Contacts of the strand formed by residues 118 - 126 (chain B) in PDB entry 2QBX


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 118 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    102B  VAL*     5.6     0.2    -      -       -      -
    116B  LYS*     4.8     2.8    -      -       -      +
    117B  GLU*     1.3    86.8    +      -       +      +
    119B  PHE*     1.3    61.1    +      -       -      +
    148B  THR*     3.8    13.4    -      -       +      +
    149B  ILE      3.1    10.8    -      -       -      +
    150B  ALA*     3.6    25.6    -      -       +      -
    187B  GLN      5.0     0.2    -      -       -      +
    188B  ASP*     4.9     2.6    -      -       -      +
    189B  TYR*     2.7    42.1    +      -       -      -
    193B  MET*     3.5    16.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 119 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     51B  TRP*     4.9     6.1    -      +       +      -
     98B  MET*     4.1    12.8    -      -       -      -
    100B  PHE*     3.9    30.7    -      +       +      -
    102B  VAL*     5.6     1.6    -      -       +      -
    118B  THR*     1.3    74.5    -      -       -      +
    120B  ASN*     1.3    68.3    +      -       -      +
    148B  THR*     3.5     1.4    -      -       -      +
    149B  ILE*     2.6    80.6    +      -       +      +
    186B  PHE*     3.8    30.1    -      +       +      -
    187B  GLN      3.4    16.6    -      -       -      +
    188B  ASP*     4.8     0.4    -      -       -      -
    189B  TYR*     3.6     9.2    -      -       -      -
    193B  MET*     3.8    26.2    -      -       +      -
    195B  LEU*     4.4    14.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 120 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    119B  PHE*     1.3    79.2    -      -       -      +
    121B  LEU*     1.3    60.0    +      -       -      +
    122B  TYR*     3.6    24.9    +      -       +      -
    145B  LYS*     3.4    21.3    +      -       -      +
    147B  ASP      3.6     3.1    -      -       -      +
    148B  THR*     2.7    32.1    +      -       -      -
    185B  ALA      3.5     0.7    -      -       -      +
    186B  PHE*     3.3     6.8    -      -       -      -
    187B  GLN*     2.8    55.8    +      -       -      +
    189B  TYR*     3.3    21.0    +      -       -      -
    411B  SO4      5.6     0.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 121 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     96B  VAL*     4.4    14.1    -      -       +      -
     98B  MET*     4.0    26.2    -      -       +      -
    119B  PHE      4.2     0.4    +      -       -      -
    120B  ASN*     1.3    73.0    -      -       -      +
    122B  TYR*     1.3    68.7    +      -       -      +
    145B  LYS*     3.7     5.0    -      -       -      +
    146B  VAL*     2.7    58.1    +      -       +      -
    147B  ASP      3.0    16.0    +      -       -      +
    149B  ILE*     4.3    10.3    -      -       +      -
    172B  ARG*     4.3     6.3    -      -       +      -
    174B  PHE*     5.8     0.2    -      -       +      -
    184B  LEU*     4.3    11.7    -      -       +      -
    185B  ALA      3.4     4.3    -      -       -      +
    186B  PHE*     3.4    36.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 122 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     80B  TRP*     3.6    23.1    -      +       -      -
    120B  ASN*     3.6    24.6    +      -       +      -
    121B  LEU*     1.3    75.1    -      -       -      +
    123B  TYR*     1.3    61.0    +      -       -      +
    140B  GLU*     3.8    23.1    +      -       +      -
    143B  TRP*     3.7    30.1    -      -       +      -
    144B  VAL      3.1     8.3    -      -       -      +
    145B  LYS*     3.4    39.7    +      -       +      +
    146B  VAL*     4.1     4.5    -      -       -      +
    184B  LEU*     3.3     9.4    -      -       -      +
    185B  ALA*     2.8    39.0    +      -       +      +
    187B  GLN*     2.8    34.4    +      -       +      -
    411B  SO4      3.3    16.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 123 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    122B  TYR*     1.3    74.4    -      -       -      +
    124B  TYR*     1.3    68.5    +      -       -      +
    125B  GLU*     3.9    30.4    +      -       +      -
    143B  TRP*     3.4     5.8    -      -       -      -
    144B  VAL*     2.7    72.4    +      -       +      +
    145B  LYS      5.3     0.4    -      -       -      -
    146B  VAL*     3.6    15.3    -      -       +      -
    174B  PHE*     3.4    48.7    -      +       +      -
    175B  GLY*     4.7    10.2    +      -       -      -
    176B  PRO      5.2     2.8    +      -       -      -
    177B  VAL*     4.6     2.0    -      -       +      -
    182B  PHE*     4.9     2.7    -      -       +      -
    183B  TYR      3.2    13.0    -      -       -      +
    184B  LEU*     3.7    13.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 124 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    127A  ASP*     4.1     6.6    +      -       -      -
    179A  ARG*     3.2    25.6    +      -       +      +
    123B  TYR*     1.3    79.2    -      -       -      +
    125B  GLU*     1.3    77.2    +      -       -      +
    126B  ALA*     3.8    13.0    -      -       +      -
    130B  SER*     4.6     6.7    -      -       -      -
    135B  PHE*     3.4    24.6    -      +       -      -
    136B  PRO*     4.0    19.1    -      -       +      -
    142B  PRO*     3.6    37.0    -      -       +      +
    143B  TRP*     3.6    22.9    -      -       +      -
    144B  VAL*     5.4     2.0    -      -       -      -
    182B  PHE*     3.2     4.4    -      -       -      -
    183B  TYR*     2.9    43.7    +      +       -      -
----------------------------------------------------------
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Residues in contact with GLU 125 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    179A  ARG*     2.9    34.4    +      -       -      +
    405A  SO4      3.9    12.6    +      -       -      +
    123B  TYR*     3.9    24.2    +      -       +      -
    124B  TYR*     1.3    82.4    -      -       -      +
    126B  ALA*     1.3    61.0    +      -       -      +
    176B  PRO      4.1     5.7    -      -       -      +
    177B  VAL*     3.3    29.5    -      -       +      +
    178B  SER*     3.0    26.8    +      -       -      -
    179B  ARG*     3.4    19.6    +      -       -      +
    181B  GLY      3.3    10.2    -      -       -      +
    182B  PHE*     3.9     4.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 126 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    127A  ASP*     3.5    12.6    -      -       -      +
    179A  ARG*     4.2     1.1    -      -       -      +
     85B  PHE*     3.8     4.1    -      -       +      -
    124B  TYR*     3.8    14.3    +      -       +      -
    125B  GLU*     1.3    76.9    -      -       -      +
    127B  ASP*     1.3    64.8    +      -       -      +
    128B  PHE      3.3    20.0    -      -       -      +
    130B  SER*     3.9     6.3    -      -       -      +
    179B  ARG*     4.2     1.8    -      -       -      +
    180B  SER      3.4     2.9    +      -       -      -
    181B  GLY      2.8    33.2    +      -       -      +
    183B  TYR*     4.1    13.2    -      -       +      -
----------------------------------------------------------
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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