Contacts of the strand formed by residues 611 - 622 (chain C) in PDB entry 6DBV


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 PHE 611 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    593C  ILE*     5.8     7.2    -      -       +      -
    597C  LEU*     4.0    33.4    -      -       +      -
    607C  CYS*     3.1    27.1    -      -       +      -
    608C  THR      4.8     3.1    -      -       -      -
    609C  SER      2.5    10.4    +      -       -      +
    610C  GLY*     1.3    74.0    -      -       -      -
    612C  THR*     1.3    67.7    +      -       -      +
    649C  ILE*     3.5    21.3    -      -       +      -
    650C  SER      3.0    20.0    -      -       -      -
    651C  ILE*     3.4    21.1    -      -       +      -
    652C  ARG*     5.6     0.2    -      -       -      +
    662C  ILE*     4.7     5.8    -      -       +      -
    718C  ARG*     4.6    14.8    -      -       +      -
    719C  SER      3.6    15.5    -      -       -      +
    720C  PHE*     3.9    28.0    -      +       +      -
    721C  ARG*     3.3    24.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 612 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    610C  GLY      5.6     0.2    -      -       -      -
    611C  PHE*     1.3    82.0    +      -       -      +
    613C  VAL*     1.3    66.8    +      -       -      +
    614C  VAL*     4.3     6.9    +      -       +      +
    648C  SER      4.1     0.5    -      -       -      +
    649C  ILE*     3.3     5.2    -      -       -      +
    650C  SER*     3.0    37.7    +      -       -      -
    651C  ILE      6.0     1.1    -      -       -      -
    652C  ARG*     5.1     9.7    -      -       -      +
    721C  ARG*     3.2    18.8    +      -       -      +
    723C  PHE*     3.6    46.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 613 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    582C  LEU*     6.3     0.2    -      -       +      -
    586C  LEU*     3.8    15.5    -      -       +      -
    612C  THR*     1.3    73.4    -      -       -      +
    614C  VAL*     1.3    72.8    +      -       -      +
    615C  VAL*     4.4     5.6    -      -       +      -
    646C  ILE*     4.1    20.0    -      -       +      -
    648C  SER      3.2    10.1    -      -       -      +
    649C  ILE*     3.6    27.1    -      -       +      -
    720C  PHE*     3.6    24.2    -      -       +      -
    721C  ARG      3.1     5.5    +      -       -      -
    722C  PHE*     3.3    29.4    -      -       +      +
    723C  PHE      3.1    22.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 614 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    612C  THR*     4.8    10.1    -      -       +      +
    613C  VAL*     1.3    78.7    -      -       -      +
    615C  VAL*     1.3    61.9    +      -       -      +
    647C  MET*     2.9    32.4    +      -       +      +
    648C  SER*     2.9    26.7    +      -       -      +
    723C  PHE*     3.7    18.8    -      -       +      +
    725C  ARG*     4.4    20.6    -      -       +      +
    978C  TRP*     3.7    30.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 615 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    578C  TYR*     4.2     8.7    -      -       -      +
    582C  LEU*     4.4    17.9    -      -       +      -
    613C  VAL*     4.4     6.1    -      -       +      -
    614C  VAL*     1.3    79.4    -      -       -      +
    616C  LYS*     1.3    72.7    -      -       -      +
    617C  GLU*     5.1     2.0    -      -       +      -
    644C  PHE*     4.4    10.1    -      -       +      -
    645C  THR      4.3     2.2    -      -       -      +
    646C  ILE*     5.0     6.3    -      -       +      -
    722C  PHE*     4.4    22.7    -      -       +      -
    723C  PHE      3.2    11.8    +      -       -      +
    724C  PHE*     3.7    32.3    -      -       +      -
    725C  ARG*     3.3    29.5    +      -       -      +
    978C  TRP*     5.0     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 616 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    614C  VAL      4.2     1.2    +      -       -      -
    615C  VAL*     1.3    76.2    -      -       -      +
    617C  GLU*     1.3    74.6    +      -       -      +
    618C  SER*     6.0     2.9    -      -       -      -
    644C  PHE*     3.2     9.2    -      -       -      +
    645C  THR*     3.0    54.2    +      -       -      +
    647C  MET*     4.0    16.2    -      -       +      +
    668C  PRO*     3.2    37.2    +      -       -      +
    669C  ASN*     5.3     0.6    +      -       -      +
    673C  SER      5.6     0.2    +      -       -      -
    674C  CYS*     6.1     1.8    -      -       -      -
    725C  ARG      4.1     2.9    -      -       -      -
    727C  THR*     3.8    15.0    -      -       +      +
    728C  GLY*     6.1     0.2    -      -       -      -
    977C  ALA      4.1     7.3    +      -       -      +
    978C  TRP*     4.0    37.8    -      -       +      +
    979C  ALA      4.0    14.1    +      -       -      +
    982C  GLY*     6.0     2.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 617 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    578C  TYR*     4.3     6.7    +      -       -      +
    615C  VAL*     5.1     0.9    -      -       +      -
    616C  LYS*     1.3    82.3    -      -       -      +
    618C  SER*     1.3    63.5    +      -       -      +
    642C  PHE*     3.9    18.7    -      -       +      -
    643C  SER      3.4    14.6    -      -       -      +
    644C  PHE*     3.9     7.0    -      -       +      +
    701C  ARG*     2.7    36.4    +      -       -      -
    724C  PHE*     4.3     5.0    -      -       -      -
    725C  ARG      2.6    28.1    +      -       -      +
    726C  GLY*     3.0    21.0    +      -       -      -
    727C  THR*     3.7     3.9    +      -       -      +
    728C  GLY*     2.9    22.1    +      -       -      -
    729C  TYR*     4.1    12.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 618 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    616C  LYS*     6.0     3.1    -      -       -      -
    617C  GLU*     1.3    80.8    -      -       -      +
    619C  CYS*     1.3    64.0    +      -       -      +
    642C  PHE*     3.7     2.3    -      -       -      -
    643C  SER*     3.0    34.6    +      -       -      +
    674C  CYS*     4.7     3.1    -      -       -      -
    728C  GLY*     3.1    22.7    -      -       -      -
    729C  TYR*     3.7     7.0    -      -       -      -
    979C  ALA      5.7     0.2    -      -       -      -
    980C  SER*     4.4     9.2    -      -       -      -
    983C  ASN*     2.3    38.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with CYS 619 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    618C  SER*     1.3    81.2    -      -       -      +
    620C  ASP*     1.3    61.8    +      -       -      +
    640C  VAL*     3.6    25.8    -      -       -      -
    641C  ARG      3.8     6.3    -      -       -      -
    642C  PHE*     3.7    24.9    -      -       +      -
    680C  MET*     5.7     0.2    -      -       -      -
    690C  LEU*     5.6     2.5    -      -       -      -
    694C  LEU*     5.3     3.4    -      -       -      -
    728C  GLY      3.2     8.0    +      -       -      +
    729C  TYR*     3.4    27.7    -      -       +      -
    730C  ASP*     4.8     4.3    +      -       -      +
    733C  MET*     3.5    30.1    -      -       -      +
    737C  MET*     5.1     4.9    -      -       +      -
    983C  ASN*     3.8     0.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 620 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    619C  CYS*     1.3    76.3    -      -       -      +
    621C  GLY*     1.3    83.8    +      -       -      +
    640C  VAL*     3.3     8.1    -      -       -      +
    641C  ARG*     3.0    29.3    +      -       -      +
    684C  GLU*     4.4    10.2    -      -       -      +
    728C  GLY      5.8     0.9    -      -       -      +
    730C  ASP*     3.5    15.0    -      -       -      +
    733C  MET*     5.7     2.5    -      -       -      -
    980C  SER*     5.8     3.8    -      -       -      +
    983C  ASN*     4.4    14.6    -      -       +      +
    984C  GLU*     3.1    14.7    -      -       -      +
    987C  ASN*     5.5     5.3    -      -       -      +
   1102C   CA      2.4    24.0    -      -       -      -
   1103C   CA      2.5    18.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 621 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    620C  ASP*     1.3    98.4    +      -       -      +
    622C  MET*     1.3    62.3    +      -       -      -
    623C  GLY      4.0     1.0    +      -       -      -
    638C  LYS*     6.0     0.4    -      -       -      -
    639C  ALA      2.9    13.2    -      -       -      -
    640C  VAL*     3.6    14.2    -      -       -      +
    641C  ARG      4.7     0.2    -      -       -      -
    684C  GLU*     5.1     9.8    +      -       -      +
    733C  MET*     6.2     0.2    -      -       -      +
    987C  ASN*     4.2     6.7    +      -       -      -
   1102C   CA      3.6    12.0    -      -       -      -
   1103C   CA      4.2     1.0    -      -       -      -
     46H    T      5.2     0.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with MET 622 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    621C  GLY*     1.3    73.2    -      -       -      -
    623C  GLY*     1.3    66.6    +      -       -      +
    625C  VAL*     3.5    15.9    -      -       +      -
    637C  GLU      3.7     1.0    -      -       -      +
    638C  LYS*     3.4     9.7    -      -       -      +
    639C  ALA*     2.7    33.3    +      -       +      +
    987C  ASN*     3.1    59.5    +      -       -      +
    990C  PHE*     3.9    18.2    -      -       +      -
    991C  ARG*     2.6    43.3    -      -       +      +
     45H    G      4.7     4.9    -      -       -      +
     46H    T      4.3     5.8    -      -       -      +
----------------------------------------------------------
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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