU*     3.2    11.4    -      -       -      +
    349A  HIS*     4.5    17.4    +      +       -      -
----------------------------------------------------------
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Residues in contact with ILE 108 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     93A  THR*     4.0     2.0    -      -       -      +
     94A  ALA*     2.7    31.2    +      -       -      +
     95A  ILE*     2.9    32.1    +      -       +      +
     97A  TRP*     5.1     0.4    -      -       +      -
    106A  LYS*     4.3    22.2    -      -       +      -
    107A  HIS*     1.3    77.1    -      -       -      +
    109A  SER*     1.3    66.3    +      -       -      +
    112A  GLU*     3.1    12.1    -      -       +      +
    113A  LEU*     3.8    31.0    -      -       +      +
    116A  ASP*     6.0     1.1    -      -       -      +
    143A  PRO*     3.5    37.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 109 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     90A  GLY      3.3    12.2    +      -       -      -
     91A  ASP*     4.2    12.6    +      -       -      -
     92A  ARG      3.3    10.8    -      -       -      -
     93A  THR*     4.1     3.3    -      -       -      +
     94A  ALA*     4.0     0.4    -      -       -      -
    107A  HIS      3.8     1.8    -      -       -      -
    108A  ILE*     1.3    77.2    -      -       -      +
    110A  TYR*     1.3    53.0    +      -       -      +
    111A  ARG*     3.3     8.7    +      -       -      +
    112A  GLU*     2.7    41.0    +      -       -      +
    113A  LEU*     2.9    30.1    +      -       -      +
----------------------------------------------------------
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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