Contacts of the strand formed by residues 610 - 616 (chain A) in PDB entry 6Q6Q


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 LEU 610 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    608A  GLN      4.1     4.7    -      -       -      +
    609A  GLU*     1.3    79.7    -      -       -      +
    611A  PHE*     1.3    59.5    +      -       -      +
    639A  VAL*     4.0    17.3    -      -       +      -
    679A  LEU*     3.7    35.7    -      -       +      -
    680A  ALA      3.5    13.5    -      -       -      +
    681A  ASP*     3.4    31.0    -      -       -      +
    828A  HIS*     4.8     5.4    -      -       +      -
    830A  ARG*     3.6    42.2    -      -       +      +
    831A  ALA      2.7     9.0    +      -       -      +
    832A  VAL*     3.2     6.8    -      -       +      -
    833A  ARG*     2.8    28.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 611 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33A  LYS*     5.6     1.8    -      -       -      -
    601A  ASP*     5.7     0.2    -      -       -      -
    609A  GLU*     5.9     0.4    -      -       -      -
    610A  LEU*     1.3    74.1    -      -       -      +
    612A  LEU*     1.3    86.1    +      -       -      +
    613A  THR*     4.3     5.8    +      -       -      -
    678A  VAL      3.8     0.5    -      -       -      +
    679A  LEU*     3.4     5.7    -      -       -      +
    680A  ALA      3.1    30.5    +      -       -      -
    681A  ASP      4.5     1.2    +      -       -      -
    682A  SER*     3.9     5.4    -      -       -      +
    683A  GLU*     3.6    66.4    -      -       +      +
    686A  ALA*     4.3     8.6    -      -       +      +
    687A  LYS*     4.1     8.5    -      -       -      -
    833A  ARG*     3.4    29.2    -      -       +      -
    835A  VAL*     3.4    43.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 612 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    611A  PHE*     1.3    87.0    -      -       -      +
    613A  THR*     1.3    63.9    +      -       -      +
    614A  PHE*     3.6    34.3    -      -       +      -
    642A  MET*     4.1    13.5    -      -       +      -
    677A  ALA*     3.8    17.9    -      -       +      -
    678A  VAL      3.3    19.7    -      -       -      +
    679A  LEU*     4.0    12.6    -      -       +      -
    820A  VAL*     4.2     7.9    -      -       +      +
    821A  THR*     3.6    24.7    -      -       -      +
    824A  ALA*     4.6     5.2    -      -       +      -
    832A  VAL*     3.7    14.8    -      -       +      -
    833A  ARG      3.1     8.8    +      -       -      +
    834A  CYS*     3.4    23.1    -      -       +      +
    835A  VAL      5.3     0.2    -      -       -      +
    836A  LEU*     5.6     0.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with THR 613 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    611A  PHE*     4.2     9.1    -      -       -      -
    612A  LEU*     1.3    75.0    -      -       -      +
    614A  PHE*     1.3    71.9    +      -       -      +
    677A  ALA*     3.5     3.3    -      -       -      -
    678A  VAL*     2.7    45.7    +      -       +      +
    686A  ALA*     3.5    42.1    -      -       +      +
    687A  LYS*     3.9    16.8    -      -       -      +
    690A  ALA*     4.0    10.7    -      -       +      +
    836A  LEU*     5.9     1.8    -      -       -      -
    840A  GLU*     3.3    16.8    +      -       -      -
   3006A  MLI      5.3     1.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 614 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    612A  LEU*     3.6    11.2    -      -       +      -
    613A  THR*     1.3    86.5    +      -       -      +
    615A  VAL*     1.3    68.5    +      -       -      +
    616A  THR*     4.3     6.7    +      -       +      +
    663A  LEU*     4.8     3.4    -      -       +      -
    674A  LEU*     4.0    37.0    -      -       +      -
    676A  CYS      3.5    14.8    -      -       -      +
    677A  ALA*     4.1    11.4    -      -       +      -
    690A  ALA*     4.6     0.5    -      -       -      +
    817A  ILE*     3.7    23.8    -      -       +      -
    820A  VAL*     3.5    34.1    -      -       +      -
    834A  CYS*     3.4    26.0    -      -       -      -
    836A  LEU*     4.2    17.3    -      -       +      -
    840A  GLU*     3.8    11.8    +      -       -      +
    844A  ILE*     4.9     4.7    -      -       +      -
   3006A  MLI      3.8    13.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 615 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    613A  THR      4.4     0.2    +      -       -      -
    614A  PHE*     1.3    72.8    -      -       -      +
    616A  THR*     1.3    61.2    +      -       -      +
    674A  LEU*     4.1     1.4    -      -       -      -
    675A  VAL*     3.1    20.5    +      -       +      +
    676A  CYS*     3.2    35.9    +      -       +      +
    678A  VAL*     4.1    11.7    -      -       +      -
    690A  ALA*     3.6    42.0    -      -       +      +
    693A  VAL*     4.4     9.2    -      -       +      -
    695A  ILE*     4.0    25.1    -      -       +      -
   3006A  MLI      3.7    13.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with THR 616 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    614A  PHE*     4.6     5.6    -      -       +      +
    615A  VAL*     1.3    81.9    -      -       -      +
    617A  SER*     1.3    70.0    +      -       -      +
    618A  SER*     3.6     3.1    +      -       -      -
    672A  GLY*     3.6    28.6    -      -       -      +
    673A  GLN      3.2     6.5    -      -       -      +
    674A  LEU*     4.4     6.5    -      -       +      -
    675A  VAL*     4.1     5.1    -      -       -      +
    695A  ILE*     5.3     2.4    -      -       -      +
    697A  TYR*     4.2     5.4    +      -       -      -
    840A  GLU*     5.9     4.3    -      -       +      +
    843A  LEU*     4.1    12.2    -      -       +      +
    844A  ILE*     4.0    25.6    -      -       +      -
   3006A  MLI      3.4    28.0    +      -       -      +
----------------------------------------------------------
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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