Contacts of the strand formed by residues 683 - 688 (chain G) in PDB entry 6MZL


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 683 (chain G).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    677G  PHE*     3.3    25.1    -      -       -      +
    678G  SER*     3.0     9.7    +      -       -      -
    680G  ASN*     5.0    10.5    -      -       -      -
    682G  ARG*     1.3   130.4    -      -       +      +
    684G  LEU*     1.3    69.0    +      -       -      +
    695G  LEU*     4.1     9.2    -      -       +      -
    696G  TRP      3.6     4.0    -      -       -      +
    697G  ASP*     3.1    32.5    -      -       +      -
    719G  PHE*     3.8    17.3    -      +       +      -
    724G  GLU*     3.2    34.3    -      -       +      -
    742G  LYS      4.4     7.4    -      -       -      -
    743G  ALA*     5.4     9.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 684 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    643G  ALA*     5.4     0.9    -      -       +      -
    651G  VAL*     5.2     2.0    -      -       +      -
    653G  LEU*     5.6     3.1    -      -       +      -
    665G  PHE*     3.7    36.8    -      -       +      -
    675G  LEU*     4.3     9.6    -      -       +      -
    676G  THR      3.4     3.8    -      -       -      +
    677G  PHE*     3.5    34.1    -      -       +      -
    682G  ARG      4.8     1.8    -      -       -      +
    683G  PHE*     1.3    81.4    -      -       -      +
    685G  ALA*     1.3    58.5    +      -       -      +
    686G  THR*     4.0    16.4    -      -       +      -
    695G  LEU*     3.0    12.3    -      -       -      +
    696G  TRP*     2.8    49.0    +      -       +      +
    697G  ASP      4.7     6.1    -      -       -      -
    698G  ILE*     4.7     8.7    -      -       +      +
    719G  PHE*     3.5     6.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 685 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    675G  LEU*     3.3     3.1    -      -       -      -
    676G  THR*     2.8    45.3    +      -       -      +
    684G  LEU*     1.3    73.7    -      -       -      +
    686G  THR*     1.3    63.1    +      -       -      +
    693G  VAL*     3.9    18.6    -      -       +      -
    694G  LEU      3.3     4.7    -      -       -      -
    695G  LEU*     5.4     0.4    -      -       -      -
    717G  LEU*     4.0    14.8    -      -       +      -
    719G  PHE*     3.4    21.8    -      -       +      -
    726G  LEU*     4.7     3.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 686 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    651G  VAL*     4.5    12.8    -      -       +      -
    668G  HIS*     5.6     1.0    -      -       -      +
    672G  ILE*     5.4     5.6    -      -       -      -
    674G  SER      3.6     7.9    -      -       -      -
    675G  LEU*     3.8    24.2    -      -       +      -
    684G  LEU*     4.0     9.6    -      -       +      -
    685G  ALA*     1.3    78.7    -      -       -      +
    687G  GLY*     1.3    62.2    +      -       -      +
    688G  ALA*     5.1     1.7    -      -       -      +
    692G  ARG      3.6     1.9    -      -       -      +
    693G  VAL*     3.5     1.9    -      -       -      -
    694G  LEU*     2.9    35.9    +      -       -      +
    696G  TRP*     2.7    39.7    +      -       +      +
    717G  LEU*     4.1     0.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 687 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    672G  ILE*     4.0     3.3    -      -       -      +
    673G  HIS      3.6     5.4    +      -       -      -
    674G  SER*     3.2    29.2    +      -       -      +
    686G  THR*     1.3    74.4    -      -       -      +
    688G  ALA*     1.3    59.2    +      -       -      +
    692G  ARG      3.4     6.5    -      -       -      -
    693G  VAL*     4.2     4.9    -      -       -      -
    714G  VAL*     3.7    29.3    -      -       -      +
    717G  LEU*     3.4     9.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 688 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    668G  HIS*     3.5    44.9    -      -       +      +
    670G  GLY      4.4     6.3    -      -       -      +
    671G  PRO      4.3     5.8    -      -       -      +
    672G  ILE*     4.7     7.6    -      -       +      +
    673G  HIS*     4.8     1.8    -      -       -      +
    686G  THR      5.1     1.1    -      -       -      +
    687G  GLY*     1.3    75.8    -      -       -      +
    689G  THR*     1.3    53.3    +      -       -      +
    690G  ASP      3.0     3.1    -      -       -      +
    691G  GLY*     2.9    26.9    +      -       -      -
    692G  ARG      2.9    13.4    +      -       -      +
    714G  VAL*     3.7    10.6    +      -       -      +
----------------------------------------------------------
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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