Contacts of the strand formed by residues 693 - 697 (chain A) in PDB entry 6F3T


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 VAL 693 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    685A  ALA*     4.3     9.4    -      -       +      -
    686A  THR      3.3    10.1    -      -       -      +
    691A  GLY      5.1     0.2    -      -       -      +
    692A  ARG*     1.3    75.9    -      -       -      +
    694A  LEU*     1.3    61.1    +      -       -      +
    695A  LEU*     4.3     1.8    -      -       +      -
    706A  GLU*     3.7     1.0    -      -       -      -
    707A  LEU*     2.7    57.1    +      -       +      +
    710A  HIS*     4.7     4.9    -      -       +      -
    714A  VAL*     4.1    27.1    -      -       +      -
    717A  LEU*     3.9    23.3    -      -       +      -
    726A  LEU*     3.9    20.6    -      -       +      -
    728A  SER*     4.2    11.0    -      -       -      +
    738A  TRP*     4.8     3.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 694 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    667A  GLY      4.0     2.5    -      -       -      -
    668A  HIS*     3.6    47.1    -      -       +      +
    685A  ALA*     3.4     4.7    -      -       -      -
    686A  THR*     2.9    31.7    +      -       -      +
    692A  ARG*     3.7    28.7    -      -       +      +
    693A  VAL*     1.3    75.3    -      -       -      +
    695A  LEU*     1.3    62.9    +      -       -      +
    696A  TRP*     3.5    36.3    +      -       +      +
    703A  MET*     4.0    17.3    -      -       +      -
    705A  GLY      3.4     4.3    -      -       -      +
    706A  GLU*     3.8    23.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 695 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    684A  LEU      3.5     2.5    -      -       -      +
    685A  ALA*     3.8    26.0    -      -       +      -
    693A  VAL*     4.3     1.3    -      -       +      -
    694A  LEU*     1.3    76.1    -      -       -      +
    696A  TRP*     1.3    56.9    +      -       -      +
    703A  MET*     3.5     5.9    -      -       -      +
    704A  VAL*     2.8    32.3    +      -       +      +
    705A  GLY*     2.8    31.9    +      -       -      +
    707A  LEU*     4.1    24.0    -      -       +      -
    726A  LEU*     3.9    17.5    -      -       +      -
    740A  ALA*     6.3     0.4    -      -       -      -
    743A  ALA*     3.7    29.4    -      -       +      -
    744A  PHE*     3.8    30.7    -      -       +      -
    768A  LEU*     5.5     0.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with TRP 696 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    355A  MET*     4.6     5.4    -      -       +      -
    651A  VAL*     5.0     1.7    -      -       +      +
    665A  PHE*     3.5    67.0    -      +       +      +
    666A  THR      3.1    29.4    -      -       -      -
    668A  HIS*     4.8     3.6    -      +       -      -
    683A  PHE*     3.2     9.1    -      -       -      +
    684A  LEU*     2.8    61.3    +      -       +      +
    686A  THR*     2.8    32.1    +      -       +      +
    694A  LEU*     3.5    33.4    +      -       +      -
    695A  LEU*     1.3    74.7    -      -       -      +
    697A  ASP*     1.3    60.4    +      -       -      +
    698A  ILE      3.6     0.5    +      -       -      -
    702A  LEU      3.4     4.9    -      -       -      +
    703A  MET*     3.7    44.4    -      -       +      -
    704A  VAL*     4.3     3.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with ASP 697 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    374A  PHE*     5.9     0.3    -      -       -      -
    665A  PHE*     4.2     1.7    -      -       -      -
    682A  ARG*     3.9     9.5    +      -       -      +
    683A  PHE*     3.9    21.2    -      -       +      -
    696A  TRP*     1.3    70.7    -      -       -      +
    698A  ILE*     1.3    54.5    +      -       -      +
    699A  GLY*     3.1    16.8    +      -       -      -
    700A  HIS*     3.1    38.4    +      -       +      +
    701A  GLY*     2.7    34.5    +      -       -      -
    702A  LEU*     2.8    12.0    +      -       +      +
    704A  VAL*     3.7    23.1    -      -       +      +
    747A  LEU*     4.3    12.0    -      -       -      +
----------------------------------------------------------
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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