Contacts of the strand formed by residues 235 - 240 (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 TYR 235 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    294A  GLU*     4.5     5.2    +      -       -      -
    234B  GLY*     1.3    73.6    -      -       -      -
    236B  CYS*     1.3    59.2    +      -       -      +
    237B  LEU*     4.0    10.5    -      -       +      -
    279B  PHE*     4.0     3.1    -      -       -      -
    280B  GLU*     3.4    27.4    -      -       +      +
    282B  LYS*     3.7    23.1    -      -       +      -
    299B  TYR*     3.7    19.5    -      +       +      -
    302B  MET*     3.5    28.6    -      -       +      +
    303B  ASP      4.9     6.8    +      -       -      -
    304B  HIS*     3.7    35.2    -      +       -      -
    307B  MET*     3.6    29.7    -      -       +      +
    309B  CYS      4.1     2.6    +      -       -      -
    310B  PHE*     3.7     9.3    -      -       +      +
    311B  ILE      3.0    25.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with CYS 236 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    234B  GLY      3.9     0.2    +      -       -      -
    235B  TYR*     1.3    73.0    -      -       -      +
    237B  LEU*     1.3    65.3    +      -       -      +
    238B  ILE*     3.7     8.0    +      -       -      -
    274B  PHE*     4.0    26.5    -      -       -      -
    279B  PHE*     3.9    12.3    -      -       +      -
    280B  GLU      2.9     8.3    +      -       -      -
    281B  ILE*     3.4    23.6    -      -       +      +
    282B  LYS      2.9    24.0    +      -       -      -
    311B  ILE*     3.3    30.1    -      -       +      -
    313B  CYS*     4.1    13.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 237 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    235B  TYR*     4.2     7.0    -      -       +      -
    236B  CYS*     1.3    73.2    -      -       -      +
    238B  ILE*     1.3    65.0    +      -       -      +
    239B  ILE*     5.0     5.4    -      -       +      -
    282B  LYS*     3.5    26.9    -      -       +      +
    284B  HIS*     5.6     0.9    -      -       +      -
    295B  ILE*     3.9    19.3    -      -       +      -
    296B  LEU*     3.8    29.6    -      -       +      -
    299B  TYR*     3.7    35.2    -      -       +      -
    310B  PHE*     3.8    22.9    -      -       +      -
    311B  ILE      2.9     9.8    +      -       -      +
    312B  CYS*     3.6    11.4    -      -       -      -
    313B  CYS*     2.9    26.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 238 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    236B  CYS*     4.2     7.0    -      -       -      +
    237B  LEU*     1.3    79.5    -      -       -      +
    239B  ILE*     1.3    58.7    +      -       -      +
    240B  ASN*     3.6     9.9    +      -       +      +
    267B  ALA*     4.0    11.2    -      -       +      +
    270B  LEU*     3.9    25.8    -      -       +      -
    271B  THR*     3.7    16.2    -      -       -      +
    281B  ILE*     3.7    28.9    -      -       +      -
    282B  LYS      3.0     8.7    +      -       -      +
    283B  PRO*     4.2    11.8    -      -       +      +
    284B  HIS*     2.8    33.6    +      -       -      +
    313B  CYS*     3.5    12.1    -      -       +      +
    315B  LEU*     3.9    28.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 239 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    237B  LEU*     5.0     5.6    -      -       +      -
    238B  ILE*     1.3    75.0    -      -       -      +
    240B  ASN*     1.3    59.0    +      -       -      +
    241B  ASN*     3.9    19.1    -      -       -      +
    284B  HIS*     3.5    11.7    -      -       +      -
    287B  CYS*     4.1     5.2    -      -       -      -
    292B  ILE*     4.0    35.4    -      -       +      -
    295B  ILE*     3.9    40.4    -      -       +      -
    296B  LEU*     5.6     2.0    -      -       +      -
    312B  CYS*     4.6    10.1    -      -       -      -
    313B  CYS      2.8    16.9    +      -       -      +
    314B  ILE*     4.2    21.8    -      -       +      -
    315B  LEU*     2.9    30.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASN 240 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    238B  ILE*     4.2    13.9    -      -       +      +
    239B  ILE*     1.3    72.2    -      -       -      +
    241B  ASN*     1.3    62.0    +      -       -      +
    242B  HIS*     3.6     2.9    +      -       -      +
    263B  THR*     2.5    43.8    +      -       -      +
    264B  HIS*     4.4     4.4    -      -       -      +
    267B  ALA*     3.3    27.7    -      -       +      +
    283B  PRO*     6.2     1.1    -      -       +      -
    284B  HIS      2.9    10.4    +      -       -      +
    285B  ASP*     3.3    27.3    +      -       -      +
    286B  ASP*     2.9    19.4    +      -       -      +
    315B  LEU*     3.7     5.5    -      -       +      +
----------------------------------------------------------
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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