Contacts of the strand formed by residues 271 - 279 (chain C) 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 GLN 271 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     54C  LEU*     4.1     4.0    -      -       -      -
     55C  PHE      2.9    33.5    +      -       -      +
     57C  PRO*     4.1    14.5    -      -       +      +
     88C  ASP*     6.2     0.2    -      -       -      +
    269C  TYR*     4.0     8.2    +      -       +      +
    270C  LEU*     1.3    77.5    -      -       -      +
    272C  PRO*     1.3    75.9    -      -       +      +
    273C  ARG*     3.3    32.5    +      -       +      +
----------------------------------------------------------
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Residues in contact with PRO 272 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     52C  GLN*     4.0    19.6    +      -       -      +
     53C  ASP      3.5     8.1    -      -       -      +
     54C  LEU*     4.0    21.5    -      -       +      -
     88C  ASP*     5.2     8.7    -      -       -      +
    270C  LEU      4.9     0.7    -      -       -      +
    271C  GLN*     1.3    86.4    -      -       +      +
    273C  ARG*     1.3    69.0    +      -       -      +
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Residues in contact with ARG 273 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     52C  GLN*     3.4     5.0    -      -       -      +
     53C  ASP      2.9    33.5    +      -       -      +
     55C  PHE*     3.8    14.1    -      -       +      +
     57C  PRO*     3.6    27.4    -      -       +      +
    271C  GLN*     3.5    32.1    -      -       +      +
    272C  PRO*     1.3    84.2    -      -       -      +
    274C  THR*     1.3    62.1    +      -       -      +
    275C  PHE*     3.9    22.4    -      -       +      -
    290C  ASP*     3.4    29.6    +      -       -      +
    292C  ALA*     3.8    32.8    +      -       -      +
    293C  LEU*     4.1     3.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with THR 274 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    754A  LEU*     5.0    10.6    -      -       +      +
     50C  SER*     4.9     8.1    -      -       -      -
     51C  THR      3.5    16.8    -      -       -      +
     52C  GLN*     3.3    20.5    -      -       +      +
    273C  ARG*     1.3    71.0    -      -       -      +
    275C  PHE*     1.3    76.7    +      -       -      +
    290C  ASP*     4.0     1.7    -      -       -      +
    291C  CYS*     3.2    38.5    +      -       +      +
    292C  ALA*     4.8     2.7    +      -       -      +
    301C  CYS*     4.9     2.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 275 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     35C  GLY      6.0     0.2    -      -       -      -
     36C  VAL*     4.1    17.3    -      -       +      -
     49C  HIS      3.9     0.5    -      -       -      +
     50C  SER*     3.4     4.0    -      -       -      -
     51C  THR      2.9    32.0    +      -       -      -
     55C  PHE*     3.8    44.2    -      +       +      -
     56C  LEU      3.9    15.3    -      -       -      -
     58C  PHE*     3.6    27.4    -      +       -      -
    273C  ARG*     3.9    16.1    -      -       +      -
    274C  THR*     1.3    81.9    -      -       -      +
    276C  LEU*     1.3    60.8    +      -       -      +
    277C  LEU*     3.7    18.7    -      -       +      +
    288C  ALA*     4.4    11.2    -      -       +      -
    289C  VAL      3.4     5.4    -      -       -      -
    290C  ASP*     3.4    35.2    -      -       +      -
    291C  CYS*     4.4     3.8    -      -       -      -
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Residues in contact with LEU 276 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     48C  LEU*     4.3    13.2    -      -       +      -
     49C  HIS      3.6    17.7    -      -       -      +
     50C  SER*     3.2    23.1    -      -       -      +
    275C  PHE*     1.3    71.2    -      -       -      +
    277C  LEU*     1.3    61.9    +      -       -      +
    288C  ALA*     3.2     4.6    -      -       -      -
    289C  VAL*     2.9    51.8    +      -       +      +
    291C  CYS*     4.1    10.9    -      -       -      -
    300C  LYS      4.2    18.8    -      -       -      +
    301C  CYS*     4.4     8.7    -      -       -      +
    304C  LYS*     4.3    24.7    -      -       +      +
    305C  SER      4.5     4.3    -      -       -      +
    306C  PHE*     4.2    20.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 277 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     36C  VAL*     3.8    17.5    -      -       +      -
     37C  TYR      5.4     0.9    -      -       -      +
     39C  PRO*     5.4     5.2    -      -       +      -
     47C  VAL      3.9     0.3    -      -       -      +
     48C  LEU*     3.4     6.8    -      -       -      +
     49C  HIS*     2.9    37.7    +      -       +      +
     51C  THR*     3.4    32.5    -      -       +      -
     55C  PHE*     4.8     5.2    -      -       +      -
    275C  PHE*     3.7    20.4    -      -       +      +
    276C  LEU*     1.3    73.3    -      -       -      +
    278C  LYS*     1.3    59.8    +      -       -      +
    279C  TYR*     4.3    17.9    -      -       +      +
    285C  ILE*     3.7    30.7    -      -       +      -
    287C  ASP      3.7     1.3    -      -       -      -
    288C  ALA*     3.6    23.6    -      -       +      -
    306C  PHE*     5.2     0.2    -      -       -      -
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Residues in contact with LYS 278 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     47C  VAL      3.7     2.7    -      -       -      -
     48C  LEU*     3.7    25.0    -      -       +      +
    277C  LEU*     1.3    73.0    -      -       -      +
    279C  TYR*     1.3    70.3    +      -       -      +
    280C  ASN*     6.1     2.7    -      -       -      +
    285C  ILE*     3.2     6.9    -      -       -      -
    286C  THR*     3.1    41.8    +      -       -      +
    287C  ASP*     2.9    31.7    +      -       +      +
    306C  PHE*     4.0    21.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 279 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38C  TYR*     4.6     8.6    -      +       -      -
     39C  PRO*     4.3    16.1    -      -       -      +
     40C  ASP*     6.1     0.9    -      -       -      -
     42C  VAL      5.5     3.8    +      -       -      -
     44C  ARG*     3.6    47.9    +      -       +      +
     46C  SER*     3.0     8.7    -      -       -      +
     47C  VAL*     2.9    54.2    +      -       +      +
     49C  HIS*     3.9    25.3    +      -       +      -
    277C  LEU*     4.3    16.1    -      -       +      +
    278C  LYS*     1.3    80.6    -      -       -      +
    280C  ASN*     1.3    60.3    +      -       -      +
    283C  GLY      3.9    16.4    -      -       -      -
    284C  THR      3.6     3.1    -      -       -      +
    285C  ILE*     3.7    30.7    -      -       +      +
----------------------------------------------------------
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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