Contacts of the helix formed by residues 16 - 27 (chain B) in PDB entry 4WNB


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 16 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     14B  TYR*     3.1    42.9    +      -       +      +
     15B  GLY*     1.3    78.4    -      -       -      +
     17B  PRO*     1.3    76.6    -      -       +      +
     18B  THR*     3.4    12.6    +      -       -      +
     19B  PHE*     3.0    39.9    +      -       -      +
     20B  ILE*     3.1     9.0    +      -       -      +
     87B  TYR*     4.6     2.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with PRO 17 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     15B  GLY      4.3     1.6    -      -       -      +
     16B  ASP*     1.3    86.5    -      -       +      +
     18B  THR*     1.3    57.3    +      -       -      +
     20B  ILE*     3.2     2.9    +      -       +      +
     21B  VAL*     2.8    38.2    +      -       +      +
     37B  ARG*     5.4     3.8    -      -       -      +
     48B  ILE*     4.3    19.3    -      -       +      -
     86B  ALA*     4.3     8.1    -      -       +      -
     87B  TYR*     3.5    41.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with THR 18 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16B  ASP*     3.2    11.0    +      -       -      +
     17B  PRO*     1.3    78.3    -      -       -      +
     19B  PHE*     1.3    52.4    +      -       -      +
     21B  VAL*     4.7     3.8    -      -       -      -
     22B  SER*     2.7    48.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 19 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     40A  ALA      3.8    11.4    -      -       -      -
     41A  ILE      4.6     9.0    -      -       -      -
     13B  LEU*     4.7    11.0    -      -       +      -
     14B  TYR      4.1    10.3    -      -       -      +
     15B  GLY*     4.2    14.4    -      -       -      -
     16B  ASP*     3.0    26.1    +      -       -      +
     18B  THR*     1.3    78.3    -      -       -      +
     20B  ILE*     1.3    61.3    +      -       +      +
     22B  SER*     3.8     4.7    -      -       -      -
     23B  THR*     2.7    64.0    +      -       +      +
     50B  VAL*     4.2    10.1    -      -       +      -
     54B  THR*     4.2     3.6    -      -       +      -
     58B  LEU*     3.9    25.1    -      -       +      -
     61B  ARG*     5.8     0.4    -      -       -      -
     84B  TRP*     3.9    22.4    -      +       -      -
----------------------------------------------------------
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Residues in contact with ILE 20 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     15B  GLY*     3.7    10.8    -      -       -      +
     16B  ASP      3.1     8.5    +      -       -      +
     17B  PRO      3.7     6.1    -      -       -      +
     19B  PHE*     1.3    79.0    -      -       +      +
     21B  VAL*     1.3    61.9    +      -       -      +
     23B  THR*     3.2     5.4    +      -       -      -
     24B  ALA*     3.1    23.6    +      -       -      +
     34B  HIS*     3.4    18.8    -      -       +      +
     48B  ILE*     3.8    19.1    -      -       +      +
     49B  PHE*     3.6    22.9    -      -       -      +
     50B  VAL*     3.7    19.8    -      -       +      +
     51B  ASN      5.8     0.2    +      -       -      -
     84B  TRP      4.1     7.6    -      -       -      +
     85B  TYR      4.0     4.7    -      -       -      +
     86B  ALA*     3.5    41.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 21 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     17B  PRO*     2.8    27.3    +      -       +      +
     18B  THR*     4.1     3.8    -      -       -      +
     20B  ILE*     1.3    70.4    -      -       -      +
     22B  SER*     1.3    66.2    +      -       -      +
     24B  ALA*     3.3     1.8    +      -       -      +
     25B  LEU*     3.0    39.1    +      -       +      +
     34B  HIS      3.7    17.9    -      -       -      +
     35B  HIS*     3.9    25.6    -      -       +      +
     48B  ILE*     4.3     8.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 22 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     40A  ALA*     3.6    17.8    +      -       -      +
     18B  THR*     2.7    37.3    +      -       -      +
     19B  PHE*     3.4     6.4    +      -       -      -
     21B  VAL*     1.3    76.6    -      -       -      +
     23B  THR*     1.3    61.1    +      -       -      +
     25B  LEU*     4.3     2.6    -      -       -      +
     26B  ALA*     2.9    30.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 23 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     40A  ALA*     3.3    37.2    -      -       +      +
     41A  ILE*     4.0    11.7    -      -       +      -
     19B  PHE*     2.7    47.0    +      -       +      +
     20B  ILE*     3.2     7.3    +      -       -      -
     22B  SER*     1.3    74.4    +      -       -      +
     24B  ALA*     1.3    68.3    +      -       -      +
     26B  ALA*     3.2     2.1    +      -       -      +
     27B  THR*     3.0    27.0    +      -       -      +
     50B  VAL*     5.0     2.4    -      -       -      +
     51B  ASN*     5.0     0.3    +      -       -      -
     54B  THR*     3.2    25.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 24 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     20B  ILE      3.1    15.0    +      -       -      +
     21B  VAL      3.8     3.6    -      -       -      +
     23B  THR*     1.3    82.3    +      -       -      +
     25B  LEU*     1.3    63.8    +      -       +      +
     27B  THR*     2.8    22.1    +      -       -      -
     29B  ASP*     3.0    28.3    +      -       -      +
     34B  HIS*     3.5    33.2    -      -       +      +
     51B  ASN*     4.1    11.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 25 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     21B  VAL*     3.0    34.2    +      -       +      +
     22B  SER*     4.3     2.9    -      -       -      +
     24B  ALA*     1.3    81.0    -      -       +      +
     26B  ALA*     1.3    58.1    +      -       -      +
     28B  ARG*     3.0    22.1    +      -       -      +
     29B  ASP      4.0    15.5    -      -       -      +
     30B  PHE*     3.8    34.7    -      -       +      -
     35B  HIS*     4.3    20.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 26 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33A  MET*     5.0     2.6    -      -       -      +
     36A  ASN*     3.6    34.4    -      -       +      +
     37A  TRP*     3.7    25.7    +      -       +      +
     40A  ALA*     3.8     8.3    -      -       +      -
     41A  ILE*     6.0     0.4    -      -       +      -
     68A  MET*     4.9     1.0    -      -       -      +
     71A  VAL*     3.8     9.0    -      -       -      +
     22B  SER      2.9    21.1    +      -       -      +
     23B  THR*     3.7     3.8    -      -       -      +
     25B  LEU*     1.3    77.5    -      -       -      +
     27B  THR*     1.3    58.8    +      -       +      +
     28B  ARG*     3.2     3.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 27 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37A  TRP*     3.6    25.8    -      -       +      +
     41A  ILE*     4.9     2.9    -      -       +      -
     71A  VAL*     3.7    11.0    -      -       +      +
     74A  MET*     3.5    13.3    -      -       -      +
     23B  THR      3.0    12.3    +      -       -      +
     24B  ALA      2.8    17.2    +      -       -      -
     26B  ALA*     1.3    75.6    -      -       +      +
     28B  ARG*     1.3    70.2    +      -       -      +
     29B  ASP*     3.3     0.9    +      -       -      +
     51B  ASN*     2.9    21.1    +      -       -      -
     53B  LEU*     3.7    37.3    -      -       +      +
     54B  THR*     4.0    11.2    -      -       -      +
----------------------------------------------------------
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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