Contacts of the strand formed by residues 91 - 95 (chain A) in PDB entry 5WN0


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 91 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     62A  LEU*     4.5     9.2    -      -       +      -
     63A  LYS      3.4     2.6    +      -       -      -
     64A  ILE*     3.9    15.9    -      -       +      -
     65A  CYS      2.8    26.7    +      -       -      -
     89A  PRO*     3.3     7.7    -      -       -      +
     90A  ASP*     1.3    88.4    -      -       +      +
     92A  LEU*     1.3    63.2    +      -       -      +
     93A  CYS*     4.0    13.9    -      -       -      -
    114A  LEU*     4.4     0.2    -      -       -      -
    133A  LEU*     4.5    10.1    -      -       +      -
    134A  LEU      3.2     9.6    -      -       -      +
    135A  SER*     3.6    13.5    -      -       -      -
    162A  PHE*     3.7    32.1    -      -       +      -
    165A  PHE*     4.0    13.0    -      -       +      -
    167A  LEU*     3.6    28.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 92 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     65A  CYS*     3.1    37.2    -      -       +      +
     67A  TRP*     4.9     4.5    -      -       +      -
     75A  TRP*     4.4     5.4    -      -       +      -
     81A  LEU*     5.3     3.1    -      -       +      -
     84A  VAL*     3.7    39.0    -      -       +      -
     89A  PRO*     4.3     7.9    -      -       +      -
     91A  ILE*     1.3    73.9    -      -       -      +
     93A  CYS*     1.3    61.2    -      -       -      +
     94A  LEU*     3.5    38.4    -      -       +      -
    108A  LEU*     6.1     0.2    -      -       +      -
    111A  LEU*     5.4     0.4    -      -       +      -
    114A  LEU*     4.2     9.3    -      -       +      +
    132A  GLY      3.9     0.3    -      -       -      +
    133A  LEU*     3.5     2.8    -      -       -      -
    134A  LEU*     2.7    57.5    +      -       +      +
----------------------------------------------------------
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Residues in contact with CYS 93 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     64A  ILE*     4.4     2.5    -      -       -      -
     65A  CYS      2.7    14.4    +      -       -      +
     66A  SER*     3.2     2.1    -      -       -      +
     67A  TRP      2.8    31.5    +      -       -      -
     91A  ILE*     4.0    18.4    -      -       -      -
     92A  LEU*     1.3    75.1    -      -       -      +
     94A  LEU*     1.3    60.3    -      -       -      +
     95A  GLN*     3.5     4.3    -      -       -      +
    132A  GLY      3.3     5.6    -      -       -      +
    133A  LEU*     4.2     7.9    -      -       -      -
    167A  LEU*     4.1    10.5    -      -       -      -
    169A  THR*     3.1    29.6    -      -       -      +
    208A  CYS*     3.4    26.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 94 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     67A  TRP*     3.2    12.3    -      -       +      +
     69A  VAL*     4.1    16.8    -      -       +      -
     72A  LEU*     4.2    16.8    -      -       +      -
     75A  TRP*     4.4     8.7    -      -       +      -
     92A  LEU*     3.5    35.0    -      -       +      -
     93A  CYS*     1.3    81.6    -      -       -      +
     95A  GLN*     1.3    66.7    +      -       -      +
     97A  THR*     4.2    13.9    -      -       +      -
    108A  LEU*     5.3     1.3    -      -       +      -
    119A  TRP*     4.1    16.6    -      -       +      -
    131A  VAL*     3.3     5.5    -      -       -      +
    132A  GLY      2.8    34.0    +      -       -      +
    134A  LEU*     4.0    24.9    -      -       +      -
    169A  THR*     5.0     0.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 95 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     66A  SER*     3.1    20.5    +      -       -      -
     67A  TRP      2.8    10.2    +      -       -      -
     68A  ASN*     3.2    31.8    +      -       +      +
     69A  VAL*     2.9    27.2    +      -       -      +
     93A  CYS      3.5    18.6    -      -       -      -
     94A  LEU*     1.3    76.8    -      -       -      +
     96A  GLU*     1.3    67.6    +      -       -      +
     97A  THR*     3.4     2.6    +      -       -      -
    130A  GLY      4.0     2.7    -      -       -      -
    131A  VAL*     4.0     9.9    -      -       +      -
    169A  THR*     3.0    24.9    +      -       -      +
    170A  ALA      3.3    21.1    -      -       -      +
    171A  TYR*     4.1    11.7    -      -       +      -
    209A  GLY*     3.6    14.4    -      -       -      -
    210A  ASP*     3.8     4.8    +      -       +      +
    283A  ASP*     4.4     1.6    -      -       -      +
----------------------------------------------------------
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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