Contacts of the strand formed by residues 76 - 86 (chain F) in PDB entry 2QC8


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 ASP 76 (chain F).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     61F  ASN*     4.3    16.5    +      -       +      +
     62F  PHE      3.4     8.3    -      -       -      -
     70F  SER*     5.2     0.2    -      -       -      -
     74F  ASN      4.1     1.7    -      -       -      +
     75F  SER*     1.3    75.2    -      -       -      +
     77F  MET*     1.3    61.1    +      -       -      +
    104F  TYR*     4.4     5.9    +      -       -      +
    317G  ALA*     3.7    14.7    -      -       -      +
    319G  ARG*     3.1    17.5    +      -       -      +
    324G  ARG*     3.2    29.5    +      -       -      -
    326G  PRO*     3.7     0.7    -      -       -      +
    327G  ARG*     2.9    68.5    +      -       +      +
----------------------------------------------------------
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Residues in contact with MET 77 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     61F  ASN*     2.9     9.0    -      -       -      +
     62F  PHE*     2.9    49.2    +      -       +      +
     64F  GLY*     3.7    13.9    -      -       -      -
     69F  GLN*     3.4    42.8    -      -       +      +
     70F  SER*     3.9     6.3    -      -       -      +
     75F  SER      3.4    13.9    -      -       -      +
     76F  ASP*     1.3    74.6    -      -       -      +
     78F  TYR*     1.3    64.1    +      -       -      +
    101F  VAL*     3.5    16.4    -      -       +      -
    102F  PHE      3.4    19.7    -      -       -      +
    103F  LYS*     3.8    19.1    -      -       +      -
    104F  TYR      5.3     0.7    -      -       -      +
    109F  ALA*     4.0    11.2    -      -       +      -
    110F  GLU*     5.8     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 78 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     59F  GLU*     3.7    18.4    -      -       -      -
     60F  TRP      3.6     7.9    -      -       -      -
     61F  ASN*     4.3     3.4    -      -       +      +
     77F  MET*     1.3    76.3    -      -       -      +
     79F  LEU*     1.3    65.4    +      -       -      +
     80F  VAL*     4.1     3.6    -      -       +      -
    100F  GLU      3.6     0.4    -      -       -      +
    101F  VAL*     3.3    12.8    -      -       -      +
    102F  PHE*     3.0    45.4    +      -       +      +
    103F  LYS      3.3    26.9    -      -       -      -
    104F  TYR      3.9     6.0    +      -       -      -
    106F  ARG*     3.5    45.5    +      -       +      +
    327G  ARG*     3.4    39.0    -      -       +      +
    328G  THR*     5.6     6.5    -      -       -      -
    331G  GLN*     3.9    17.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 79 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     30F  TYR*     4.2    10.9    -      -       +      -
     32F  TRP*     3.4    58.6    -      -       +      -
     43F  LYS*     4.7     3.4    -      -       -      -
     59F  GLU*     3.5     7.6    -      -       -      +
     60F  TRP*     2.8    38.8    +      -       +      +
     61F  ASN      3.6    22.4    -      -       -      +
     62F  PHE*     3.6    29.2    -      -       +      -
     78F  TYR*     1.3    72.5    -      -       -      +
     80F  VAL*     1.3    62.8    +      -       -      +
     81F  PRO*     3.6     2.8    -      -       -      +
     99F  CYS*     4.0    19.3    -      -       +      -
    100F  GLU      3.6     1.8    -      -       -      -
    101F  VAL*     4.3     3.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 80 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     59F  GLU*     4.1    24.9    -      -       +      +
     78F  TYR*     4.9     5.4    -      -       +      -
     79F  LEU*     1.3    74.3    -      -       -      +
     81F  PRO*     1.4    80.9    -      -       +      +
     82F  ALA*     3.3     1.0    +      -       -      +
     99F  CYS*     3.3     3.0    -      -       -      +
    100F  GLU*     3.1    31.4    +      -       +      +
    102F  PHE*     3.7    34.1    -      -       +      -
    106F  ARG*     5.6     4.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with PRO 81 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     30F  TYR*     4.1    11.9    -      -       +      -
     54F  VAL*     3.8    27.6    -      -       +      +
     57F  LEU*     3.7    20.6    -      -       +      +
     58F  PRO      3.6    23.3    -      -       -      +
     59F  GLU*     4.2     5.8    -      -       +      +
     79F  LEU      3.6     9.4    -      -       -      +
     80F  VAL*     1.4    97.6    -      -       +      +
     82F  ALA*     1.3    59.3    +      -       -      +
     97F  VAL*     3.9     8.7    -      -       +      -
     98F  LEU      3.8     7.0    -      -       -      +
     99F  CYS*     4.1     4.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 82 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     54F  VAL*     3.7    15.1    -      -       -      +
     80F  VAL      3.3     5.4    +      -       -      +
     81F  PRO*     1.3    74.4    -      -       -      +
     83F  ALA*     1.3    62.5    +      -       +      +
     98F  LEU*     2.8    19.6    +      -       +      +
     99F  CYS      4.4     0.7    -      -       -      -
    100F  GLU*     4.3    11.2    -      -       +      +
    114F  ARG*     3.7    42.5    +      -       -      +
    216F  ASP*     5.0     0.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 83 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     54F  VAL*     3.8     7.0    -      -       -      -
     82F  ALA*     1.3    81.1    -      -       -      +
     84F  MET*     1.3    61.4    +      -       -      +
     85F  PHE*     4.0    22.1    -      -       +      -
     96F  LEU      3.9     0.5    -      -       -      +
     97F  VAL*     3.3     3.0    -      -       -      -
     98F  LEU*     2.7    42.6    +      -       +      +
    216F  ASP*     4.1    25.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with MET 84 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     51F  PRO*     3.7    26.0    -      -       -      +
     52F  LYS      3.6    31.6    -      -       -      +
     53F  CYS*     4.0    10.5    -      -       -      +
     54F  VAL*     3.8    20.2    -      -       +      +
     57F  LEU*     3.7    25.1    -      -       +      -
     83F  ALA*     1.3    73.3    -      -       -      +
     85F  PHE*     1.3    81.9    +      -       -      +
     95F  LYS*     4.0    20.0    -      -       +      +
     96F  LEU      3.3     9.6    -      -       -      +
     97F  VAL*     4.4     0.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 85 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     83F  ALA*     4.0    26.2    -      -       +      -
     84F  MET*     1.3    82.9    -      -       -      +
     86F  ARG*     1.3    65.5    +      -       -      +
     95F  LYS*     3.4    10.4    -      -       -      +
     96F  LEU*     2.7    38.8    +      -       +      +
    186F  ALA*     3.3    23.1    -      -       +      +
    187F  GLY*     3.6    24.0    -      -       -      -
    188F  VAL*     4.0    10.1    -      -       +      -
    216F  ASP      4.6     2.0    -      -       -      -
    217F  HIS*     3.6    40.6    -      +       -      -
    220F  VAL*     3.6    36.3    -      -       +      -
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Residues in contact with ARG 86 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     85F  PHE*     1.3    77.7    -      -       -      +
     87F  ASP*     1.3    60.1    +      -       -      +
     88F  PRO*     3.2    12.6    -      -       -      +
     92F  ASP*     2.7    40.4    +      -       -      +
     94F  ASN      4.0     4.5    -      -       -      -
     95F  LYS*     4.7    11.4    -      -       -      +
     96F  LEU*     4.2     2.2    -      -       -      +
    184F  LEU      5.1     1.4    +      -       -      -
    185F  TYR*     2.9    66.1    +      -       +      +
    186F  ALA*     3.1    21.9    +      -       -      +
    187F  GLY*     5.8     0.7    -      -       -      -
     21J  PRO*     5.0     5.5    +      -       -      +
     22J  GLN      6.2     0.4    -      -       -      -
     23J  GLY*     6.0     4.2    -      -       -      -
----------------------------------------------------------
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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