Contacts of the strand formed by residues 298 - 304 (chain B) in PDB entry 1QQJ


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 ASN 298 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    296B  ASP*     4.4     8.5    +      -       -      +
    297B  ILE*     1.3    73.2    -      -       -      +
    299B  LEU*     1.3    59.6    +      -       -      +
    317B  SER      3.8     5.9    -      -       -      +
    318B  ASN*     3.7    13.7    +      -       -      +
    394B  GLY*     3.0     6.2    -      -       -      -
    395B  HIS*     2.9    74.6    +      -       +      +
    396B  CYS*     4.4     0.8    -      -       -      +
    397B  GLN*     4.2    16.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 299 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    200B  LEU*     4.1    27.4    -      -       +      -
    202B  MET*     3.9    14.8    -      -       +      -
    230B  LEU*     3.6    31.0    -      -       +      -
    297B  ILE*     3.7     8.1    -      -       +      +
    298B  ASN*     1.3    82.2    -      -       -      +
    300B  SER*     1.3    61.7    +      -       -      +
    316B  ARG*     3.4     4.7    -      -       -      +
    317B  SER*     2.8    38.6    +      -       -      +
    318B  ASN*     4.0     3.1    -      -       -      -
    319B  PHE*     3.7    18.8    -      -       -      +
    351B  ILE*     3.6    32.8    -      -       +      -
    393B  THR      3.5     5.8    -      -       -      +
    394B  GLY*     4.0     2.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 300 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    299B  LEU*     1.3    77.5    -      -       -      +
    301B  VAL*     1.3    68.2    +      -       -      +
    313B  THR*     3.3    24.9    +      -       -      +
    315B  CYS      3.3     5.2    +      -       -      -
    316B  ARG*     4.2     6.6    +      -       -      +
    391B  ILE      3.8     0.8    -      -       -      +
    392B  ILE*     3.4     5.0    -      -       -      +
    393B  THR*     2.9    46.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 301 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    198B  MET*     4.0    17.9    -      -       +      -
    200B  LEU*     4.1    31.6    -      -       +      -
    300B  SER*     1.3    80.8    -      -       -      +
    302B  SER*     1.3    63.7    +      -       -      +
    313B  THR*     3.5     4.2    -      -       -      -
    314B  ILE*     2.8    33.2    +      -       +      +
    315B  CYS*     2.9    33.5    +      -       +      -
    390B  VAL*     3.5    30.5    -      -       +      -
    391B  ILE      3.4     4.5    -      -       -      +
    392B  ILE*     4.2     8.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 302 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    301B  VAL*     1.3    77.6    -      -       -      +
    303B  LEU*     1.3    61.6    +      -       -      +
    311B  ALA*     3.9    22.0    -      -       -      +
    312B  ALA      3.1    14.8    -      -       -      -
    313B  THR*     4.4     6.5    -      -       -      -
    314B  ILE*     4.8     0.9    -      -       -      -
    389B  GLU      3.6     0.7    +      -       -      +
    390B  VAL*     3.3     9.2    -      -       -      +
    391B  ILE*     2.9    54.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 303 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    302B  SER*     1.3    76.3    -      -       -      +
    304B  LYS*     1.3    65.4    +      -       -      +
    305B  GLY      3.8    14.6    -      -       -      +
    308B  MET*     4.2     2.6    -      -       -      +
    311B  ALA*     3.5     1.1    -      -       -      -
    312B  ALA*     2.8    33.4    +      -       -      +
    314B  ILE*     4.3    22.8    -      -       +      +
    362B  MET*     3.7    32.8    -      -       +      -
    375B  VAL*     4.1    20.6    -      -       +      -
    381B  ARG*     4.0    16.4    -      -       +      +
    384B  LEU*     3.9    16.8    -      -       +      -
    388B  ASP*     4.0    17.7    -      -       +      +
    389B  GLU      3.4     7.0    -      -       -      +
    390B  VAL*     4.8     2.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 304 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    303B  LEU*     1.3    79.5    -      -       -      +
    305B  GLY*     1.3    71.4    +      -       -      +
    308B  MET*     3.4    29.2    -      -       +      +
    309B  SER*     3.8    21.3    +      -       -      +
    310B  GLN      4.3     0.2    -      -       -      +
    311B  ALA*     3.8    26.2    -      -       +      +
    387B  GLY      3.9     1.2    -      -       -      +
    388B  ASP*     3.5     0.3    -      -       -      -
    389B  GLU*     2.9    54.6    +      -       +      +
----------------------------------------------------------
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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