Contacts of the strand formed by residues 72 - 77 (chain B) in PDB entry 6Q3W


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 LEU 72 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     68B  ARG*     4.5     7.1    -      -       +      +
     71B  GLY*     1.3    78.3    -      -       -      +
     73B  VAL*     1.3    63.1    +      -       -      +
     74B  SER*     3.8     4.4    +      -       -      +
     89B  GLN*     6.2     3.1    -      -       +      -
     90B  PHE      4.1     5.8    -      -       -      +
     91B  PRO*     4.7     2.0    -      -       +      -
    124B  GLY*     3.5     2.6    -      -       -      -
    125B  PHE      3.1    23.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 73 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     72B  LEU*     1.3    74.6    -      -       -      +
     74B  SER*     1.3    60.7    +      -       -      +
     75B  LEU*     3.8    14.8    -      -       +      -
     88B  LEU      3.9     0.2    -      -       -      +
     89B  GLN*     3.3     3.3    -      -       -      -
     90B  PHE*     2.9    70.0    +      -       +      +
     92B  LEU*     4.9    15.0    -      -       +      +
    114B  ILE*     4.1    13.5    -      -       +      -
    122B  LEU*     6.4     0.7    -      -       +      -
    123B  PRO      5.3     1.3    -      -       -      +
    124B  GLY*     4.7     4.7    -      -       -      -
    125B  PHE*     3.5    44.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with SER 74 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     24B  PHE*     3.2    27.1    -      -       -      -
     72B  LEU*     3.8     4.7    +      -       -      -
     73B  VAL*     1.3    73.6    -      -       -      +
     75B  LEU*     1.3    65.3    +      -       -      +
     88B  LEU      3.4     8.2    +      -       -      -
     89B  GLN*     4.3     9.4    -      -       -      +
    125B  PHE      2.9    10.9    +      -       -      -
    126B  SER*     3.4     5.0    -      -       -      -
    127B  ALA      3.0    26.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 75 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     24B  PHE*     4.8     2.4    -      -       -      -
     63B  LEU*     6.0     1.1    -      -       +      -
     73B  VAL*     3.8     7.6    -      -       +      -
     74B  SER*     1.3    85.4    +      -       -      +
     76B  LEU*     1.3    62.2    +      -       -      +
     86B  GLN      4.6     0.2    -      -       -      -
     87B  ARG*     3.5     2.1    -      -       -      +
     88B  LEU*     2.7    42.8    +      -       +      +
     90B  PHE*     3.8    23.6    -      -       +      -
    106B  TRP*     4.1    23.1    -      -       +      -
    107B  ALA*     5.0     2.2    -      -       +      -
    110B  VAL*     3.7    34.3    -      -       +      -
    125B  PHE*     3.8    27.8    -      -       +      -
    127B  ALA*     3.4    14.4    -      -       +      +
    129B  VAL*     5.3     6.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 76 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19B  ALA*     4.3     7.2    -      -       +      +
     23B  GLU*     4.0    20.4    -      -       +      -
     24B  PHE*     4.7     7.4    -      -       +      -
     75B  LEU*     1.3    77.2    -      -       -      +
     77B  THR*     1.3    59.9    +      -       -      +
     78B  THR*     4.5    14.4    -      -       +      -
     86B  GLN*     3.2    19.7    -      -       +      +
     87B  ARG*     3.6    19.1    -      -       +      -
    106B  TRP*     4.7     2.2    -      -       -      -
    127B  ALA      3.1     6.4    +      -       -      +
    128B  VAL*     3.1    32.1    -      -       +      +
    129B  VAL*     2.7    30.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 77 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     76B  LEU*     1.3    77.0    -      -       -      +
     78B  THR*     1.3    65.0    +      -       -      +
     79B  SER*     3.2    20.4    +      -       -      +
     82B  ALA*     4.0    14.4    -      -       +      +
     86B  GLN*     2.9    39.2    +      -       +      +
    106B  TRP*     3.6    38.6    -      -       +      -
    129B  VAL*     2.9    29.1    +      -       -      +
----------------------------------------------------------
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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