Contacts of the strand formed by residues 79 - 82 (chain L) in PDB entry 2WWB


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 79 (chain L).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     73L  VAL*     3.3     3.6    -      -       -      +
     74L  TYR*     3.0    35.2    +      -       -      -
     77L  LYS*     3.3    23.1    -      -       +      +
     78L  PHE*     1.4    76.8    -      -       +      +
     80L  VAL*     1.4    64.2    +      -       -      +
     98L  ASN*     3.3    21.8    -      -       +      +
     99L  LEU      3.2    14.8    -      -       -      +
    100L  HIS*     5.4     0.2    -      -       -      -
    101L  PRO*     4.6     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 80 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     50L  ILE*     4.5     4.3    -      -       +      -
     70L  ILE*     3.6    35.0    -      -       +      -
     72L  SER      3.6     3.6    -      -       -      -
     73L  VAL*     3.5    23.3    -      -       +      -
     79L  ALA*     1.4    72.5    -      -       -      +
     81L  GLN*     1.4    74.5    +      -       -      +
     82L  VAL*     3.8     9.9    -      -       +      -
     97L  ILE      4.0     0.2    -      -       -      +
     98L  ASN*     3.3     6.9    -      -       -      -
     99L  LEU*     2.9    36.5    +      -       +      +
    101L  PRO*     3.8    23.6    -      -       +      -
    104L  LEU*     4.3    15.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 81 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     70L  ILE*     3.6     0.9    -      -       -      +
     71L  SER*     3.0    42.0    +      -       -      +
     72L  SER*     2.9    23.0    +      -       -      +
     74L  TYR*     4.2    15.4    +      -       +      -
     79L  ALA      4.3     0.4    +      -       -      -
     80L  VAL*     1.4    80.7    -      -       -      +
     82L  VAL*     1.4    66.2    +      -       -      +
     83L  ASP*     5.5     0.2    -      -       -      +
     84L  LYS*     5.3     7.8    -      -       -      +
     86L  THR*     5.9     1.2    -      -       -      -
     95L  VAL      5.0     1.4    -      -       -      +
     96L  PRO*     3.3    47.8    -      -       -      +
     97L  ILE      3.3    11.0    -      -       -      +
     98L  ASN*     3.9     7.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 82 (chain L). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     56L  VAL*     4.7     7.0    -      -       +      +
     58L  VAL*     4.9     7.2    -      -       +      -
     66L  GLN*     4.4    14.1    -      -       -      +
     67L  GLU      4.4     4.7    -      -       -      +
     68L  GLY*     3.7    27.8    -      -       -      +
     69L  LYS      3.7    11.0    -      -       -      +
     70L  ILE*     4.3     7.6    -      -       +      -
     71L  SER*     3.7     3.1    -      -       -      -
     80L  VAL*     3.8    15.0    +      -       +      -
     81L  GLN*     1.4    84.7    -      -       -      +
     83L  ASP*     1.4    67.1    +      -       -      +
     84L  LYS*     3.6     2.8    +      -       -      +
     85L  VAL      3.4    17.3    -      -       -      +
     86L  THR      4.6     0.5    +      -       -      -
     96L  PRO      4.8     0.7    -      -       -      +
     97L  ILE*     4.4     5.4    +      -       +      +
     99L  LEU*     3.7    29.2    -      -       +      +
    104L  LEU*     5.2     3.6    -      -       +      -
----------------------------------------------------------
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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