Contacts of the strand formed by residues 76 - 83 (chain B) in PDB entry 3SBW


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 THR 76 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     68B  ASN*     4.2    20.6    -      -       +      +
     69B  ARG      3.4     3.8    -      -       -      -
     70B  LEU*     3.7    20.4    -      -       +      -
     74B  ASN      4.0     0.8    +      -       -      -
     75B  GLN*     1.3    85.0    +      -       -      +
     77B  GLU*     1.3    62.0    +      -       -      +
     78B  LYS      4.2     0.4    -      -       -      -
    122B  LEU*     4.7     2.0    -      -       +      -
    136B  GLU*     3.6    24.0    -      -       -      +
    123C  TYR*     3.7    27.6    +      -       +      +
    124C  LYS*     3.3    25.5    +      -       -      -
    125C  ARG*     3.7    14.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 77 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     68B  ASN*     3.6     2.5    -      -       -      -
     69B  ARG*     2.8    43.2    +      -       -      +
     71B  SER*     4.0    24.9    +      -       -      -
     75B  GLN*     4.5     8.5    -      -       +      +
     76B  THR*     1.3    79.8    -      -       -      +
     78B  LYS*     1.3    62.9    +      -       -      +
     79B  GLN*     2.9    27.7    +      -       -      +
    124C  LYS*     4.5     9.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 78 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     64B  MET*     5.5     1.4    -      -       -      +
     66B  ASN*     3.7    14.6    -      -       -      +
     68B  ASN*     3.0    18.1    +      -       -      +
     76B  THR      4.2     0.4    -      -       -      -
     77B  GLU*     1.3    72.7    -      -       -      +
     79B  GLN*     1.3    65.4    +      -       -      +
     80B  ALA      3.8    12.6    -      -       -      +
     81B  ALA*     3.6    24.2    -      -       -      +
     90B  VAL*     3.5    34.8    -      -       +      +
     18C  MET*     3.4    19.1    -      -       -      +
     19C  PHE*     3.6    17.6    +      -       -      +
     20C  THR*     5.2     4.0    +      -       -      +
    121C  ALA      2.5    34.1    +      -       -      +
    122C  ASP*     3.9    25.7    +      -       -      +
    124C  LYS*     5.0     1.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 79 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     67B  TRP*     2.7    23.8    +      -       +      +
     68B  ASN      4.3     1.6    -      -       -      -
     69B  ARG*     3.4    34.2    +      -       +      +
     77B  GLU*     2.9    32.4    +      -       -      +
     78B  LYS*     1.3    82.2    +      -       -      +
     80B  ALA*     1.3    59.9    +      -       -      +
     89B  PRO*     3.6     2.9    -      -       -      +
     90B  VAL*     3.0    25.5    +      -       -      +
     91B  GLN      4.6     1.6    +      -       -      -
     92B  ASP      4.6     1.4    +      -       -      +
     95B  PHE*     3.6    55.0    -      -       +      +
    121B  TYR*     4.3     4.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 80 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     66B  ASN*     3.7     2.1    -      -       -      -
     67B  TRP*     2.8    29.2    +      -       +      +
     78B  LYS*     3.8     7.9    -      -       -      +
     79B  GLN*     1.3    80.2    -      -       -      +
     81B  ALA*     1.3    63.0    +      -       -      +
     87B  SER*     4.4     2.2    -      -       -      +
     88B  GLN      3.3    15.0    -      -       -      +
     89B  PRO*     3.9     2.9    -      -       +      -
     90B  VAL*     4.3     2.9    -      -       -      +
     95B  PHE*     3.6    28.0    -      -       +      +
     97B  ILE*     4.1    17.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 81 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     64B  MET*     4.8    10.3    -      -       +      -
     65B  LEU      3.3     4.7    -      -       -      -
     66B  ASN*     3.4    19.7    -      -       -      +
     78B  LYS*     3.6     6.3    -      -       -      +
     80B  ALA*     1.3    74.9    -      -       -      +
     82B  PHE*     1.3    62.0    +      -       -      +
     83B  SER*     4.0     3.1    +      -       -      +
     86B  LEU      3.8     1.4    -      -       -      +
     87B  SER*     3.5     0.7    -      -       -      -
     88B  GLN*     2.8    36.5    +      -       -      +
     97B  ILE*     3.9     4.3    -      -       -      -
     18C  MET*     3.5    27.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 82 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     59B  TRP*     4.2    21.5    -      +       -      -
     61B  GLU*     4.7     1.6    -      -       -      -
     63B  LEU      4.2     0.7    -      -       -      +
     64B  MET*     3.4     2.8    -      -       -      +
     65B  LEU*     2.7    47.5    +      -       +      +
     81B  ALA*     1.3    73.1    -      -       -      +
     83B  SER*     1.3    66.7    +      -       -      +
     85B  GLY*     3.4    42.8    -      -       -      -
     86B  LEU*     3.4    15.9    -      -       -      -
     87B  SER*     3.8    11.0    -      -       -      +
     97B  ILE*     3.7    28.4    -      -       +      +
     99B  GLN*     3.6    41.1    -      -       +      -
    106B  PHE*     4.0    16.2    -      +       +      -
----------------------------------------------------------
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Residues in contact with SER 83 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     59B  TRP*     6.0     0.2    -      -       -      -
     63B  LEU      4.4     6.3    -      -       -      -
     64B  MET*     3.8    34.5    -      -       -      +
     81B  ALA*     4.0     4.4    +      -       -      +
     82B  PHE*     1.3    80.0    -      -       -      +
     84B  ASN*     1.3    75.2    +      -       -      +
     85B  GLY      3.3     2.2    -      -       -      -
     86B  LEU*     3.0    17.7    +      -       -      +
     88B  GLN*     4.8     8.8    +      -       -      +
----------------------------------------------------------
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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