Contacts of the strand formed by residues 92 - 98 (chain E) in PDB entry 4WFH


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 ALA 92 (chain E).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38E  LYS*     4.0    20.2    -      -       +      -
     39E  GLN      3.4    16.4    -      -       -      +
     40E  ARG*     3.7    12.6    -      -       -      +
     41E  HIS      5.0     2.5    -      -       -      +
     90E  ASP      3.0    10.0    +      -       -      +
     91E  SER*     1.3    76.6    -      -       -      +
     93E  ILE*     1.3    65.7    +      -       -      +
     94E  TYR*     3.8     6.7    -      -       +      -
    110E  THR      3.8     0.3    -      -       -      +
    111E  THR*     3.5     4.1    -      -       -      +
    112E  LEU*     2.8    33.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 93 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37E  VAL      3.9     0.3    -      -       -      +
     38E  LYS*     3.6     2.4    -      -       -      -
     39E  GLN*     2.8    45.2    +      -       +      +
     41E  HIS*     5.5     1.8    -      -       -      +
     92E  ALA*     1.3    76.4    -      -       -      +
     94E  TYR*     1.3    63.1    -      -       -      +
     95E  TYR*     3.6    40.5    +      -       +      +
    108E  GLN      5.4     0.4    -      -       -      +
    109E  GLY*     4.2     2.0    -      -       -      -
    110E  THR      3.3    16.4    -      -       -      +
    111E  THR*     3.4    25.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 94 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6E  GLN*     2.7    24.4    +      -       -      -
     18E  MET*     5.0     3.8    -      -       +      -
     20E  THR*     5.5     0.2    -      -       +      -
     36E  TRP*     4.8     1.6    -      -       +      -
     37E  VAL      3.3     3.6    -      -       -      +
     38E  LYS*     3.7    39.4    +      -       +      +
     48E  ILE*     3.7    18.6    -      -       +      -
     64E  PHE*     5.5     2.7    -      +       -      -
     81E  MET*     3.6    28.9    -      -       +      -
     83E  LEU*     3.6    25.9    -      -       +      +
     90E  ASP*     2.6    38.2    +      -       -      +
     92E  ALA*     3.8    11.7    -      -       +      -
     93E  ILE*     1.3    75.1    -      -       -      +
     95E  TYR*     1.3    58.6    +      -       -      +
    110E  THR*     2.8    33.7    +      -       +      +
    112E  LEU*     3.8    25.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 95 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37D  GLN*     3.4    10.7    +      -       -      -
     41D  THR      4.2     2.3    +      -       -      -
     42D  SER*     3.5    27.8    +      -       -      -
     43D  PRO*     4.0    11.2    -      -       +      -
      6E  GLN*     3.6     2.2    -      -       -      -
     36E  TRP*     3.2    12.2    -      -       -      -
     37E  VAL*     2.8    44.8    +      -       +      +
     39E  GLN*     3.2    34.4    +      -       +      -
     45E  LEU*     4.5     2.0    -      -       +      -
     93E  ILE*     3.6    26.7    -      -       +      +
     94E  TYR*     1.3    75.0    -      -       -      +
     96E  CYS*     1.3    63.2    +      -       -      +
     97E  THR      4.1     0.2    +      -       -      -
    106E  TRP*     3.7    32.1    -      +       +      -
    107E  GLY      3.7     8.7    -      -       -      -
    108E  GLN      4.0     2.0    -      -       -      -
    109E  GLY*     3.4    26.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with CYS 96 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4E  LEU*     3.7    12.2    -      -       -      +
      6E  GLN*     3.3    19.2    +      -       -      +
     22E  CYS*     2.0    55.0    -      -       +      -
     34E  MET*     3.4    10.5    -      -       +      -
     35E  ASN      3.4     6.5    -      -       -      +
     36E  TRP*     3.9    12.8    -      -       +      -
     95E  TYR*     1.3    75.9    -      -       -      +
     97E  THR*     1.3    61.2    +      -       -      +
    106E  TRP*     3.5     0.7    -      -       -      -
    107E  GLY      2.8    26.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with THR 97 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4E  LEU*     4.0     1.8    -      -       -      -
     34E  MET*     3.7     5.4    -      -       -      +
     35E  ASN*     2.8    43.5    +      -       +      +
     37E  VAL*     3.9    26.5    -      -       +      -
     96E  CYS*     1.3    76.0    -      -       -      +
     98E  ARG*     1.3    57.5    +      -       -      +
    103E  PHE*     3.2    40.8    -      -       +      +
    105E  TYR      2.8    19.9    +      -       -      -
    106E  TRP*     3.4    22.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 98 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      2E  VAL*     4.8     1.4    -      -       -      +
      4E  LEU*     4.7     2.9    -      -       +      -
     27E  TYR*     3.3    64.6    -      -       -      +
     32E  TYR*     3.6    45.3    +      -       +      -
     33E  ILE      3.4    12.3    -      -       -      +
     34E  MET*     4.4     4.5    -      -       -      -
     35E  ASN*     3.9     2.0    -      -       -      -
     97E  THR*     1.3    74.7    -      -       -      +
     99E  GLY*     1.3    61.0    +      -       -      +
    103E  PHE*     3.2     6.6    -      -       -      -
    104E  ASP*     3.0    58.7    +      -       -      +
    105E  TYR*     2.9    43.0    +      -       +      +
----------------------------------------------------------
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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