Contacts of the strand formed by residues 680 - 683 (chain K) in PDB entry 6R1U


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 PHE 680 (chain K).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    461K  PHE*     3.5    29.2    -      +       +      -
    462K  GLY      3.5    22.7    -      -       -      -
    463K  GLU      4.2     4.0    -      -       -      -
    464K  ARG      3.3    23.0    -      -       -      +
    465K  CYS*     3.6    23.1    -      -       +      -
    466K  ASP      4.6     0.3    +      -       -      -
    678K  ALA*     3.2    18.4    -      -       -      +
    679K  ASP*     1.3    86.9    -      -       +      +
    681K  PHE*     1.3    68.6    +      -       -      +
    696K  VAL*     3.9    11.4    -      -       +      -
    697K  PHE      3.1    17.0    -      -       -      +
    698K  TYR*     3.9    23.1    -      +       +      -
    699K  ASP*     4.7     0.4    -      -       -      +
      6M  THR*     4.3     7.9    -      -       +      -
      7M  ALA*     3.8    26.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 681 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    465K  CYS*     3.8     7.6    -      -       -      -
    466K  ASP*     3.9     9.4    -      -       +      +
    468K  ILE*     3.9    27.1    -      -       +      -
    671K  TRP*     4.7     5.4    -      +       -      -
    675K  VAL*     3.6    32.1    -      -       +      -
    680K  PHE*     1.3    80.2    -      -       -      +
    682K  GLY*     1.3    67.4    +      -       -      +
    696K  VAL*     3.5     2.0    -      -       -      -
    697K  PHE*     2.9    69.8    +      +       +      -
    699K  ASP*     5.8     2.2    -      -       +      -
    709K  LEU*     4.2    25.6    -      -       +      -
    737K  LEU*     4.4     2.2    -      -       +      -
    740K  LEU*     4.9     6.1    -      -       +      -
    741K  PHE*     3.8    29.8    -      +       -      -
----------------------------------------------------------
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Residues in contact with GLY 682 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    465K  CYS*     3.6     9.4    -      -       -      -
    466K  ASP      2.8    15.8    +      -       -      -
    467K  LEU*     4.3     4.5    -      -       -      -
    468K  ILE*     3.1    30.3    +      -       -      +
    538K  PHE*     4.0    11.9    -      -       -      -
    681K  PHE*     1.3    79.5    -      -       -      +
    683K  HIS*     1.3    61.5    +      -       -      +
    695K  ALA      3.3     8.7    -      -       -      -
    696K  VAL*     4.5     0.9    -      -       -      -
    740K  LEU*     5.0     0.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with HIS 683 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    468K  ILE      3.6     3.1    -      -       -      -
    470K  GLU*     2.7    29.9    +      -       +      +
    538K  PHE*     3.7    14.0    -      -       -      -
    682K  GLY*     1.3    73.0    -      -       -      +
    684K  VAL*     1.3    80.2    +      -       -      +
    685K  PRO*     3.3    10.4    -      -       +      +
    686K  PRO*     4.2     6.7    -      -       +      +
    690K  LYS      5.6     2.2    -      -       -      -
    691K  ARG      5.4     0.3    -      -       -      +
    693K  LEU*     3.5    15.1    +      -       +      -
    694K  PHE      2.9    30.1    +      -       -      +
    695K  ALA*     2.7    14.4    +      -       -      +
    697K  PHE*     4.7     3.1    -      -       +      -
    736K  THR*     3.5    22.9    -      -       +      +
    740K  LEU*     3.8    29.2    -      -       +      -
----------------------------------------------------------
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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