Contacts of the strand formed by residues 66 - 73 (chain B) in PDB entry 1QY4


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 LEU 66 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     66A  LEU*     3.8    25.6    -      -       +      -
     96A  ALA*     3.5    29.6    -      -       +      +
     97A  GLU*     3.8    10.1    -      -       -      -
     98A  VAL*     4.1    17.6    -      -       +      +
    129A  TYR*     3.7     9.4    -      -       +      -
    151A  ILE      3.7    21.5    -      -       -      +
    152A  TYR*     4.5     0.4    -      -       -      -
    153A  PRO*     4.0    10.5    -      -       +      -
     57B  VAL      4.8     0.2    -      -       -      +
     59B  GLN*     3.3    20.4    +      -       -      +
     64B  GLY      4.5     2.2    -      -       -      +
     65B  ASP*     1.3    91.6    +      -       -      +
     67B  ASN*     1.3    66.6    +      -       -      +
     68B  PHE*     5.1     0.9    -      -       -      -
    151B  ILE*     4.3     9.9    -      -       +      -
    152B  TYR      3.5    18.8    -      -       -      +
    153B  PRO*     3.9     2.9    -      -       +      -
    154B  ALA      3.9     0.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASN 67 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     57B  VAL      3.5     7.6    -      -       -      +
     58B  GLU*     3.6    19.7    +      -       -      +
     59B  GLN*     2.6    36.1    +      -       -      +
     66B  LEU*     1.3    77.9    -      -       -      +
     68B  PHE*     1.3    66.9    +      -       -      +
    151B  ILE*     3.3     6.5    -      -       -      +
    152B  TYR*     2.9    65.1    +      -       +      +
    154B  ALA*     3.6    25.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 68 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     98A  VAL*     4.0    21.1    -      -       +      -
    127A  VAL*     3.6    30.5    -      -       +      -
    129A  TYR*     4.4    20.2    -      +       +      -
      6B  PHE*     4.5     5.4    -      +       -      -
      8B  VAL*     4.1    17.3    -      -       +      -
     17B  ILE*     4.2     9.6    -      -       +      -
     55B  TYR      4.1     0.2    -      -       -      +
     56B  ALA*     4.4     0.5    -      -       -      +
     57B  VAL*     2.8    72.1    +      -       +      +
     66B  LEU      5.1     2.0    -      -       -      -
     67B  ASN*     1.3    79.0    -      -       -      +
     69B  ALA*     1.3    63.3    +      -       -      +
    149B  LEU*     4.2    14.8    -      -       +      -
    150B  ALA      3.1    12.8    -      -       -      +
    151B  ILE*     4.1    14.4    -      -       +      -
    152B  TYR*     4.0     3.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 69 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     17B  ILE*     4.7     1.1    -      -       -      -
     54B  VAL*     3.9    14.6    -      -       +      -
     55B  TYR      3.1    12.6    -      -       -      +
     56B  ALA*     3.9    11.9    -      -       +      -
     68B  PHE*     1.3    77.0    -      -       -      +
     70B  THR*     1.3    59.2    +      -       -      +
     71B  THR*     4.3     0.7    +      -       -      -
    148B  PHE*     4.0     0.3    -      -       -      +
    149B  LEU*     3.4     5.7    -      -       -      +
    150B  ALA*     2.6    39.5    +      -       -      +
    152B  TYR*     4.1     7.9    -      -       +      +
    301B  6PG      3.8    21.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 70 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10B  VAL*     3.9    24.0    -      -       +      -
     15B  GLY*     2.5    35.3    +      -       -      +
     17B  ILE*     3.7    10.9    -      -       +      +
     54B  VAL*     3.2     7.1    -      -       -      +
     55B  TYR*     2.8    49.0    +      -       -      +
     69B  ALA*     1.3    76.3    -      -       -      +
     71B  THR*     1.3    63.7    +      -       -      +
    102B  LEU*     4.8     2.9    -      -       +      -
    147B  ILE*     5.0     0.4    -      -       -      -
    148B  PHE      3.1    12.8    -      -       -      +
    149B  LEU*     3.9    13.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 71 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     52B  TYR*     3.9    22.7    -      -       +      -
     53B  GLU      3.2    10.1    -      -       -      +
     54B  VAL*     3.8     4.3    -      -       -      +
     69B  ALA      4.3     0.5    +      -       -      -
     70B  THR*     1.3    77.1    +      -       -      +
     72B  VAL*     1.3    73.9    -      -       -      +
     73B  LEU*     3.8     2.5    -      -       +      +
     85B  THR*     4.3     4.9    -      -       +      -
    146B  PHE      3.6     0.7    -      -       -      +
    147B  ILE*     3.2     8.5    -      -       -      +
    148B  PHE*     3.1    60.6    +      -       +      -
    301B  6PG      2.7    31.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 72 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     14B  THR      3.4    24.9    -      -       -      +
     15B  GLY*     4.1    11.4    -      -       -      +
     52B  TYR*     3.1     4.7    -      -       -      -
     53B  GLU*     2.8    38.3    +      -       -      +
     55B  TYR*     4.4    15.0    -      -       +      -
     71B  THR*     1.3    76.7    -      -       -      +
     73B  LEU*     1.3    59.7    +      -       -      +
     74B  TYR*     3.6    32.2    +      -       +      +
    145B  PRO*     4.0    23.1    -      -       +      -
    146B  PHE      3.6     2.9    -      -       -      -
    147B  ILE*     4.2     8.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 73 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     51B  VAL*     3.7    14.4    -      -       +      +
     52B  TYR*     3.7     7.9    -      -       +      -
     71B  THR*     3.8     7.1    -      -       +      -
     72B  VAL*     1.3    70.7    -      -       -      +
     74B  TYR*     1.3    66.5    +      -       -      +
     83B  PHE*     3.8     6.1    -      -       +      +
     84B  PHE*     3.8    30.1    -      -       -      +
     85B  THR*     4.3    10.3    -      -       +      -
    138B  THR*     3.5    21.1    -      -       -      +
    139B  VAL      3.4    10.5    -      -       -      +
    140B  ASN*     2.8    51.4    +      -       +      +
    145B  PRO*     3.7     1.3    -      -       -      +
    146B  PHE*     2.8    37.6    +      -       +      +
    148B  PHE*     4.7     0.9    -      -       +      -
----------------------------------------------------------
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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