Contacts of the strand formed by residues 283 - 287 (chain B) in PDB entry 5WN1


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 ASP 283 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     66B  SER*     5.7     1.5    +      -       -      +
     67B  TRP*     6.2     0.7    -      -       -      -
     68B  ASN*     4.1     8.6    +      -       -      +
     95B  GLN*     4.6     2.4    -      -       -      +
    209B  GLY      3.3     5.9    -      -       -      +
    210B  ASP*     3.2    29.5    +      -       -      +
    265B  THR*     3.0    36.2    +      -       -      +
    281B  ARG*     3.8     9.7    +      -       -      +
    282B  LEU*     1.3    77.9    -      -       -      +
    284B  TYR*     1.3    61.9    +      -       -      +
    309B  HIS*     2.6    32.0    +      -       -      +
    310B  CYS      5.0     3.1    -      -       -      +
    312B  ILE*     3.4    32.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 284 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    207B  LEU      4.2     0.7    -      -       -      -
    208B  CYS*     3.3     6.4    -      -       -      +
    209B  GLY      3.0    28.7    +      -       -      -
    211B  LEU*     4.0    26.2    -      -       +      -
    213B  VAL      2.9    24.3    +      -       -      -
    215B  HIS*     3.4    17.3    +      -       -      +
    219B  ASP*     4.6     0.5    +      -       -      -
    240B  PHE*     3.5    21.8    -      +       -      -
    251B  ASP*     3.3    22.7    -      -       -      -
    281B  ARG*     3.1    50.1    +      -       -      +
    282B  LEU      3.3    28.5    -      -       -      -
    283B  ASP*     1.3    74.6    -      -       -      +
    285B  PHE*     1.3    60.1    +      -       -      +
    286B  LEU*     3.7    15.5    -      -       +      -
    312B  ILE*     3.6    11.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 285 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     64B  ILE*     3.4    35.4    -      -       +      -
     66B  SER*     4.0     7.4    -      -       -      -
    206B  VAL*     4.5     7.4    -      -       +      -
    207B  LEU      3.5     2.0    -      -       -      -
    208B  CYS*     3.3    28.0    -      -       +      -
    251B  ASP*     4.3     1.7    +      -       -      +
    252B  SER*     2.9    42.5    +      -       -      +
    253B  PHE      5.8     0.4    -      -       -      +
    284B  TYR*     1.3    71.8    -      -       -      +
    286B  LEU*     1.3    62.6    +      -       -      +
    287B  LEU*     4.4     2.2    -      -       +      -
    298B  SER*     4.1    13.0    +      -       -      -
    312B  ILE*     3.5    37.5    -      -       +      -
    313B  THR      3.6     6.3    -      -       -      -
    314B  LEU*     3.5    47.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 286 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    205B  LEU      4.0     0.3    -      -       -      +
    206B  VAL*     3.6     0.9    -      -       -      -
    207B  LEU*     2.8    52.8    +      -       +      +
    211B  LEU*     3.9    20.9    -      -       +      -
    240B  PHE*     4.1    11.0    -      -       +      -
    243B  LEU*     4.1    11.0    -      -       +      -
    244B  LEU*     4.0    18.6    -      -       +      -
    249B  LEU*     4.0    18.7    -      -       +      +
    250B  ALA      3.2     5.2    -      -       -      +
    251B  ASP*     3.8    20.6    -      -       +      +
    284B  TYR*     3.7    27.4    -      -       +      -
    285B  PHE*     1.3    80.1    -      -       -      +
    287B  LEU*     1.3    66.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 287 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    205B  LEU      3.5     4.0    -      -       -      +
    206B  VAL*     4.0    19.5    -      -       +      -
    249B  LEU*     3.2     9.4    -      -       -      -
    250B  ALA*     2.9    31.2    +      -       -      +
    252B  SER*     4.3    13.0    -      -       -      -
    285B  PHE*     4.4     4.3    -      -       +      -
    286B  LEU*     1.3    85.7    -      -       -      +
    288B  SER*     1.3    74.0    +      -       -      +
    291B  LEU*     4.3    14.1    -      -       +      +
    292B  LEU*     4.6     9.4    -      -       +      -
    295B  LEU*     4.3    27.6    -      -       +      -
    314B  LEU*     3.9    21.1    -      -       +      -
    316B  LEU*     4.1    21.3    -      -       +      -
----------------------------------------------------------
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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