Contacts of the strand formed by residues 156 - 162 (chain P) in PDB entry 3QUM


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 GLN 156 (chain P).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19P  GLY*     2.8    42.6    +      -       -      +
     20P  TRP      3.0     7.4    +      -       -      +
     21P  GLU*     3.9    15.5    -      -       -      +
     22P  CYS*     4.4     0.2    -      -       -      -
    138P  ALA      3.4     2.4    -      -       -      +
    139P  SER*     3.1    24.4    -      -       -      -
    140P  GLY      3.0     6.5    +      -       -      +
    141P  TRP      4.2     6.3    +      -       -      +
    154P  LYS*     3.1    21.7    +      -       -      +
    155P  LEU*     1.3    82.1    +      -       -      +
    157P  CYS*     1.3    62.9    +      -       -      +
    158P  VAL*     4.1     4.9    -      -       +      +
    191P  CYS      4.5     5.8    -      -       -      +
    192P  SER*     3.2    32.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with CYS 157 (chain P). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     97H  TYR*     3.6    24.7    -      -       +      -
     98H  ARG*     2.5    33.3    +      -       -      -
     20P  TRP      3.3    10.8    +      -       -      +
     21P  GLU      4.2     5.1    -      -       -      +
     22P  CYS*     2.0    46.3    -      -       -      -
     27P  GLN*     3.8    12.1    -      -       -      -
    137P  TYR*     3.8    19.7    -      -       +      -
    138P  ALA      3.7     3.4    -      -       -      -
    139P  SER*     4.2     5.8    -      -       -      -
    156P  GLN*     1.3    75.6    -      -       -      +
    158P  VAL*     1.3    58.7    +      -       -      +
    187P  GLY*     4.1     0.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 158 (chain P). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19P  GLY*     6.2     0.7    -      -       -      -
     20P  TRP      5.1     2.0    -      -       -      +
    137P  TYR*     3.3    18.3    -      -       -      -
    138P  ALA*     3.4    13.3    +      -       +      +
    156P  GLN*     4.8     5.4    -      -       +      +
    157P  CYS*     1.3    80.9    -      -       -      +
    159P  ASP*     1.3    65.8    +      -       -      +
    160P  LEU*     3.5    17.8    +      -       +      +
    185P  ARG      5.8     0.2    -      -       -      +
    186P  TRP*     4.5    18.4    -      -       +      +
    187P  GLY*     4.1    17.0    -      -       -      +
    188P  LYS      4.7    12.1    -      -       -      +
    190P  THR*     4.7     3.8    -      -       -      +
    192P  SER*     3.0    38.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 159 (chain P). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     97H  TYR*     2.4    35.1    +      -       -      -
     98H  ARG*     3.5    14.1    +      -       -      -
    136P  CYS      3.7     8.8    -      -       -      +
    137P  TYR*     4.2     0.3    -      -       -      +
    157P  CYS      4.1     0.2    +      -       -      -
    158P  VAL*     1.3    75.1    -      -       -      +
    160P  LEU*     1.3    62.9    +      -       -      +
    185P  ARG*     3.5    33.2    +      -       -      +
    186P  GLY*     3.5    34.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 160 (chain P). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    135P  THR*     3.8     2.4    -      -       -      +
    136P  CYS*     2.8    30.2    +      -       +      +
    137P  TYR*     4.5     2.2    -      -       -      -
    138P  ALA*     4.3    10.3    -      -       +      -
    158P  VAL*     3.5    18.8    +      -       +      +
    159P  ASP*     1.3    76.9    -      -       -      +
    161P  HIS*     1.3    69.5    +      -       -      +
    183P  ALA*     4.0    16.2    -      -       +      +
    184P  GLY*     3.5    17.7    -      -       -      +
    185P  ARG*     2.9    26.9    +      -       -      +
    186P  TRP*     3.9    22.2    -      -       +      -
    199P  LEU*     4.3    16.4    -      -       +      -
    228P  TYR*     3.8    21.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with HIS 161 (chain P). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    133P  GLY*     4.4    12.6    -      -       -      -
    134P  THR      3.1    22.9    -      -       -      +
    135P  THR*     3.8    10.6    -      -       +      +
    136P  CYS*     4.2     2.2    -      -       -      +
    160P  LEU*     1.3    73.3    +      -       -      +
    162P  VAL*     1.3    64.2    +      -       -      +
    163P  ILE*     3.4    16.2    +      -       +      +
    183P  ALA*     3.8     5.6    -      -       -      -
    184P  GLY      3.2    27.8    +      -       -      +
    185P  ARG*     2.4    60.0    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 162 (chain P). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    130P  PRO*     4.4    16.6    -      -       +      +
    131P  ALA      4.5     4.7    -      -       -      +
    132P  LEU*     3.7    14.9    -      -       +      -
    133P  GLY*     2.9    24.3    +      -       -      -
    134P  THR*     2.9    22.7    +      -       -      +
    136P  CYS*     3.9    18.2    -      -       -      -
    161P  HIS*     1.3    73.3    -      -       -      +
    163P  ILE*     1.3    71.9    +      -       -      +
    181P  LEU*     4.8    17.9    -      -       +      -
    182P  CYS      4.1     4.5    -      -       -      +
    183P  ALA*     3.9    12.3    -      -       +      -
    199P  LEU*     5.5     2.7    -      -       +      -
    201P  CYS*     4.3     6.1    -      -       -      -
----------------------------------------------------------
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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