Contacts of the helix formed by residues 861 - 879 (chain u) in PDB entry 6FF7


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 ALA 861 (chain u).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     261  VAL*     4.0    22.4    -      -       +      +
    821u  HIS*     6.0     3.6    -      -       +      -
    859u  ASP*     3.2    10.8    -      -       +      +
    860u  GLU*     1.3    80.2    -      -       -      +
    862u  GLU*     1.3    64.1    +      -       -      +
    863u  GLN*     4.7     1.1    -      -       +      +
    864u  TYR*     4.0    22.4    -      -       +      +
    865u  ARG*     3.5    20.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 862 (chain u). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    860u  GLU      4.2     0.6    +      -       -      -
    861u  ALA*     1.3    72.5    -      -       -      +
    863u  GLN*     1.3    61.0    +      -       -      +
    865u  ARG*     3.5     5.3    +      -       -      +
    866u  LYS*     2.9    27.9    +      -       -      +
    902u  GLU      5.7     4.9    -      -       -      +
    903u  GLN*     6.0     2.0    -      -       -      -
    904u  THR*     5.6    12.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 863 (chain u). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    824u  ALA*     4.3    21.2    -      -       +      +
    825u  LEU*     6.0     1.6    -      -       -      -
    861u  ALA*     4.7     1.2    -      -       +      +
    862u  GLU*     1.3    76.9    -      -       -      +
    864u  TYR*     1.3    60.5    +      -       -      +
    866u  LYS*     3.3     8.1    +      -       -      +
    867u  MET*     2.9    27.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 864 (chain u). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    820u  GLN      5.4     5.6    -      -       -      +
    821u  HIS*     5.4     9.2    -      -       +      -
    824u  ALA*     4.6     9.7    -      -       +      +
    856u  ASP*     5.4     2.2    -      -       -      +
    859u  ASP*     5.3     7.0    -      -       +      -
    861u  ALA*     4.0    21.3    +      -       +      +
    862u  GLU      3.3     0.4    -      -       -      -
    863u  GLN*     1.3    76.2    -      -       -      +
    865u  ARG*     1.3    59.8    +      -       -      +
    867u  MET*     3.2     9.0    +      -       -      +
    868u  VAL*     3.0    26.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 865 (chain u). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    856u  ASP      4.6    13.6    +      -       -      +
    857u  LEU*     4.8    13.2    -      -       -      +
    859u  ASP*     5.4     5.8    -      -       +      +
    861u  ALA      3.5    16.3    +      -       -      +
    862u  GLU*     3.5     5.5    +      -       -      +
    863u  GLN      3.4     0.2    -      -       -      -
    864u  TYR*     1.3    78.3    -      -       -      +
    866u  LYS*     1.3    57.2    +      -       -      +
    868u  VAL*     3.4     7.3    +      -       -      +
    869u  MET*     2.9    29.3    +      -       -      +
    899u  ALA*     5.1    11.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 866 (chain u). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    862u  GLU      2.9    19.0    +      -       -      +
    863u  GLN*     3.5    10.1    -      -       -      +
    864u  TYR      3.2     0.4    -      -       -      -
    865u  ARG*     1.3    74.4    -      -       -      +
    867u  MET*     1.3    58.6    +      -       -      +
    869u  MET*     3.4     6.5    +      -       -      +
    870u  GLU*     2.9    29.8    +      -       -      +
    909u  VAL*     6.5     0.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with MET 867 (chain u). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    824u  ALA*     4.4    14.1    -      -       +      -
    830u  TYR*     5.8     5.4    -      -       +      +
    834u  VAL*     5.1     3.5    -      -       -      +
    863u  GLN      2.9    14.4    +      -       -      +
    864u  TYR*     3.2    11.6    +      -       -      +
    866u  LYS*     1.3    74.5    -      -       -      +
    868u  VAL*     1.3    59.7    +      -       -      +
    870u  GLU*     3.3     6.3    +      -       -      +
    871u  THR*     2.9    28.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 868 (chain u). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    853u  ILE*     4.6    19.7    -      -       +      +
    856u  ASP*     4.8    17.3    -      -       +      +
    857u  LEU*     5.3     4.5    -      -       +      +
    864u  TYR      3.0    16.0    +      -       -      +
    865u  ARG*     3.8     8.1    -      -       -      +
    867u  MET*     1.3    75.5    -      -       -      +
    869u  MET*     1.3    58.0    +      -       -      +
    871u  THR*     3.3     8.8    +      -       -      -
    872u  ILE*     2.9    28.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with MET 869 (chain u). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    865u  ARG      2.9    18.2    +      -       -      +
    866u  LYS*     3.6     8.5    -      -       -      +
    867u  MET      3.2     0.2    -      -       -      -
    868u  VAL*     1.3    78.3    -      -       -      +
    870u  GLU*     1.3    56.4    +      -       -      +
    872u  ILE*     3.8     6.4    -      -       -      +
    873u  GLU*     2.9    30.3    +      -       -      +
    909u  VAL      5.8     2.2    -      -       -      +
    910u  MET*     5.3    16.8    -      -       +      -
    913u  GLY*     5.2     4.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 870 (chain u). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    834u  VAL*     5.0    11.4    -      -       +      +
    866u  LYS      2.9    17.0    +      -       -      +
    867u  MET*     3.7     7.2    -      -       -      +
    869u  MET*     1.3    73.4    -      -       -      +
    871u  THR*     1.3    61.0    +      -       -      +
    873u  GLU*     4.1     4.9    -      -       -      +
    874u  LYS*     3.0    33.1    +      -       -      +
    909u  VAL*     6.2     4.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 871 (chain u). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    834u  VAL*     4.7    14.7    -      -       -      +
    837u  THR*     5.3    11.4    -      -       -      -
    853u  ILE*     6.4     1.8    -      -       -      -
    867u  MET      2.9    14.7    +      -       -      -
    868u  VAL*     3.4    13.0    -      -       -      -
    869u  MET      3.3     0.2    -      -       -      -
    870u  GLU*     1.3    76.9    -      -       -      +
    872u  ILE*     1.3    56.9    +      -       -      +
    874u  LYS*     3.9     2.4    -      -       -      +
    875u  ILE*     3.0    32.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 872 (chain u). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    850u  ILE*     6.4     3.6    -      -       +      -
    868u  VAL      2.9    16.3    +      -       -      +
    869u  MET*     3.8     6.5    -      -       -      +
    871u  THR*     1.3    76.8    -      -       -      +
    873u  GLU*     1.3    56.1    +      -       -      +
    875u  ILE*     4.0     3.7    -      -       -      +
    876u  MET*     2.9    35.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 873 (chain u). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    869u  MET      2.9    18.0    +      -       -      +
    870u  GLU*     4.1     5.4    -      -       -      +
    871u  THR      3.4     0.2    -      -       -      -
    872u  ILE*     1.3    75.6    -      -       -      +
    874u  LYS*     1.3    57.8    +      -       -      +
    876u  MET*     4.4     2.2    -      -       -      +
    877u  GLY*     2.9    26.5    +      -       -      -
    909u  VAL      5.5     1.1    -      -       -      +
    912u  ASN      5.0     0.7    -      -       -      +
    913u  GLY*     3.7    30.7    -      -       -      +
    916u  THR*     4.6    13.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 874 (chain u). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    834u  VAL*     5.7     5.4    -      -       +      +
    838u  VAL*     5.1    16.3    -      -       +      +
    870u  GLU      3.0    18.3    +      -       -      +
    871u  THR*     4.1     2.9    -      -       -      +
    873u  GLU*     1.3    75.9    -      -       -      +
    875u  ILE*     1.3    60.0    +      -       -      +
    877u  GLY*     5.1     0.2    -      -       -      -
    878u  ASN*     2.9    31.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 875 (chain u). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    837u  THR      5.8     0.7    -      -       -      +
    838u  VAL*     5.8     4.9    -      -       -      +
    841u  ALA*     4.4    22.9    -      -       +      -
    846u  ALA*     5.8     9.0    -      -       +      +
    850u  ILE*     6.4     1.8    -      -       +      -
    871u  THR      3.0    19.5    +      -       -      +
    872u  ILE*     4.1     3.6    -      -       -      +
    874u  LYS*     1.3    77.5    -      -       -      +
    876u  MET*     1.3    57.7    +      -       -      +
    878u  ASN*     4.8     2.2    -      -       -      -
    879u  LEU*     2.8    37.4    +      -       +      +
----------------------------------------------------------
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Residues in contact with MET 876 (chain u). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    872u  ILE      2.9    19.3    +      -       -      +
    873u  GLU*     4.4     2.2    -      -       -      +
    875u  ILE*     1.3    76.5    -      -       -      +
    877u  GLY*     1.3    59.4    +      -       -      +
    878u  ASN      3.5     0.2    -      -       -      -
    880u  GLY*     3.5    34.2    +      -       -      +
    881u  ALA*     5.7     1.6    -      -       +      -
    916u  THR*     5.4     7.0    -      -       -      +
    917u  VAL*     5.4     8.3    -      -       +      -
    920u  ALA*     4.3    18.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 877 (chain u). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    873u  GLU      2.9    18.3    +      -       -      -
    874u  LYS      3.9     0.7    -      -       -      -
    876u  MET*     1.3    78.2    -      -       -      +
    878u  ASN*     1.3    60.2    +      -       -      +
    880u  GLY      5.0     0.2    -      -       -      -
    916u  THR*     5.3     8.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with ASN 878 (chain u). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    838u  VAL*     6.0     5.8    -      -       +      +
    874u  LYS      2.9    18.9    +      -       -      +
    875u  ILE*     4.1     2.2    -      -       -      +
    877u  GLY*     1.3    80.0    -      -       -      +
    879u  LEU*     1.3    65.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 879 (chain u). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    841u  ALA*     5.3    12.1    -      -       +      +
    842u  ASN*     6.2     1.6    -      -       -      -
    846u  ALA*     4.7    17.9    -      -       +      +
    875u  ILE*     2.8    21.4    +      -       +      +
    877u  GLY      5.2     0.2    -      -       -      -
    878u  ASN*     1.3    77.3    -      -       +      +
    880u  GLY*     1.3    59.4    +      -       -      +
----------------------------------------------------------
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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