Contacts of the strand formed by residues 417 - 423 (chain A) in PDB entry 1QIJ


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 GLY 417 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    317A  THR      4.0     1.2    -      -       -      +
    318A  GLN*     3.3    11.1    -      -       -      -
    319A  ILE*     3.1    25.4    +      -       -      +
    411A  TYR*     4.9     0.5    -      -       -      -
    415A  GLY      3.5     3.8    +      -       -      -
    416A  ASN*     1.3    80.0    -      -       -      +
    418A  THR*     1.3    64.5    +      -       -      -
    419A  TYR*     4.7     3.8    -      -       -      -
    494A  LEU*     4.1    18.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with THR 418 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    319A  ILE*     3.5    15.0    -      -       +      +
    321A  LEU*     4.1    14.1    -      -       +      -
    408A  VAL*     3.6    22.7    -      -       +      -
    411A  TYR*     4.2     4.5    -      -       -      -
    412A  THR*     2.8    37.1    +      -       -      +
    415A  GLY*     5.6     0.3    -      -       -      -
    417A  GLY*     1.3    78.1    +      -       -      -
    419A  TYR*     1.3    64.3    +      -       -      +
    420A  LEU*     4.9     0.4    -      -       +      +
    494A  LEU*     3.5    11.7    -      -       -      +
    495A  PHE*     2.8    47.8    +      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 419 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    319A  ILE      3.0     8.8    +      -       -      -
    320A  LEU*     3.3    15.5    -      -       +      +
    321A  LEU*     2.9    28.6    +      -       -      +
    417A  GLY*     4.7     3.6    -      -       -      -
    418A  THR*     1.3    81.0    -      -       -      +
    420A  LEU*     1.3    59.6    +      -       -      +
    476A  PHE*     4.0    14.6    -      +       -      -
    480A  GLY      3.5    20.5    +      -       -      -
    481A  ASN*     3.3    27.3    +      -       -      +
    482A  PRO*     3.4    33.0    -      -       +      -
    483A  ASN*     4.4     0.7    -      -       -      -
    492A  TRP*     3.8    31.0    -      +       +      +
    493A  PRO      3.8    14.1    -      -       -      -
    494A  LEU*     3.2    32.3    -      -       +      +
    495A  PHE*     4.8     1.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 420 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    321A  LEU*     3.0    43.7    -      -       +      +
    322A  GLY*     3.8     7.6    -      -       -      -
    404A  LEU*     4.1    11.0    -      -       +      -
    405A  MET*     3.6    34.3    -      -       +      -
    408A  VAL*     4.6     6.1    -      -       +      -
    418A  THR      4.3     0.4    -      -       -      -
    419A  TYR*     1.3    73.7    -      -       -      +
    421A  TYR*     1.3    65.8    +      -       -      +
    492A  TRP*     3.2    17.4    +      -       -      +
    493A  PRO      5.3     0.6    +      -       -      -
    495A  PHE*     4.0    29.9    -      -       +      +
    501A  LYS      4.5     1.2    +      -       -      +
    502A  PHE*     3.5    22.0    -      -       +      +
    503A  ILE      3.3    15.2    +      -       -      -
    516A  LEU*     4.4     9.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 421 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    223A  ILE*     5.7     0.2    -      -       +      -
    224A  LEU      4.7     1.6    -      -       -      -
    225A  GLN*     3.5    34.5    +      -       +      +
    226A  SER*     4.5     1.6    +      -       -      -
    320A  LEU*     4.0    10.3    -      -       +      -
    321A  LEU*     3.0    23.5    +      -       -      -
    322A  GLY*     3.2    37.2    +      -       -      -
    323A  VAL*     3.5    22.0    +      -       -      -
    324A  ASN*     4.9     1.1    +      -       -      -
    420A  LEU*     1.3    79.3    -      -       -      +
    422A  PHE*     1.3    66.2    +      -       -      +
    423A  PHE*     3.6    19.7    -      +       +      -
    443A  GLU*     4.3     9.4    -      -       +      +
    473A  TRP*     3.6    30.3    -      +       -      -
    492A  TRP*     3.7    15.3    -      +       +      -
    502A  PHE*     4.4     2.5    -      -       -      -
    503A  ILE*     3.3    11.4    -      -       +      +
    505A  LEU*     4.0    21.3    -      -       +      -
    516A  LEU*     4.3     4.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 422 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    323A  VAL*     3.6    26.7    -      -       +      -
    324A  ASN      4.3     0.7    -      -       -      -
    325A  LYS*     3.7    33.9    -      -       +      -
    401A  ILE*     4.9     7.9    -      -       +      -
    421A  TYR*     1.3    76.3    -      -       -      +
    423A  PHE*     1.3    61.3    +      -       -      +
    424A  ASN*     3.3    27.6    +      -       +      +
    502A  PHE*     3.5    23.6    -      +       +      -
    503A  ILE      3.0     5.7    +      -       -      -
    504A  ASP*     3.3    22.3    -      -       -      +
    505A  LEU      2.9    21.9    +      -       -      -
    516A  LEU*     3.7    26.5    -      -       +      -
    517A  ARG*     5.0     7.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 423 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    323A  VAL      2.9    10.3    +      -       -      +
    324A  ASN*     3.4    17.4    -      -       -      +
    325A  LYS      2.9    25.6    +      -       -      -
    421A  TYR*     3.6    13.2    -      +       +      -
    422A  PHE*     1.3    71.7    -      -       -      +
    424A  ASN*     1.3    58.7    +      -       -      +
    425A  HIS*     3.2    31.4    -      -       +      -
    438A  VAL*     3.6    13.6    -      -       +      +
    442A  TYR*     4.5     4.9    -      -       +      -
    443A  GLU*     3.7    29.8    -      -       +      -
    446A  PHE*     3.8    27.6    -      +       -      -
    465A  LEU*     4.2     8.5    -      -       +      -
    469A  ILE*     4.0    22.9    -      -       +      -
    505A  LEU*     3.4    29.4    -      -       +      -
----------------------------------------------------------
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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