Contacts of the strand formed by residues 843 - 850 (chain A) in PDB entry 6N8P


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 843 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    714A  ARG*     4.9     0.2    +      -       -      -
    777A  VAL*     3.7    22.0    -      -       +      +
    814A  VAL*     4.2     7.4    -      -       +      -
    815A  SER      3.6    21.5    -      -       -      +
    816A  GLU*     3.0    32.0    +      -       -      +
    817A  GLU      5.6     1.6    -      -       -      -
    819A  PHE*     3.9    20.9    -      -       +      -
    835A  LEU*     4.1    11.0    -      -       +      -
    842A  ARG*     1.3    70.2    -      -       -      +
    844A  ARG*     1.3    63.3    +      -       -      +
    845A  ARG      3.8    15.3    -      -       -      +
    846A  VAL*     4.3     1.1    -      -       +      -
    866A  VAL*     3.7    30.5    -      -       +      -
    867A  LEU      3.9     3.1    -      -       -      -
    868A  THR*     4.5     1.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 844 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    714A  ARG*     4.0    20.4    +      -       -      +
    777A  VAL*     4.2    13.0    -      -       -      +
    816A  GLU*     5.8     1.3    -      -       -      -
    842A  ARG      3.4     2.4    +      -       -      -
    843A  VAL*     1.3    74.4    -      -       -      +
    845A  ARG*     1.3    72.5    +      -       +      +
    867A  LEU*     2.7    24.7    +      -       +      +
    868A  THR      4.4     9.4    -      -       -      +
    869A  ASN*     4.5     8.5    -      -       +      +
    898A  ILE*     4.2    21.1    -      -       +      +
    899A  ALA*     3.7    38.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 845 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    777A  VAL*     5.3     3.1    -      -       -      -
    843A  VAL*     3.8     5.9    -      -       -      +
    844A  ARG*     1.3    99.7    -      -       +      +
    846A  VAL*     1.3    64.2    +      -       -      +
    847A  SER*     3.2    20.7    +      -       -      -
    865A  ALA      4.1     0.6    -      -       -      +
    866A  VAL*     3.7     2.1    -      -       -      -
    867A  LEU*     2.9    39.8    +      -       +      +
    898A  ILE      6.1     0.4    -      -       -      -
    899A  ALA      5.2     7.4    -      -       -      -
    901A  CYS      3.4    26.3    +      -       -      -
    902A  VAL*     4.5     8.5    -      -       -      +
    903A  PHE*     3.2    41.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 846 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    777A  VAL*     3.6    23.1    +      -       +      +
    778A  GLY*     4.0    10.3    -      -       -      -
    814A  VAL*     4.0    28.3    -      -       +      -
    843A  VAL*     4.3     3.8    -      -       +      +
    845A  ARG*     1.3    78.8    +      -       -      +
    847A  SER*     1.3    72.9    +      -       -      +
    864A  LEU*     3.7    28.9    -      -       +      -
    865A  ALA      3.4    12.1    -      -       -      +
    866A  VAL*     3.8    16.6    -      -       +      -
    903A  PHE*     5.4     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 847 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    845A  ARG*     3.2    24.3    +      -       -      -
    846A  VAL*     1.3    84.7    +      -       -      +
    848A  VAL*     1.3    66.0    +      -       -      +
    849A  ALA*     6.2     0.2    -      -       -      -
    864A  LEU*     3.8     5.5    -      -       -      +
    865A  ALA*     2.8    35.1    +      -       -      +
    903A  PHE*     4.1    24.5    -      -       -      +
    904A  THR      5.4     2.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 848 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    780A  LEU*     4.4    22.9    -      -       +      +
    788A  PRO*     3.7    31.2    -      -       +      -
    847A  SER*     1.3    75.0    -      -       -      +
    849A  ALA*     1.3    62.5    +      -       -      +
    850A  HIS*     6.0     0.2    -      -       +      -
    862A  HIS*     4.4    16.8    -      -       +      -
    863A  HIS      3.7    13.0    -      -       -      +
    864A  LEU*     4.2     3.9    -      -       +      +
    878A  LEU*     5.4     0.7    -      -       +      -
    904A  THR      4.3     2.9    -      -       -      +
    905A  LYS*     4.0    14.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 849 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    847A  SER      3.5     0.6    +      -       -      -
    848A  VAL*     1.3    77.7    -      -       -      +
    850A  HIS*     1.3    60.3    +      -       -      +
    851A  PHE*     3.5    34.1    -      -       +      -
    862A  HIS*     3.6     1.7    -      -       -      +
    863A  HIS*     2.9    33.6    +      -       -      +
    865A  ALA*     4.1    20.9    -      -       +      +
    904A  THR      4.6     6.5    -      -       -      +
    905A  LYS      3.2     9.9    -      -       -      +
    907A  GLY*     4.6     4.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with HIS 850 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    849A  ALA*     1.3    72.2    -      -       -      +
    851A  PHE*     1.3    64.5    +      -       -      +
    852A  GLY*     5.9     0.4    -      -       -      -
    860A  GLY*     3.0    34.0    +      -       -      -
    861A  GLU      3.6    17.0    -      -       -      -
    862A  HIS*     3.6    36.8    -      +       +      -
    905A  LYS*     2.8    14.3    +      -       +      +
    906A  TYR*     3.6    45.9    -      +       +      +
    927A  TRP*     5.7     1.2    -      -       -      -
----------------------------------------------------------
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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