Contacts of the strand formed by residues 280 - 285 (chain B) in PDB entry 4PS1


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 GLU 280 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    246A  LYS*     6.4     2.0    -      -       -      -
    288A  THR*     4.4     6.9    +      -       -      +
    232B  PRO*     3.8    26.5    -      -       +      +
    234B  GLY      2.9    13.6    +      -       -      +
    235B  TYR*     3.4    20.3    -      -       +      -
    236B  CYS      2.9    21.3    +      -       -      -
    279B  PHE*     1.3    71.6    -      -       -      +
    281B  ILE*     1.3    63.5    +      -       -      +
    282B  LYS*     2.7    43.1    +      -       +      +
    307B  MET*     4.9     1.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 281 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    246A  LYS*     5.6     9.2    -      -       -      +
    236B  CYS*     3.4    18.2    -      -       +      +
    238B  ILE*     3.7    30.5    -      -       +      -
    271B  THR*     3.9    22.9    -      -       +      +
    274B  PHE*     3.7    29.8    -      -       +      -
    275B  GLU*     3.5    39.1    +      -       +      +
    279B  PHE*     3.7     7.2    +      -       +      +
    280B  GLU*     1.3    73.7    -      -       -      +
    282B  LYS*     1.3    71.4    -      -       -      +
    283B  PRO*     3.4    18.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with LYS 282 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    286A  ASP      5.2     9.2    +      -       -      +
    288A  THR*     3.5    27.3    +      -       -      +
    291A  GLN*     5.5     4.6    +      -       -      +
    235B  TYR*     3.7    17.3    -      -       +      -
    236B  CYS      2.9     8.7    +      -       -      -
    237B  LEU*     3.5    19.9    -      -       +      -
    238B  ILE      3.0    18.9    +      -       -      -
    280B  GLU*     2.7    46.6    +      -       -      +
    281B  ILE*     1.3    80.3    +      -       -      +
    283B  PRO*     1.3    64.5    -      -       -      +
    284B  HIS*     3.5    15.9    -      -       -      +
    299B  TYR*     3.3    26.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with PRO 283 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    243A  ASN*     4.1    22.5    +      -       -      +
    286A  ASP*     4.3    12.0    -      -       -      +
    238B  ILE*     3.4    20.6    -      -       +      +
    240B  ASN*     6.2     0.4    -      -       +      -
    267B  ALA*     6.3     2.5    -      -       +      -
    271B  THR*     5.7     2.0    -      -       -      +
    281B  ILE*     3.4    17.7    -      -       +      +
    282B  LYS*     1.3    89.4    -      -       -      +
    284B  HIS*     1.3    70.0    +      -       -      +
    285B  ASP*     4.3     9.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with HIS 284 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    285A  ASP*     3.6    41.3    +      -       +      +
    286A  ASP*     5.0     6.5    +      -       +      -
    237B  LEU*     5.6     1.8    -      -       +      -
    238B  ILE      2.8     9.0    +      -       -      +
    239B  ILE*     3.5    10.7    -      -       +      -
    240B  ASN      2.9    23.0    +      -       -      -
    282B  LYS*     3.5    25.8    +      -       +      +
    283B  PRO*     1.3    78.2    +      -       -      +
    285B  ASP*     1.3    64.5    +      -       -      +
    287B  CYS*     3.8     9.0    -      -       -      -
    295B  ILE*     3.6    50.3    -      -       +      +
    299B  TYR*     4.8     8.8    +      +       -      -
----------------------------------------------------------
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Residues in contact with ASP 285 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    240B  ASN*     3.3    32.9    +      -       -      +
    283B  PRO*     5.0     6.6    -      -       -      +
    284B  HIS*     1.3    78.7    +      -       -      +
    286B  ASP*     1.3    81.9    +      -       +      +
    287B  CYS*     3.5     4.8    -      -       -      -
    291B  GLN*     5.3     2.3    +      -       -      -
----------------------------------------------------------
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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