Contacts of the strand formed by residues 392 - 394 (chain M) in PDB entry 2PPB


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 392 (chain M).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    129M  ILE*     5.1     1.2    -      -       -      +
    134M  ARG*     2.6    50.1    +      -       -      +
    135M  VAL      3.7     8.3    -      -       -      -
    136M  ILE*     4.0    21.7    -      -       -      +
    385M  PHE      4.6     5.6    -      -       -      -
    386M  PHE*     3.1    14.2    +      -       -      -
    389M  SER*     2.9    16.8    +      -       -      +
    390M  GLN      4.7     1.0    -      -       -      +
    391M  LEU*     1.3    76.2    -      -       -      +
    393M  GLN*     1.3    67.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 393 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    134M  ARG*     3.0    37.1    -      -       -      +
    135M  VAL      3.3    10.9    +      -       -      +
    137M  VAL*     4.3    10.2    -      -       -      +
    390M  GLN      3.8     5.8    -      -       -      +
    391M  LEU*     2.5    28.9    +      -       -      +
    392M  SER*     1.3    79.6    +      -       -      +
    394M  PHE*     1.3    68.3    +      -       -      +
    395M  LYS*     4.3     0.2    -      -       -      -
    406M  HIS*     3.8    24.5    +      -       +      +
    409M  ARG*     3.9    11.5    -      -       -      +
     12Y    G      2.9    53.0    +      -       -      +
     13Y    C      4.1     2.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 394 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    132M  ALA*     3.2    28.7    -      -       +      -
    133M  ASP      4.0     2.5    -      -       -      -
    134M  ARG*     3.7    11.0    -      -       -      +
    393M  GLN*     1.3    72.6    -      -       +      +
    395M  LYS*     1.3    67.3    +      -       -      +
    396M  ASP*     3.1     4.9    +      -       -      +
    406M  HIS*     3.5    13.2    +      -       -      -
    632M  ASN*     3.2    39.9    -      -       +      -
    633M  GLN*     3.2    28.7    -      -       -      +
     20X    G      2.7    48.7    -      -       -      +
     21X    C      3.5    20.4    -      -       -      -
     12Y    G      5.6     7.2    -      -       -      +
----------------------------------------------------------
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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