Contacts of the strand formed by residues 273 - 279 (chain 3) in PDB entry 6Q8W


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 GLU 273 (chain 3).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    2433  ARG*     4.4    15.5    +      -       -      +
    2693  THR*     3.6     7.4    -      -       -      -
    2703  ARG      3.1    41.9    +      -       -      +
    2713  SER*     3.9    11.3    -      -       -      +
    2723  GLY*     1.3    78.5    -      -       -      +
    2743  LEU*     1.3    62.6    +      -       -      +
    2753  LEU*     3.4    17.9    +      -       +      +
    3023  ASP*     4.1    20.9    -      -       +      +
    6293  ILE*     4.7     2.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 274 (chain 3). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    2433  ARG*     2.9    14.8    +      -       -      -
    2673  ALA*     4.7     3.1    -      -       +      -
    2683  ASP      3.9     7.2    -      -       -      +
    2693  THR*     3.7    22.2    -      -       +      -
    2733  GLU*     1.3    72.4    -      -       -      +
    2753  LEU*     1.3    61.5    +      -       -      +
    2763  ARG      4.7     1.1    -      -       -      +
    2773  ILE*     3.8    23.3    -      -       +      -
    2983  HIS*     3.5    47.4    +      -       +      +
    3013  ALA*     4.1     6.1    -      -       +      -
    3023  ASP*     3.3    27.4    -      -       +      +
    6083  TYR*     3.7    26.5    -      -       +      -
    6293  ILE*     4.2    14.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 275 (chain 3). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    2393  THR      4.4     0.3    -      -       -      +
    2403  ALA*     3.1    20.0    -      -       +      +
    2433  ARG*     3.1    55.4    +      -       +      +
    2443  ALA*     3.7    25.1    -      -       +      -
    2493  MET*     3.7    23.1    -      -       +      -
    2683  ASP      2.9    13.1    +      -       -      +
    2693  THR      4.4     0.2    -      -       -      -
    2703  ARG*     3.6    42.2    -      -       +      +
    2733  GLU*     3.4    14.5    +      -       +      +
    2743  LEU*     1.3    75.2    -      -       -      +
    2763  ARG*     1.3    60.2    +      -       +      +
    2983  HIS*     3.5    12.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 276 (chain 3). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    1233  ASP*     4.7     8.7    +      -       -      -
    1243  LYS*     6.1     0.8    -      -       -      +
    2273  THR*     6.0     3.6    -      -       -      -
    2363  LEU*     6.0     4.2    -      -       -      +
    2373  ASP*     4.3    15.0    -      -       +      +
    2403  ALA*     3.5    21.9    +      -       +      -
    2463  ASN*     3.8    35.5    +      -       -      +
    2493  MET*     3.2    35.1    -      -       +      +
    2683  ASP*     2.8    42.7    +      -       +      +
    2743  LEU*     3.9     0.6    -      -       -      +
    2753  LEU*     1.3    84.6    -      -       +      +
    2773  ILE*     1.3    70.7    +      -       -      +
    2783  ARG*     3.4    44.3    -      -       +      +
    2983  HIS*     4.4     4.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 277 (chain 3). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    2373  ASP*     5.3     0.7    +      -       -      +
    2653  ILE*     4.4    18.8    -      -       +      -
    2663  THR      3.5     3.4    -      -       -      +
    2673  ALA*     3.5    34.5    -      -       +      -
    2743  LEU*     3.8    14.6    -      -       +      -
    2763  ARG*     1.3    80.8    -      -       -      +
    2783  ARG*     1.3    76.4    +      -       -      +
    2903  ILE*     5.3     0.9    -      -       +      -
    2943  GLY      3.9    17.0    -      -       -      +
    2953  ARG*     3.5    37.4    +      -       +      +
    2983  HIS*     4.1    19.9    +      -       +      -
    6083  TYR*     3.9    25.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 278 (chain 3). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    2283  ASP*     4.2    17.5    +      -       -      +
    2463  ASN*     6.1     1.6    -      -       -      +
    2513  GLU*     4.3    16.6    +      -       -      -
    2653  ILE*     3.4     9.2    -      -       -      +
    2663  THR*     2.9    47.1    +      -       -      +
    2683  ASP*     2.7    52.3    +      -       -      +
    2763  ARG*     3.4    36.4    -      -       +      +
    2773  ILE*     1.3    80.3    -      -       -      +
    2793  ALA*     1.3    67.8    +      -       -      +
    2903  ILE*     4.5     2.5    -      -       -      -
    2953  ARG*     3.7     7.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 279 (chain 3). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    2283  ASP*     3.4    12.9    +      -       +      +
    2663  THR*     4.1     5.7    +      -       -      -
    2783  ARG*     1.3    82.8    +      -       -      +
    2803  ARG*     1.3    58.5    +      -       -      +
    2813  GLU      4.2     0.7    +      -       -      -
    2883  ILE*     3.1    30.7    -      -       -      +
    2893  TRP      4.6     0.2    -      -       -      +
    2903  ILE*     3.5    17.5    -      -       +      -
    2953  ARG*     3.5    18.2    -      -       -      +
----------------------------------------------------------
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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