Contacts of the strand formed by residues 883 - 887 (chain F) in PDB entry 5YWB


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 THR 883 (chain F).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    679F  VAL*     5.3     2.9    -      -       +      -
    703F  ILE*     4.2    26.0    -      -       +      +
    704F  PRO      4.3     6.1    -      -       -      +
    705F  ARG*     3.3    27.6    -      -       -      +
    706F  GLY      3.4     3.3    +      -       -      +
    707F  GLN      4.3     7.6    -      -       -      +
    849F  ASN*     3.0    17.6    +      -       -      +
    850F  VAL*     3.8    24.6    -      -       +      +
    851F  VAL*     2.9    30.4    +      -       -      +
    882F  ARG*     1.3    72.1    -      -       -      +
    884F  VAL*     1.3    63.6    +      -       -      +
    885F  VAL*     4.7     0.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 884 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    703F  ILE*     5.5     0.2    -      -       -      +
    707F  GLN      3.3    11.0    +      -       -      +
    708F  LEU*     3.7    27.3    -      -       +      +
    709F  THR*     3.3    22.9    +      -       -      -
    851F  VAL*     3.6    21.8    -      -       +      +
    853F  LEU*     4.9     2.9    -      -       +      -
    873F  ILE*     4.8     4.7    -      -       +      +
    877F  LEU*     3.7    35.7    -      -       +      -
    878F  ARG*     5.7     0.7    -      -       -      +
    882F  ARG      4.5     7.4    -      -       -      +
    883F  THR*     1.3    79.8    -      -       -      +
    885F  VAL*     1.3    67.5    +      -       -      +
    886F  LEU*     4.2    20.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 885 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    703F  ILE*     4.5    28.0    -      -       +      -
    709F  THR*     3.9    16.6    -      -       +      +
    711F  ILE*     4.0    27.8    -      -       +      -
    723F  LEU*     4.2     4.9    -      -       +      +
    850F  VAL*     4.3    15.3    -      -       +      -
    851F  VAL      2.9     7.2    +      -       -      -
    852F  PHE*     3.3    39.5    -      -       +      +
    853F  LEU      2.9    24.3    +      -       -      +
    883F  THR*     4.7     0.9    -      -       +      -
    884F  VAL*     1.3    77.2    -      -       -      +
    886F  LEU*     1.3    60.3    +      -       -      +
    887F  VAL      4.2     0.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 886 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    708F  LEU*     4.5     1.3    -      -       +      -
    709F  THR      3.2    19.1    +      -       -      +
    710F  MET*     3.4    35.0    -      -       +      +
    711F  ILE      3.5     1.2    +      -       -      -
    853F  LEU*     3.6    28.9    -      -       +      -
    856F  PRO*     3.7     9.0    -      -       +      -
    857F  PHE*     3.4    26.7    -      -       +      -
    869F  MET*     5.7     0.2    -      -       +      -
    873F  ILE*     3.5    41.5    -      -       +      -
    884F  VAL*     4.0    12.7    -      -       +      +
    885F  VAL*     1.3    73.4    -      -       -      +
    887F  VAL*     1.3    64.7    +      -       -      +
    888F  THR*     3.5    16.7    +      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 887 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    711F  ILE*     3.6    46.7    -      -       +      +
    719F  LYS*     3.6    42.4    -      -       +      +
    723F  LEU*     3.7    23.1    -      -       +      -
    853F  LEU      3.0    11.0    +      -       -      +
    854F  ASP*     4.7    10.0    -      -       -      +
    855F  ASP*     2.8    33.3    +      -       -      +
    856F  PRO*     4.3     0.2    -      -       -      +
    886F  LEU*     1.3    77.3    -      -       -      +
    888F  THR*     1.3    61.0    +      -       -      +
   2501F  ADP      5.4     0.2    -      -       -      +
----------------------------------------------------------
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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