Contacts of the strand formed by residues 778 - 782 (chain A) 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 ASP 778 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    678A  LEU      5.2     2.7    -      -       -      +
    679A  ILE*     3.7     9.2    -      -       +      +
    680A  LEU      3.3    20.8    +      -       -      +
    718A  LYS*     2.9    22.6    +      -       -      +
    719A  TYR*     2.8    39.6    +      -       +      +
    754A  LEU*     3.9    22.8    -      -       +      +
    755A  HIS      4.0     4.0    -      -       -      +
    756A  LYS*     5.7     1.0    -      -       -      +
    776A  LEU*     3.3     9.3    -      -       -      +
    777A  VAL*     1.3    90.0    -      -       -      +
    779A  ILE*     1.3    59.2    -      -       -      +
    780A  PHE*     5.1     0.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 779 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    680A  LEU*     3.3    24.2    -      -       +      +
    681A  ALA      4.6     0.4    -      -       -      +
    682A  GLU*     4.1    20.4    -      -       +      +
    754A  LEU*     3.9     0.7    -      -       -      +
    755A  HIS*     2.8    33.1    +      -       -      +
    756A  LYS      3.8     9.4    -      -       -      +
    757A  MET*     3.7    50.5    -      -       +      +
    758A  PRO*     5.2     1.1    -      -       +      -
    778A  ASP*     1.3    74.5    -      -       -      +
    780A  PHE*     1.3    72.1    +      -       -      +
     74J  MET*     4.1    17.3    -      -       +      -
    136J  ILE*     4.8     2.5    -      -       +      -
    137J  THR*     4.0    19.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 780 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    679A  ILE*     3.7    42.6    -      -       +      -
    680A  LEU      2.9    10.5    +      -       -      +
    681A  ALA*     3.7     6.0    -      -       +      -
    682A  GLU*     2.9    30.7    +      -       -      +
    700A  ILE*     4.5     4.7    -      -       +      -
    719A  TYR*     3.8    22.7    -      +       +      -
    741A  GLN*     3.3    24.2    -      -       -      -
    743A  PHE*     5.0     1.1    -      +       +      -
    752A  ILE*     3.7    33.7    -      -       +      -
    753A  TYR      3.3     7.4    -      -       -      -
    754A  LEU*     3.6    41.5    -      -       +      -
    778A  ASP*     5.1     0.9    -      -       +      -
    779A  ILE*     1.3    74.9    -      -       -      +
    781A  VAL*     1.3    60.8    -      -       -      +
    782A  VAL*     3.9     4.4    +      -       +      +
     85J  PHE*     4.7     4.0    -      +       -      -
----------------------------------------------------------
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Residues in contact with VAL 781 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    682A  GLU*     3.7     3.6    -      -       -      +
    684A  SER*     4.8     2.0    -      -       -      -
    751A  PRO      3.7     1.2    -      -       -      +
    752A  ILE*     3.4     2.9    -      -       -      -
    753A  TYR*     3.0    33.7    +      -       +      +
    755A  HIS*     3.5    28.3    -      -       +      +
    779A  ILE      4.2     0.2    +      -       -      -
    780A  PHE*     1.3    71.7    -      -       -      +
    782A  VAL*     1.3    65.5    +      -       -      +
    783A  GLY      4.0     0.3    +      -       -      -
   1077A  LEU*     3.8    42.2    -      -       +      +
    137J  THR*     3.3    35.0    -      -       +      +
    139J  PRO*     4.8     2.2    -      -       +      -
    140J  LEU*     4.3    15.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 782 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    681A  ALA*     4.3     4.5    -      -       +      -
    682A  GLU      3.1     9.3    +      -       -      +
    683A  TYR*     3.6    36.7    -      -       +      -
    684A  SER*     2.8    31.0    +      -       -      -
    743A  PHE*     3.7    26.7    -      -       +      -
    748A  PHE*     5.1     2.5    -      -       +      -
    750A  ALA*     3.7    25.1    -      -       +      -
    751A  PRO      3.4     6.1    -      -       -      +
    752A  ILE*     3.7    12.6    -      -       +      -
    780A  PHE*     4.2     7.9    -      -       +      +
    781A  VAL*     1.3    76.8    -      -       -      +
    783A  GLY*     1.3    67.4    +      -       -      +
    785A  GLN*     5.6     1.8    -      -       +      -
----------------------------------------------------------
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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