Contacts of the strand formed by residues 741 - 748 (chain A) in PDB entry 6N8Q


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 THR 741 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    630A  PRO*     4.7    11.4    -      -       +      +
    710A  THR      5.2     0.9    +      -       -      -
    735A  ALA      3.6     1.2    -      -       -      +
    736A  GLY*     3.3     3.8    -      -       -      -
    737A  THR*     3.0    40.9    +      -       -      +
    739A  GLY*     4.2     5.0    +      -       -      -
    740A  GLY*     1.3    75.3    -      -       -      +
    742A  ILE*     1.3    64.1    -      -       -      +
    743A  TYR*     3.5    39.3    +      -       +      +
    767A  GLU*     3.9    16.2    -      -       +      +
    768A  ILE      3.3     9.6    -      -       -      +
    769A  GLN*     3.1    20.1    +      -       +      +
    776A  VAL*     4.2     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 742 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    734A  TRP*     3.6    34.5    -      -       +      -
    735A  ALA      3.2     7.4    -      -       -      +
    740A  GLY      3.7    16.8    -      -       -      +
    741A  THR*     1.3    74.7    -      -       -      +
    743A  TYR*     1.3    64.5    +      -       -      +
    744A  ALA      4.0     0.3    +      -       -      -
    766A  LYS      4.0     0.2    -      -       -      +
    767A  GLU*     3.4     3.1    +      -       -      -
    768A  ILE*     2.7    60.2    +      -       +      +
    770A  LEU*     3.7    26.7    -      -       +      -
    776A  VAL*     4.1    10.1    -      -       +      -
    779A  ILE*     4.1    15.0    -      -       +      -
    813A  VAL*     3.9    25.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 743 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    611A  PHE*     4.0    18.4    -      +       +      -
    625A  LYS*     3.6    29.7    +      -       -      -
    626A  CYS      5.5     0.2    +      -       -      -
    627A  THR*     3.8    21.9    -      -       +      +
    629A  HIS      4.7     2.9    +      -       -      -
    630A  PRO*     4.4    13.7    -      -       -      +
    733A  LEU      3.8     1.0    -      -       -      +
    734A  TRP*     3.3     5.2    -      -       -      +
    735A  ALA*     2.8    42.3    +      -       +      +
    737A  THR*     3.6    26.5    -      -       +      +
    741A  THR*     3.5    18.5    -      -       +      +
    742A  ILE*     1.3    74.7    -      -       -      +
    744A  ALA*     1.3    58.8    +      -       -      +
    745A  PHE*     3.8    20.2    -      -       +      -
    764A  GLN*     3.7    11.9    -      -       -      -
    766A  LYS      3.6     3.6    -      -       -      +
    767A  GLU*     3.5    33.1    +      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 744 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    723A  LEU*     4.1     9.6    -      -       +      -
    733A  LEU      3.5     4.0    -      -       -      -
    734A  TRP*     3.5    40.8    -      -       +      -
    742A  ILE      4.0     0.2    +      -       -      -
    743A  TYR*     1.3    73.4    -      -       -      +
    745A  PHE*     1.3    61.5    +      -       -      +
    764A  GLN*     3.6     4.0    -      -       -      -
    765A  ALA*     2.8    22.8    +      -       -      -
    766A  LYS*     3.0    31.4    +      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 745 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    611A  PHE*     3.6    25.4    -      +       -      -
    623A  PHE*     3.6    41.5    -      +       +      -
    625A  LYS*     3.5    26.0    -      -       +      -
    723A  LEU*     3.9     3.8    -      -       -      +
    732A  SER*     3.1     7.8    -      -       -      -
    733A  LEU*     2.9    42.0    +      -       +      +
    735A  ALA*     6.0     0.2    -      -       +      -
    743A  TYR*     3.8    14.8    -      -       +      -
    744A  ALA*     1.3    80.8    -      -       -      +
    746A  SER*     1.3    64.7    +      -       -      +
    747A  LEU*     3.7     8.5    +      -       +      +
    762A  ALA*     4.6     1.1    -      -       +      -
    763A  GLU*     3.4    10.8    -      -       -      +
    764A  GLN*     3.5    38.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 746 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    723A  LEU*     3.7    16.8    -      -       -      +
    724A  LYS*     5.2     9.9    -      -       -      +
    730A  CYS*     2.9    26.5    -      -       -      +
    731A  PRO      3.8     3.8    -      -       -      -
    745A  PHE*     1.3    72.9    -      -       -      +
    747A  LEU*     1.3    60.6    +      -       -      +
    748A  ARG      4.2     0.2    -      -       -      -
    761A  ARG      3.9     0.2    -      -       -      +
    762A  ALA*     3.2     7.6    -      -       -      -
    763A  GLU*     2.9    37.3    +      -       -      -
    765A  ALA*     4.1     8.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 747 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    600A  TRP*     4.3     3.8    -      -       +      -
    602A  LEU*     3.8    28.3    -      -       +      -
    613A  LEU*     3.6    17.5    -      -       +      -
    718A  PHE*     3.9    14.6    -      -       +      -
    730A  CYS*     4.4     3.6    -      -       -      +
    731A  PRO*     2.8    46.5    +      -       +      +
    732A  SER*     3.8    23.1    -      -       -      +
    733A  LEU*     3.9     3.4    -      -       +      +
    745A  PHE*     3.8    17.3    -      -       +      +
    746A  SER*     1.3    86.2    +      -       -      +
    748A  ARG*     1.3    60.5    +      -       -      +
    749A  VAL*     3.7     1.8    -      -       +      +
    760A  VAL*     5.2     3.8    -      -       +      -
    761A  ARG      3.6     2.7    -      -       -      +
    762A  ALA*     3.6    21.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 748 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    746A  SER      4.2     0.6    -      -       -      -
    747A  LEU*     1.3    70.0    -      -       -      +
    749A  VAL*     1.3    58.8    +      -       -      +
    750A  PRO*     4.0     2.0    -      -       -      +
    759A  PRO      4.5     1.0    -      -       -      +
    760A  VAL*     3.3     7.3    -      -       -      +
    761A  ARG*     2.8    47.4    +      -       +      +
----------------------------------------------------------
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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