Contacts of the strand formed by residues 577 - 581 (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 CYS 577 (chain G).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    568G  ARG*     3.0    43.7    -      -       -      +
    569G  LEU      3.9     1.3    -      -       -      -
    570G  TRP*     3.2    24.4    -      -       +      -
    576G  THR*     1.3    84.6    +      -       -      +
    578G  LEU*     1.3    65.8    +      -       -      +
    579G  VAL      3.3    30.3    -      -       -      -
    580G  GLY*     3.7     3.4    -      -       -      -
     84K  ALA      5.3     2.9    -      -       -      +
     86K  THR*     4.7    14.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 578 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    940E  VAL      6.0     1.6    -      -       -      +
    944E  LEU*     5.7     9.9    -      -       +      -
    556G  ASN      4.9     0.4    -      -       -      +
    557G  TYR*     4.1    31.4    -      -       +      -
    569G  LEU*     2.9    16.5    +      -       +      +
    570G  TRP      4.3     1.8    -      -       -      +
    571G  SER*     3.3    39.3    -      -       -      +
    572G  LEU      5.2     0.4    -      -       -      +
    574G  THR*     5.1     4.0    -      -       -      +
    576G  THR*     3.0    10.8    +      -       +      -
    577G  CYS*     1.3    75.6    -      -       -      +
    579G  VAL*     1.3    69.4    +      -       +      +
     84K  ALA      4.9     7.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 579 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    568G  ARG*     3.2     3.3    -      -       -      -
    569G  LEU*     2.9    56.0    +      -       +      +
    577G  CYS*     3.3     6.1    -      -       -      -
    578G  LEU*     1.3    88.6    -      -       +      +
    580G  GLY*     1.3    57.4    +      -       -      +
    581G  TYR*     3.6    25.8    -      -       +      -
    614G  THR      4.8     8.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 580 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    566G  THR*     4.3     3.1    -      -       -      -
    567G  VAL      3.4     8.1    -      -       -      -
    568G  ARG*     3.7    15.9    -      -       -      -
    577G  CYS*     3.7     6.9    -      -       -      -
    579G  VAL*     1.3    77.3    -      -       -      +
    581G  TYR*     1.3    64.3    +      -       -      +
     81K  GLU*     5.3     8.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 581 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    566G  THR*     3.0    10.0    +      -       -      -
    567G  VAL*     2.9    50.4    +      -       +      +
    569G  LEU*     4.8     6.1    -      -       +      +
    579G  VAL*     3.6    25.8    -      -       +      -
    580G  GLY*     1.3    85.7    -      -       -      +
    582G  LYS*     1.3    82.2    +      -       -      +
    600G  PHE*     3.3    30.8    -      +       -      -
    612G  TRP*     3.8    33.4    -      +       -      +
    613G  ALA      4.5     3.3    +      -       -      -
    614G  THR      5.1     3.9    +      -       -      -
    617G  TYR*     5.3    22.7    -      -       +      +
----------------------------------------------------------
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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