Contacts of the strand formed by residues 714 - 719 (chain F) 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 VAL 714 (chain F).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    673F  HIS*     3.3    18.1    -      -       -      +
    674F  SER*     2.9    15.1    +      -       -      +
    687F  GLY*     3.8    17.9    -      -       -      -
    688F  ALA      3.7    14.5    +      -       -      +
    691F  GLY*     3.7    33.0    -      -       -      -
    692F  ARG      4.0     1.6    -      -       -      +
    693F  VAL*     4.2     4.3    -      -       +      -
    710F  HIS*     4.0    16.6    -      -       +      -
    713F  THR*     1.3    69.2    -      -       -      +
    715F  CYS*     1.3    60.8    +      -       -      +
    716F  SER      4.6     0.4    -      -       -      +
    717F  LEU*     3.8    35.9    -      -       +      -
    728F  SER*     4.5     2.5    -      -       -      +
    729F  GLY      4.0    11.0    -      -       -      +
    730F  SER*     4.6     0.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with CYS 715 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    673F  HIS*     4.2     6.9    -      -       -      +
    674F  SER*     2.8    17.1    +      -       -      -
    713F  THR*     3.4    30.4    +      -       -      +
    714F  VAL*     1.3    70.3    -      -       -      +
    716F  SER*     1.3    59.8    +      -       -      +
    729F  GLY      3.3     8.2    +      -       -      +
    730F  SER*     4.8     0.9    -      -       -      -
    731F  MET*     3.9    27.4    -      -       -      +
    766F  GLN      3.3    23.8    -      -       -      +
    767F  GLU      3.5     9.9    -      -       -      +
    768F  LEU*     4.9     3.3    -      -       -      +
     62H  LYS*     3.8    26.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 716 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    674F  SER*     3.8     0.2    +      -       -      -
    714F  VAL*     3.8     0.4    -      -       -      -
    715F  CYS*     1.3    78.2    -      -       -      +
    717F  LEU*     1.3    62.5    +      -       -      +
    728F  SER*     3.4     4.2    +      -       -      -
    729F  GLY*     2.8    42.6    +      -       -      +
    766F  GLN*     3.4    14.9    +      -       -      +
    767F  GLU      4.3     2.5    -      -       -      -
    768F  LEU*     3.6    37.5    +      -       -      +
    769F  LEU*     3.6    11.7    -      -       -      +
    780F  VAL*     4.9     0.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 717 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    674F  SER*     4.0    14.7    +      -       -      -
    676F  THR*     3.3    27.2    -      -       +      +
    685F  ALA*     3.6    27.4    -      -       +      +
    686F  THR      4.0     0.7    -      -       -      +
    687F  GLY*     3.4    31.6    -      -       -      +
    693F  VAL*     3.8    16.4    -      -       +      -
    714F  VAL*     3.8    17.7    -      -       +      -
    715F  CYS      4.2     1.2    +      -       -      -
    716F  SER*     1.3    73.3    -      -       -      +
    718F  ARG*     1.3    70.7    +      -       -      +
    726F  LEU*     4.8     7.4    -      -       +      -
    727F  ALA      3.8     3.1    -      -       -      +
    728F  SER*     3.4    28.9    -      -       -      +
    769F  LEU*     3.9     5.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 718 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    476F  VAL*     6.1     3.6    -      -       -      +
    477F  ASP      5.9     0.2    +      -       -      -
    634F  ARG*     3.2    35.5    -      -       -      +
    676F  THR*     4.0     9.8    -      -       -      +
    677F  PHE      5.7     2.2    +      -       -      -
    717F  LEU*     1.3    82.3    +      -       -      +
    719F  PHE*     1.3    83.2    +      -       -      +
    720F  SER*     3.4     2.3    +      -       -      +
    726F  LEU*     3.8     7.7    -      -       -      +
    727F  ALA*     3.0    33.4    +      -       +      +
    768F  LEU*     5.3     9.1    -      -       -      +
    769F  LEU*     3.4    41.1    +      -       +      -
    770F  LEU*     4.1    13.3    -      -       -      +
    771F  GLY*     3.3    31.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 719 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    676F  THR*     4.2    10.1    +      -       -      -
    677F  PHE      3.2    31.1    +      -       -      +
    678F  SER*     3.6     8.5    -      -       -      -
    679F  PRO*     4.1    16.3    -      -       +      +
    683F  PHE*     3.7    10.3    -      +       +      -
    684F  LEU*     3.6    46.9    -      -       -      -
    685F  ALA*     3.8     5.2    -      -       +      -
    695F  LEU*     3.9    16.8    -      -       +      -
    718F  ARG*     1.3    86.3    -      -       -      +
    720F  SER*     1.3    64.3    +      -       -      +
    724F  GLU*     5.8    11.2    -      -       +      -
    725F  ILE      4.6     4.7    -      -       -      -
    726F  LEU*     3.6    37.2    -      -       +      -
----------------------------------------------------------
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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