Contacts of the strand formed by residues 76 - 86 (chain B) 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 B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     61B  ASN*     4.4    16.8    +      -       +      -
     62B  PHE      3.5     8.5    -      -       -      +
     74B  ASN      4.4     0.7    -      -       -      +
     75B  SER*     1.3    75.5    -      -       -      +
     77B  MET*     1.3    62.8    +      -       -      +
    104B  TYR*     4.5     4.5    +      -       -      +
    317C  ALA*     3.5    14.2    -      -       -      -
    319C  ARG*     3.0     7.7    +      -       -      +
    324C  ARG*     2.9    40.5    +      -       -      -
    326C  PRO*     3.7     2.1    -      -       -      +
    327C  ARG*     2.9    62.5    +      -       +      +
    328C  THR      4.9     0.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with MET 77 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     61B  ASN*     2.9    26.7    -      -       -      +
     62B  PHE*     3.0    34.6    +      -       +      +
     64B  GLY*     3.7    11.9    -      -       -      -
     69B  GLN*     3.4    45.5    -      -       +      +
     70B  SER*     3.7     7.0    -      -       -      +
     75B  SER      3.5    11.0    -      -       -      +
     76B  ASP*     1.3    79.3    -      -       -      +
     78B  TYR*     1.3    65.8    +      -       -      +
    101B  VAL*     4.0    12.8    -      -       +      -
    102B  PHE      3.5     7.6    -      -       -      +
    103B  LYS*     3.7    39.3    -      -       +      +
    104B  TYR      5.1     1.3    -      -       -      +
    109B  ALA*     4.3     4.9    -      -       +      -
    110B  GLU*     5.5     0.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 78 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     59B  GLU*     3.9    17.5    -      -       -      -
     60B  TRP      3.5     8.1    -      -       -      +
     61B  ASN*     4.3     2.9    -      -       +      +
     62B  PHE*     4.8     0.2    -      -       -      -
     77B  MET*     1.3    74.1    -      -       -      +
     79B  LEU*     1.3    65.3    +      -       -      +
     80B  VAL*     4.8     4.0    -      -       +      -
    100B  GLU      3.5     0.6    -      -       -      +
    101B  VAL*     3.4    10.6    -      -       -      +
    102B  PHE*     2.9    47.8    +      -       +      +
    103B  LYS      3.4    26.5    -      -       -      -
    104B  TYR      4.0     2.8    +      -       -      -
    106B  ARG*     3.6    47.0    +      -       +      +
    327C  ARG*     3.3    37.7    -      -       +      +
    328C  THR*     5.3    10.1    -      -       -      -
    331C  GLN*     4.1    15.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 79 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     30B  TYR*     4.3    12.3    -      -       +      -
     32B  TRP*     3.6    60.3    -      -       +      -
     43B  LYS*     4.6     0.4    -      -       -      -
     59B  GLU*     3.4     9.0    -      -       -      +
     60B  TRP*     2.8    50.5    +      -       +      +
     61B  ASN      4.0    22.4    -      -       -      +
     62B  PHE*     3.7    20.9    -      -       +      -
     78B  TYR*     1.3    74.3    -      -       -      +
     80B  VAL*     1.3    62.2    +      -       -      +
     81B  PRO*     4.0     1.4    -      -       -      +
     99B  CYS*     4.0    17.9    -      -       +      -
    100B  GLU      3.6     1.6    -      -       -      -
    101B  VAL*     4.3     3.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 80 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     59B  GLU*     4.0    24.7    -      -       +      +
     78B  TYR*     4.8     5.4    -      -       +      -
     79B  LEU*     1.3    76.5    -      -       -      +
     81B  PRO*     1.3    80.5    -      -       +      +
     82B  ALA*     4.2     0.3    -      -       -      +
     99B  CYS*     3.4     3.1    -      -       -      +
    100B  GLU*     3.0    30.0    +      -       +      +
    102B  PHE*     3.7    35.2    -      -       +      -
    106B  ARG*     5.6     4.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with PRO 81 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     30B  TYR*     4.2    10.3    -      -       +      -
     54B  VAL*     3.8    19.1    -      -       +      +
     57B  LEU*     3.7    29.4    -      -       +      +
     58B  PRO      3.7    18.4    -      -       -      +
     59B  GLU*     4.2     7.2    -      -       +      +
     79B  LEU      4.0     5.2    -      -       -      +
     80B  VAL*     1.3    97.2    -      -       +      +
     82B  ALA*     1.3    59.3    +      -       -      +
     97B  VAL*     3.7    15.3    -      -       +      -
     99B  CYS*     3.9    10.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 82 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     54B  VAL*     3.7    15.8    -      -       -      +
     80B  VAL      4.2     4.9    -      -       -      +
     81B  PRO*     1.3    75.0    -      -       -      +
     83B  ALA*     1.3    61.4    +      -       +      +
     98B  LEU*     2.9    21.1    +      -       +      +
     99B  CYS      4.5     0.4    -      -       -      -
    100B  GLU*     4.3     7.9    -      -       +      +
    114B  ARG*     3.7    46.7    +      -       -      +
    216B  ASP*     5.1     0.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 83 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     54B  VAL*     4.1     6.1    -      -       -      -
     82B  ALA*     1.3    80.3    -      -       -      +
     84B  MET*     1.3    61.1    +      -       -      +
     85B  PHE*     3.7    23.4    -      -       +      -
     96B  LEU      3.9     0.5    -      -       -      +
     97B  VAL*     3.4     3.3    -      -       -      -
     98B  LEU*     2.8    38.0    +      -       +      +
    216B  ASP*     3.8    28.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with MET 84 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     51B  PRO*     4.0    18.8    -      -       -      +
     52B  LYS      4.1     2.9    -      -       -      +
     53B  CYS*     3.6    35.4    -      -       -      +
     54B  VAL*     4.1    18.4    -      -       +      +
     57B  LEU*     3.7    24.2    -      -       +      -
     83B  ALA*     1.3    73.3    -      -       -      +
     85B  PHE*     1.3    82.5    +      -       -      +
     95B  LYS*     4.0    30.3    -      -       +      +
     96B  LEU      3.4    10.1    -      -       -      +
     97B  VAL*     4.5     1.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 85 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     83B  ALA*     3.7    27.8    -      -       +      -
     84B  MET*     1.3    83.9    -      -       -      +
     86B  ARG*     1.3    67.7    +      -       -      +
     95B  LYS*     3.4    11.4    -      -       -      +
     96B  LEU*     2.8    37.9    +      -       +      +
    186B  ALA*     3.5    19.5    -      -       +      +
    187B  GLY*     3.8    23.3    -      -       -      -
    188B  VAL*     4.0    11.4    -      -       +      -
    216B  ASP      4.5     0.9    -      -       -      -
    217B  HIS*     3.8    38.4    -      +       -      -
    220B  VAL*     3.5    42.2    -      -       +      -
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Residues in contact with ARG 86 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     21A  PRO*     4.9     5.5    +      -       -      +
     22A  GLN      6.0     1.4    +      -       -      -
     85B  PHE*     1.3    76.2    -      -       -      +
     87B  ASP*     1.3    59.3    +      -       -      +
     88B  PRO*     3.2     7.8    -      -       -      +
     92B  ASP*     2.6    42.3    +      -       -      +
     94B  ASN      4.1     4.0    -      -       -      -
     95B  LYS*     4.7    11.9    -      -       -      +
     96B  LEU*     4.2     2.4    -      -       -      +
    184B  LEU      5.0     0.6    +      -       -      -
    185B  TYR*     2.9    73.6    +      -       +      +
    186B  ALA*     3.0    33.2    +      -       -      +
    187B  GLY*     5.7     1.1    -      -       -      -
----------------------------------------------------------
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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