Contacts of the strand formed by residues 883 - 887 (chain B) 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 B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    679B  VAL*     5.3     3.1    -      -       +      -
    703B  ILE*     4.2    26.2    -      -       +      +
    704B  PRO      4.3     5.6    -      -       -      +
    705B  ARG*     3.3    27.1    -      -       -      +
    706B  GLY      3.4     3.1    +      -       -      +
    707B  GLN      4.3     7.0    -      -       -      +
    849B  ASN*     3.0    16.7    +      -       -      +
    850B  VAL*     3.8    25.1    -      -       +      +
    851B  VAL*     2.9    30.5    +      -       -      +
    882B  ARG*     1.3    72.9    -      -       -      +
    884B  VAL*     1.3    65.7    +      -       -      +
    885B  VAL*     4.7     0.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 884 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    703B  ILE*     5.5     0.2    -      -       -      +
    707B  GLN      3.3    12.0    +      -       -      +
    708B  LEU*     3.7    27.4    -      -       +      -
    709B  THR*     3.3    22.5    +      -       -      -
    851B  VAL*     3.6    21.3    -      -       +      +
    853B  LEU*     4.9     3.1    -      -       +      -
    873B  ILE*     4.8     4.3    -      -       +      +
    877B  LEU*     3.7    35.9    -      -       +      -
    878B  ARG*     6.3     0.2    -      -       -      -
    882B  ARG      4.0     8.5    +      -       -      +
    883B  THR*     1.3    78.0    -      -       -      +
    885B  VAL*     1.3    68.5    +      -       -      +
    886B  LEU*     4.0    19.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 885 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    703B  ILE*     4.5    28.0    -      -       +      -
    709B  THR*     3.9    15.5    -      -       +      +
    711B  ILE*     4.0    27.8    -      -       +      -
    723B  LEU*     4.2     4.8    -      -       +      +
    850B  VAL*     4.3    14.8    -      -       +      -
    851B  VAL      2.9     7.7    +      -       -      -
    852B  PHE*     3.3    39.5    -      -       +      +
    853B  LEU      2.9    24.3    +      -       -      +
    883B  THR*     4.7     0.7    -      -       +      -
    884B  VAL*     1.3    77.0    -      -       -      +
    886B  LEU*     1.3    60.8    +      -       -      +
    887B  VAL*     4.2     0.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 886 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    708B  LEU*     4.5     1.1    -      -       +      +
    709B  THR      3.2    17.7    +      -       -      +
    710B  MET*     3.4    35.7    -      -       +      +
    711B  ILE      3.5     1.2    +      -       -      -
    853B  LEU*     3.6    28.0    -      -       +      -
    856B  PRO*     3.7     8.7    -      -       +      -
    857B  PHE*     3.4    26.2    -      -       +      -
    869B  MET*     5.7     0.4    -      -       +      -
    873B  ILE*     3.5    41.5    -      -       +      -
    884B  VAL*     4.0    12.9    +      -       +      -
    885B  VAL*     1.3    74.1    -      -       -      +
    887B  VAL*     1.3    63.7    +      -       -      +
    888B  THR*     3.5    16.9    +      -       +      -
    893B  TYR*     5.2     0.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 887 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    711B  ILE*     3.6    46.9    -      -       +      +
    719B  LYS*     3.6    42.4    -      -       +      +
    723B  LEU*     3.7    22.7    -      -       +      -
    853B  LEU      3.0    11.3    +      -       -      +
    854B  ASP*     4.7     9.4    -      -       -      +
    855B  ASP*     2.8    32.9    +      -       -      +
    886B  LEU*     1.3    78.0    -      -       -      +
    888B  THR*     1.3    60.8    +      -       -      +
   2501B  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