Contacts of the strand formed by residues 452 - 456 (chain B) in PDB entry 2PY5


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 ILE 452 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    232B  TRP*     4.0    24.5    -      -       +      -
    234B  ASN*     3.0    27.5    +      -       -      +
    236B  ARG*     5.0     0.2    +      -       -      -
    237B  PHE*     3.4     7.8    -      -       -      -
    299B  ILE*     4.5     1.1    -      -       +      -
    445B  ALA*     3.8    32.1    -      -       +      +
    448B  CYS      3.0     9.0    +      -       -      +
    449B  TYR*     3.4    35.0    +      -       +      +
    451B  ARG*     1.3    76.2    -      -       -      +
    453B  ILE*     1.3    58.5    +      -       -      +
    454B  TYR      3.8    15.0    -      -       -      +
    455B  CYS*     4.1     2.5    -      -       -      -
    460B  ILE*     4.0     9.4    -      -       +      -
    461B  HIS      3.5    16.4    -      -       -      +
    462B  LEU*     3.7    15.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 453 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    232B  TRP*     4.9     0.2    -      -       -      -
    233B  LEU*     3.5     3.6    -      -       +      +
    234B  ASN*     2.9    30.2    +      -       -      +
    237B  PHE*     3.8    19.5    -      -       +      -
    242B  ILE*     3.7    32.3    -      -       +      -
    452B  ILE*     1.3    76.2    -      -       -      +
    454B  TYR*     1.3    66.5    +      -       +      +
    461B  HIS*     2.8    14.5    +      -       +      +
    462B  LEU*     3.6    24.5    -      -       -      +
    463B  THR*     3.7    24.5    -      -       +      +
    489B  PHE*     3.9    17.7    -      -       +      -
    494B  TYR*     3.8    23.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 454 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    231B  THR*     3.8     3.0    -      -       +      +
    232B  TRP*     3.2    26.9    -      -       -      -
    233B  LEU*     4.0    12.6    -      -       +      -
    452B  ILE*     3.8     5.2    -      -       -      +
    453B  ILE*     1.3    81.4    -      -       +      +
    455B  CYS*     1.3    75.7    +      -       -      +
    456B  ASP*     3.6    26.5    +      -       +      +
    460B  ILE*     3.5     2.4    -      -       -      -
    461B  HIS*     2.9    55.6    +      +       +      +
    494B  TYR*     3.8    24.9    -      +       +      -
    496B  ARG      4.6     2.2    -      -       -      -
    497B  GLN*     4.0    11.0    -      -       -      -
    498B  LYS*     2.8    42.6    +      -       -      +
    500B  TYR*     3.6    23.7    -      +       -      -
----------------------------------------------------------
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Residues in contact with CYS 455 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    230B  PHE*     3.7    36.8    -      -       +      +
    231B  THR*     3.3     1.2    -      -       -      -
    232B  TRP*     2.9    39.1    +      -       -      +
    299B  ILE*     5.1     0.2    -      -       -      -
    441B  THR*     4.1     6.3    -      -       +      -
    445B  ALA*     3.5    31.6    -      -       -      -
    452B  ILE*     4.1     4.5    -      -       -      -
    454B  TYR*     1.3    86.6    -      -       -      +
    456B  ASP*     1.3    63.1    +      -       -      +
    459B  SER      3.2     8.5    -      -       -      +
    460B  ILE*     4.0     9.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with ASP 456 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    230B  PHE      3.5     2.0    -      -       -      -
    231B  THR*     2.8    27.2    +      -       +      -
    454B  TYR*     3.6    25.5    +      -       +      +
    455B  CYS*     1.3    74.7    -      -       -      +
    457B  THR*     1.3    67.3    +      -       -      +
    458B  ASP*     2.7    22.7    +      -       -      +
    459B  SER*     3.0    22.1    +      -       -      -
    461B  HIS*     5.7     0.2    -      -       -      +
    498B  LYS*     3.9    20.0    -      -       -      +
----------------------------------------------------------
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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