Contacts of the strand formed by residues 883 - 886 (chain H) in PDB entry 6C3P


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 VAL 883 (chain H).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    707H  GLN      3.4    15.2    +      -       -      +
    708H  LEU*     3.5    36.5    -      -       +      +
    709H  THR      3.6     0.9    +      -       -      -
    850H  VAL*     3.3    23.3    -      -       +      +
    852H  LEU*     4.6    13.0    -      -       +      -
    872H  ILE*     4.7     5.2    -      -       +      -
    875H  LEU*     3.6    43.3    -      -       +      -
    876H  LEU*     5.0     6.1    -      -       +      -
    881H  ARG      4.2     4.9    -      -       -      +
    882H  THR*     1.3    76.1    -      -       -      +
    884H  VAL*     1.3    70.9    +      -       -      +
    885H  LEU*     5.1     0.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 884 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    703H  ILE*     4.1    23.6    -      -       +      -
    709H  THR*     3.6    31.4    -      -       +      -
    711H  ILE*     3.7    18.8    -      -       +      -
    723H  LEU*     4.9     2.7    -      -       +      -
    849H  VAL*     5.4     6.1    -      -       +      -
    850H  VAL      3.0    12.5    +      -       -      +
    851H  PHE*     3.3    22.0    -      -       +      -
    852H  LEU*     2.7    32.7    +      -       -      +
    882H  THR*     4.4     7.9    -      -       +      -
    883H  VAL*     1.3    79.9    -      -       -      +
    885H  LEU*     1.3    59.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 885 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    708H  LEU*     3.8    24.2    -      -       +      -
    709H  THR      3.3     9.3    +      -       -      +
    710H  MET*     3.5    30.8    -      -       +      -
    711H  ILE*     3.2    25.9    +      -       -      +
    723H  LEU*     5.6     0.2    -      -       -      -
    852H  LEU*     3.2    31.6    -      -       +      -
    855H  PRO*     4.8     6.5    -      -       +      -
    856H  PHE*     5.4    10.1    -      -       +      -
    868H  MET*     5.7     2.7    -      -       +      -
    872H  ILE*     4.2    22.4    -      -       +      -
    883H  VAL*     5.1     1.1    -      -       +      -
    884H  VAL*     1.3    78.1    -      -       -      +
    886H  VAL*     1.3    96.0    +      -       -      +
    887H  THR*     4.4     6.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 886 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    711H  ILE*     3.2    37.2    -      -       +      +
    719H  LYS*     4.4    13.2    -      -       +      -
    720H  SER*     5.3     0.2    -      -       -      +
    723H  LEU*     3.6    23.6    -      -       +      -
    852H  LEU      3.7     1.4    +      -       -      -
    853H  ASP*     3.2    17.0    -      -       -      +
    854H  ASP*     3.2    36.4    +      -       -      +
    855H  PRO*     3.4    18.7    -      -       -      +
    856H  PHE*     5.3     0.7    -      -       -      -
    885H  LEU*     1.3    93.3    -      -       -      +
    887H  THR*     1.3    62.9    +      -       -      +
----------------------------------------------------------
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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