Contacts of the strand formed by residues 546 - 554 (chain B) in PDB entry 6ZGI


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 LEU 546 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    518B  LEU*     3.7    27.1    -      -       +      +
    541B  PHE*     3.8    17.6    -      -       +      +
    542B  ASN*     3.5     1.0    -      -       -      -
    543B  PHE*     2.9    37.4    +      -       +      +
    544B  ASN      3.3     1.4    +      -       -      -
    545B  GLY*     1.3    76.2    -      -       -      +
    547B  THR*     1.3    69.6    +      -       -      +
    565B  PHE*     4.3    28.5    -      -       +      -
    567B  ARG*     5.5     4.7    -      -       -      +
    573B  THR*     4.4    27.4    -      -       +      +
    587B  ILE*     6.0     1.3    -      -       +      -
    976C  VAL*     6.4     1.3    -      -       +      -
    978C  ASN*     5.5     7.6    -      -       +      +
    979C  ASP*     5.1    10.8    -      -       +      +
    982C  SER*     4.6     4.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with THR 547 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    389B  ASP*     6.0     1.3    -      -       +      +
    541B  PHE*     3.2    11.0    -      -       -      +
    542B  ASN*     3.8    26.0    -      -       +      +
    545B  GLY      3.6     8.9    +      -       -      +
    546B  LEU*     1.3    81.0    -      -       -      +
    548B  GLY*     1.3    59.9    +      -       -      +
    978C  ASN*     3.3    28.9    +      -       -      +
    981C  LEU*     5.3     2.6    -      -       -      +
    982C  SER*     3.9    22.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 548 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    540B  ASN*     3.4     7.1    +      -       -      +
    541B  PHE*     2.9    45.9    +      -       -      -
    547B  THR*     1.3    77.0    -      -       -      +
    549B  THR*     1.3    64.8    +      -       -      -
    978C  ASN*     4.1    15.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with THR 549 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    322B  PRO*     3.9    23.8    -      -       +      -
    538B  CYS*     4.0    11.4    -      -       -      -
    539B  VAL      3.6     7.9    -      -       -      +
    540B  ASN*     3.1    27.7    +      -       -      +
    541B  PHE*     3.6    10.2    -      -       -      -
    548B  GLY*     1.3    73.5    -      -       -      -
    550B  GLY*     1.3    62.7    +      -       -      +
    587B  ILE*     4.6     4.3    -      -       -      +
    588B  THR      4.8     0.2    -      -       -      +
    589B  PRO*     5.2     4.0    -      -       -      +
    590B  CYS*     5.2     0.7    -      -       -      -
    745C  ASP*     4.8    28.4    +      -       +      +
    978C  ASN*     5.0     2.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 550 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    537B  LYS      3.3     1.9    -      -       -      +
    538B  CYS*     4.0    10.8    -      -       -      -
    539B  VAL*     2.9    37.9    +      -       -      +
    541B  PHE*     3.8     9.0    -      -       -      -
    549B  THR*     1.3    79.4    -      -       -      +
    551B  VAL*     1.3    65.0    +      -       -      -
    552B  LEU*     5.0     0.4    -      -       -      +
    587B  ILE*     4.7     1.6    -      -       -      -
    588B  THR      3.4    12.3    -      -       -      -
    589B  PRO*     4.9     2.7    -      -       -      -
    590B  CYS*     4.9     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 551 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    536B  ASN*     3.8    26.9    -      -       -      +
    537B  LYS*     3.7     3.8    -      -       -      -
    538B  CYS*     3.7    22.4    -      -       +      +
    550B  GLY*     1.3    76.2    -      -       -      -
    552B  LEU*     1.3    67.2    +      -       -      +
    553B  THR*     4.3    11.9    +      -       +      -
    586B  ASP      3.4     4.9    -      -       -      +
    587B  ILE*     3.4     2.1    -      -       -      +
    588B  THR*     2.9    38.4    +      -       -      +
    590B  CYS*     4.1    11.7    -      -       +      -
    837C  TYR*     4.0    20.6    -      -       +      +
    841C  LEU*     5.2    10.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 552 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    326B  ILE*     3.8    28.5    -      -       +      -
    533B  LEU*     3.9    16.6    -      -       +      -
    534B  VAL      4.1    13.2    -      -       -      +
    535B  LYS*     3.6    10.7    -      -       +      +
    536B  ASN      3.2    23.0    +      -       -      +
    537B  LYS      4.5     2.4    +      -       -      -
    539B  VAL*     4.7    10.1    -      -       +      -
    541B  PHE*     4.2    19.1    -      -       +      -
    543B  PHE*     4.0    18.2    -      -       +      -
    551B  VAL*     1.3    78.2    -      -       -      +
    553B  THR*     1.3    64.1    +      -       -      +
    576B  VAL*     5.4     0.4    -      -       +      -
    585B  LEU*     4.5    15.0    -      -       +      -
    586B  ASP      3.3     3.1    -      -       -      +
    587B  ILE*     3.9    26.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 553 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    535B  LYS*     5.4     2.9    -      -       -      -
    536B  ASN*     3.8    20.6    -      -       -      +
    551B  VAL*     4.3    13.1    +      -       +      +
    552B  LEU*     1.3    79.4    -      -       -      +
    554B  GLU*     1.3    66.0    +      -       -      +
    585B  LEU*     3.3    12.2    -      -       -      +
    586B  ASP*     2.9    46.8    +      -       -      +
    588B  THR*     4.8     3.1    +      -       -      +
    841C  LEU*     5.0    16.4    -      -       +      +
    842C  GLY*     4.1    11.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 554 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    535B  LYS*     3.5    33.6    +      -       +      +
    553B  THR*     1.3    79.3    +      -       -      +
    555B  SER*     1.3    58.4    +      -       -      +
    556B  ASN*     5.5     2.3    +      -       -      -
    583B  GLU*     4.8     9.2    -      -       -      +
    584B  ILE      4.3     4.5    -      -       -      +
    585B  LEU*     4.4     2.5    -      -       +      -
    586B  ASP*     4.2     5.4    -      -       -      +
----------------------------------------------------------
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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