Contacts of the strand formed by residues 402 - 413 (chain A) 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 ARG 402 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8A  GLU      4.1     6.5    +      -       -      +
      9A  ASP*     3.7    27.4    +      -       -      +
     10A  SER      3.2    20.2    +      -       -      +
     11A  ASP*     2.7    31.3    +      -       -      +
     13A  PRO*     3.0    29.4    -      -       -      +
    393A  THR*     6.2     2.6    -      -       -      -
    394A  GLY      4.7     2.2    +      -       -      -
    395A  HIS*     3.5    51.9    +      -       +      +
    396A  CYS      3.2    13.0    -      -       -      +
    397A  GLN*     4.3    11.5    +      -       -      +
    401A  TYR*     1.3    78.7    -      -       -      +
    403A  VAL*     1.3    64.4    +      -       -      +
    404A  GLY      3.7     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 403 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11A  ASP      4.1     1.8    -      -       -      -
     15A  GLN      3.9    21.1    -      -       -      +
     16A  ASN*     3.7    22.2    -      -       -      +
    264A  VAL*     3.8    19.7    -      -       +      -
    268A  ALA*     3.9    12.6    -      -       +      +
    269A  LEU*     4.2    12.1    -      -       +      -
    272A  PHE*     3.9    20.0    -      -       +      -
    395A  HIS*     3.3     1.8    -      -       -      -
    396A  CYS*     2.8    43.7    +      -       +      +
    401A  TYR*     4.1    12.5    -      -       +      -
    402A  ARG*     1.3    75.0    -      -       -      +
    404A  GLY*     1.3    57.4    +      -       -      +
    405A  PHE*     4.2     4.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 404 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11A  ASP*     2.9    38.8    +      -       -      +
     12A  PHE*     4.0     4.9    -      -       -      -
     16A  ASN*     3.0    18.9    +      -       -      +
    264A  VAL*     3.8     6.8    -      -       -      +
    394A  GLY      3.6     6.5    -      -       -      -
    395A  HIS*     3.8     3.6    -      -       -      -
    402A  ARG      3.7     1.2    -      -       -      -
    403A  VAL*     1.3    76.2    -      -       -      +
    405A  PHE*     1.3    64.6    +      -       -      -
    406A  GLY      3.5     2.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 405 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12A  PHE*     4.9     4.3    -      -       -      -
    202A  MET*     3.5    26.2    -      -       +      -
    228A  MET*     3.6    22.9    -      -       +      -
    229A  VAL*     4.4     7.9    -      -       -      -
    230A  LEU*     3.7    22.2    -      -       +      +
    260A  SER*     4.0    16.6    +      -       -      -
    261A  PRO*     5.6     0.3    -      -       -      +
    262A  TRP*     4.7    12.7    -      -       -      +
    264A  VAL*     3.5    29.2    -      -       +      -
    269A  LEU*     3.8    33.0    -      -       +      -
    297A  ILE*     3.7    23.1    -      -       +      -
    394A  GLY*     3.0    26.4    +      -       -      +
    396A  CYS*     4.8     0.7    -      -       -      -
    403A  VAL      4.2     9.0    -      -       -      -
    404A  GLY*     1.3    77.0    -      -       -      -
    406A  GLY*     1.3    63.5    +      -       -      +
    407A  GLN      3.5     1.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 406 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11A  ASP*     2.9    21.1    +      -       -      +
     12A  PHE*     4.2    15.2    -      -       -      -
    230A  LEU*     3.8     2.0    -      -       -      +
    262A  TRP*     5.3     4.7    -      -       -      -
    393A  THR*     3.6    24.4    -      -       -      +
    394A  GLY      4.1     1.7    +      -       -      -
    404A  GLY      3.5     1.2    +      -       -      -
    405A  PHE*     1.3    79.0    -      -       -      +
    407A  GLN*     1.3    62.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 407 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    169A  SER*     3.2    19.7    +      -       -      +
    170A  GLY*     6.1     0.2    -      -       -      -
    230A  LEU*     4.3     0.9    -      -       -      -
    260A  SER*     3.2    18.5    -      -       -      -
    261A  PRO*     3.8     4.8    -      -       -      +
    391A  ILE*     3.9    30.0    -      -       +      +
    392A  ILE      3.3     9.6    -      -       -      +
    393A  THR*     4.0     7.1    -      -       +      +
    405A  PHE      3.5     1.0    +      -       -      -
    406A  GLY*     1.3    77.0    -      -       -      +
    408A  CYS*     1.3    61.7    +      -       -      +
    409A  ALA*     3.7    15.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with CYS 408 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    169A  SER*     3.4     4.5    -      -       -      -
    230A  LEU*     3.8    21.3    -      -       +      -
    231A  MET*     3.9     8.1    -      -       -      -
    232A  ASN*     3.6    21.3    +      -       -      +
    258A  THR*     3.5    39.7    -      -       -      -
    260A  SER      4.0     7.9    -      -       -      +
    390A  VAL      3.8     1.6    -      -       -      +
    391A  ILE*     3.7     1.1    -      -       -      -
    392A  ILE*     2.9    40.2    +      -       +      +
    407A  GLN*     1.3    75.5    -      -       -      +
    409A  ALA*     1.3    59.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 409 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    169A  SER*     2.8    15.8    +      -       -      +
    170A  GLY*     2.7    33.0    +      -       -      +
    171A  THR      4.2     0.5    +      -       -      -
    234A  TRP*     4.9     1.3    -      -       -      -
    258A  THR*     3.7    13.6    -      -       -      +
    389A  GLU*     5.1     7.0    -      -       -      +
    390A  VAL      3.4     6.1    -      -       -      -
    391A  ILE*     3.9    20.0    -      -       +      +
    407A  GLN*     3.7    20.2    -      -       -      +
    408A  CYS*     1.3    73.6    -      -       -      +
    410A  GLY*     1.3    58.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 410 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    170A  GLY*     4.9     3.1    -      -       -      -
    171A  THR      4.0    13.2    -      -       -      -
    173A  ILE*     5.0     0.7    -      -       -      -
    234A  TRP*     3.6    24.7    -      -       -      -
    258A  THR*     5.3     0.4    -      -       -      -
    388A  ASP      4.0     0.2    -      -       -      +
    389A  GLU*     3.4     5.9    -      -       -      +
    390A  VAL      2.9    32.6    +      -       -      +
    409A  ALA*     1.3    77.0    -      -       -      +
    411A  LYS*     1.3    61.1    +      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 411 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    170A  GLY      5.6     0.8    +      -       -      -
    171A  THR      4.4     3.2    +      -       -      -
    172A  PRO*     3.5    12.4    -      -       +      +
    173A  ILE*     2.9    24.7    +      -       -      +
    306A  GLU*     5.0    11.1    +      -       -      +
    387A  GLY*     3.3    30.7    -      -       -      +
    388A  ASP      3.3    12.8    -      -       -      +
    389A  GLU*     4.1    21.3    -      -       +      +
    410A  GLY*     1.3    73.7    -      -       -      -
    412A  VAL*     1.3    69.2    +      -       -      +
    413A  LEU*     3.6     8.4    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 412 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    173A  ILE*     3.3    10.1    -      -       +      +
    175A  ARG*     4.4     2.7    -      -       +      +
    196A  LEU*     3.5    34.5    -      -       +      -
    234A  TRP*     4.3    13.0    -      -       +      -
    384A  LEU*     4.3    18.4    -      -       +      -
    385A  LEU      3.9    13.0    -      -       -      +
    386A  ASP*     3.9    19.3    -      -       -      +
    387A  GLY*     2.9    29.1    +      -       -      -
    388A  ASP*     2.9    20.5    +      -       +      +
    390A  VAL*     5.9     0.2    -      -       +      -
    411A  LYS*     1.3    74.6    -      -       -      +
    413A  LEU*     1.3    76.0    +      -       -      +
    414A  PRO*     4.3     0.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 413 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    172A  PRO*     3.7    36.6    -      -       +      -
    173A  ILE      2.8     8.1    +      -       -      +
    174A  ARG*     3.6    43.3    -      -       +      +
    175A  ARG*     2.9    29.1    +      -       -      +
    386A  ASP*     4.3     0.4    -      -       -      -
    411A  LYS*     4.8     9.2    -      -       +      +
    412A  VAL*     1.3    82.3    -      -       -      +
    414A  PRO*     1.3    72.8    -      -       +      +
----------------------------------------------------------
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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