Contacts of the strand formed by residues 786 - 795 (chain K) in PDB entry 6R90


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 786 (chain K).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    740K  ILE*     3.3     8.7    -      -       -      +
    741K  GLU*     2.8    53.4    +      -       +      +
    749K  THR*     4.5    20.2    -      -       +      +
    784K  GLU*     3.9    11.4    -      -       +      +
    785K  GLU*     1.3    80.5    -      -       -      +
    787K  GLU*     1.3    63.4    +      -       -      +
    788K  VAL*     3.8    14.4    -      -       +      -
    809K  GLN*     6.3     3.8    -      -       +      -
    810K  ASN*     5.1    14.4    -      -       -      +
     71L  ARG*     6.1     2.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 787 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    382K  PHE*     4.9     6.5    -      -       -      -
    722K  ARG*     3.2    27.9    +      -       -      -
    738K  SER*     4.7     4.5    -      -       -      -
    739K  ARG      3.4     5.2    -      -       -      +
    740K  ILE*     3.9    20.9    -      -       +      +
    786K  VAL*     1.3    73.9    -      -       -      +
    788K  VAL*     1.3    62.5    +      -       -      +
    789K  HIS*     3.4    14.9    +      -       +      +
    810K  ASN*     5.1     9.0    +      -       -      -
    811K  GLU      5.0     1.6    -      -       -      +
    812K  TYR*     3.0    53.0    +      -       +      +
     71L  ARG*     3.8    21.4    -      -       -      +
     74L  HIS*     5.8     0.5    -      -       -      -
     75L  GLN*     4.8     9.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 788 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    738K  SER*     3.3     1.4    -      -       -      -
    739K  ARG*     2.9    54.2    +      -       +      +
    741K  GLU*     3.6    31.4    -      -       +      +
    749K  THR*     5.0     1.6    -      -       -      +
    786K  VAL*     3.8    15.0    -      -       +      -
    787K  GLU*     1.3    74.5    -      -       -      +
    789K  HIS*     1.3    64.0    +      -       -      +
    790K  ASN*     3.8    17.7    +      -       -      +
    806K  GLN*     4.0    24.0    -      -       +      +
    807K  PHE      5.6     0.9    -      -       -      +
    808K  LEU      6.1     2.2    -      -       -      +
    809K  GLN*     6.6     0.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with HIS 789 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    722K  ARG*     3.3    32.3    -      -       -      +
    736K  LEU*     6.3     0.2    -      -       -      +
    737K  SER      3.3     7.8    +      -       -      +
    738K  SER*     3.9    10.1    -      -       -      -
    787K  GLU*     3.4    25.9    +      -       -      +
    788K  VAL*     1.3    73.4    -      -       -      +
    790K  ASN*     1.3    72.9    +      -       -      +
    806K  GLN*     4.0     2.6    -      -       -      +
    807K  PHE*     3.2    32.6    +      -       +      +
    808K  LEU      5.5     2.6    +      -       -      -
    811K  GLU      3.8    16.9    +      -       -      +
    812K  TYR*     3.2    44.6    -      +       +      -
    813K  ALA*     3.2    26.6    +      -       +      +
----------------------------------------------------------
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Residues in contact with ASN 790 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    719K  GLU*     5.3     0.4    +      -       -      +
    736K  LEU*     3.5     4.5    -      -       -      +
    737K  SER*     2.9    37.5    +      -       -      +
    739K  ARG*     3.0    25.0    +      -       -      +
    757K  SER*     3.6    26.0    -      -       -      +
    788K  VAL*     3.8    13.7    +      -       -      +
    789K  HIS*     1.3    91.6    +      -       -      +
    791K  LEU*     1.3    63.7    +      -       -      +
    792K  LEU*     4.7     2.0    -      -       +      -
    804K  ALA*     4.5     4.3    -      -       -      +
    805K  HIS      3.3     9.2    +      -       -      +
    806K  GLN*     3.1    31.2    +      -       -      +
    807K  PHE*     3.6     9.3    -      -       -      -
    813K  ALA*     5.7     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 791 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    734K  GLY*     4.0     7.4    -      -       -      -
    735K  VAL      3.2    35.9    -      -       -      +
    736K  LEU*     4.1     4.0    -      -       +      +
    790K  ASN*     1.3    72.1    -      -       -      +
    792K  LEU*     1.3    68.8    +      -       -      +
    793K  ILE*     4.2     5.4    +      -       +      +
    803K  HIS*     4.4     0.5    -      -       -      -
    804K  ALA*     3.4     4.3    -      -       -      -
    805K  HIS*     2.9    34.1    +      -       -      +
    807K  PHE*     3.5    16.7    -      -       +      -
    816K  LEU*     4.0    15.3    -      -       +      -
    829K  PHE*     4.5    11.0    -      -       +      -
    831K  VAL*     4.3    19.1    -      -       +      -
    851K  PHE*     4.7     2.5    -      -       +      -
    858K  LEU*     3.7    37.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 792 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    717K  LEU*     4.7    11.7    -      -       +      -
    719K  GLU*     3.4    17.5    -      -       +      +
    734K  GLY*     3.4     4.9    -      -       -      -
    735K  VAL*     2.8    40.4    +      -       +      +
    737K  SER*     3.7    19.5    -      -       -      +
    756K  ALA*     3.6    22.0    -      -       +      +
    757K  SER*     3.5    36.1    -      -       -      +
    790K  ASN*     4.7     0.9    -      -       +      -
    791K  LEU*     1.3    76.3    -      -       -      +
    793K  ILE*     1.3    61.4    -      -       -      +
    794K  ILE*     3.3    22.9    -      -       +      +
    801K  VAL*     4.4     4.3    -      -       +      -
    803K  HIS      3.4     4.3    -      -       -      +
    804K  ALA*     4.0    11.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 793 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    732K  CYS*     3.9    21.3    -      -       +      -
    733K  PHE      3.4     5.8    -      -       -      +
    734K  GLY*     5.5     1.1    -      -       -      -
    791K  LEU*     5.1     7.0    -      -       +      +
    792K  LEU*     1.3    75.6    -      -       -      +
    794K  ILE*     1.3    57.4    +      -       -      +
    801K  VAL*     3.6     2.8    -      -       -      -
    802K  LEU*     2.6    44.6    +      -       +      -
    803K  HIS*     2.8    36.4    +      -       +      +
    829K  PHE*     5.0     9.0    -      -       +      -
    853K  TYR*     3.3    42.8    -      -       +      -
    858K  LEU*     4.0    27.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 794 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    387K  LEU*     4.4    15.3    -      -       +      -
    715K  VAL*     5.9     0.7    -      -       +      -
    717K  LEU*     5.6     5.4    -      -       +      -
    732K  CYS*     3.3     4.5    -      -       -      +
    733K  PHE*     2.9    42.4    +      -       +      +
    735K  VAL*     3.6    26.5    -      -       +      -
    792K  LEU*     3.3    44.0    -      -       +      +
    793K  ILE*     1.3    74.9    -      -       -      +
    795K  ASP*     1.3    76.1    +      -       -      +
    799K  PHE*     3.7    31.9    -      -       +      +
    800K  GLU      3.4     4.9    -      -       -      +
    801K  VAL*     5.1     7.4    -      -       +      -
    802K  LEU*     3.6     4.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with ASP 795 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    731K  GLN      4.6     6.0    -      -       -      +
    732K  CYS*     5.3     0.7    -      -       -      -
    794K  ILE*     1.3    75.7    -      -       -      +
    796K  GLN*     1.3    60.3    +      -       -      +
    797K  HIS*     2.8    20.1    +      -       -      +
    798K  THR*     2.6    49.6    +      -       -      +
    799K  PHE*     2.9    30.1    +      -       -      +
    800K  GLU      3.0    14.3    +      -       -      +
    802K  LEU*     3.4    27.9    -      -       +      +
----------------------------------------------------------
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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