Contacts of the strand formed by residues 278 - 285 (chain A) in PDB entry 1GQF


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 LYS 278 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    230A  PHE*     3.4    10.5    -      -       +      -
    265A  PHE*     4.0    22.4    -      -       +      -
    270A  CYS      5.5     1.3    -      -       -      -
    273A  LEU*     3.2    42.4    +      -       +      -
    274A  LEU*     4.5     5.4    -      -       -      +
    276A  LYS      2.6    28.6    +      -       -      +
    277A  PRO*     1.3    74.6    -      -       -      +
    279A  LEU*     1.3    64.3    +      -       -      +
    280A  PHE*     4.2     7.6    -      -       +      -
    325A  ALA      4.2     3.8    +      -       -      -
    326A  ASP*     2.9    22.2    +      -       -      +
    327A  PHE*     3.5    48.2    -      -       +      -
    328A  LEU      3.2    22.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 279 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    198A  PHE*     4.6     4.7    -      -       +      -
    229A  CYS*     4.7     4.5    -      -       -      -
    230A  PHE      2.7    18.5    +      -       -      +
    231A  ALA*     3.2     8.4    -      -       +      +
    232A  CYS      2.8    27.9    +      -       -      +
    277A  PRO*     4.0    13.2    -      -       +      -
    278A  LYS*     1.3    77.4    -      -       -      +
    280A  PHE*     1.3    65.5    +      -       -      +
    281A  PHE*     3.4    28.0    -      -       +      -
    328A  LEU*     3.8    30.5    -      -       +      +
    366A  ILE*     5.0     1.3    -      -       +      -
    394A  LEU*     4.8     0.7    -      -       +      -
    398A  LEU*     3.7    34.5    -      -       +      -
    400A  PHE*     3.9    21.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 280 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    215A  LEU*     4.5     8.1    -      -       +      -
    230A  PHE*     4.5     5.4    -      +       -      -
    232A  CYS*     3.4    33.7    -      -       +      -
    234A  LEU*     4.7    11.2    -      -       +      -
    258A  ILE*     5.8     1.3    -      -       +      -
    261A  LEU*     4.5     7.6    -      -       +      -
    262A  THR*     3.7    27.6    -      -       -      -
    265A  PHE*     4.4    17.0    -      +       -      -
    278A  LYS*     3.9    17.3    -      -       +      -
    279A  LEU*     1.3    78.4    -      -       -      +
    281A  PHE*     1.3    62.4    +      -       -      +
    282A  ILE*     3.9     7.5    +      -       +      +
    327A  PHE*     3.4    32.5    -      +       -      -
    328A  LEU*     3.0     8.9    +      -       -      +
    329A  PHE*     3.4    30.0    -      +       +      +
    330A  ALA      3.0    24.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 281 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    193A  PHE*     3.7    37.5    -      +       -      -
    231A  ALA*     4.4     2.5    -      -       +      -
    232A  CYS      2.8    15.0    +      -       -      +
    233A  ILE*     3.1    22.2    -      -       +      +
    234A  LEU      2.8    25.1    +      -       -      -
    279A  LEU*     3.4    39.7    -      -       +      -
    280A  PHE*     1.3    74.2    -      -       -      +
    282A  ILE*     1.3    60.2    +      -       -      +
    328A  LEU*     5.4     4.3    -      -       +      -
    330A  ALA*     3.9    18.8    -      -       +      +
    349A  PHE*     5.2     2.9    -      -       +      -
    353A  LEU*     3.5    39.3    -      -       +      -
    357A  LEU*     5.4     1.6    -      -       +      -
    366A  ILE*     4.7    13.5    -      -       +      -
    370A  LEU*     4.4    14.4    -      -       +      -
    400A  PHE*     5.4     1.3    -      +       -      -
----------------------------------------------------------
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Residues in contact with ILE 282 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    234A  LEU*     3.5    37.0    -      -       +      -
    243A  ILE*     4.9     2.2    -      -       +      -
    258A  ILE*     4.1    25.1    -      -       +      -
    280A  PHE*     3.9     6.7    +      -       +      +
    281A  PHE*     1.3    81.8    -      -       -      +
    283A  GLN*     1.3    63.6    +      -       -      +
    284A  ALA*     3.9    15.0    -      -       +      -
    329A  PHE*     4.2    24.0    -      -       +      -
    330A  ALA      3.2    12.5    +      -       -      +
    331A  TYR*     3.5    35.2    -      -       +      -
    332A  SER*     3.0    27.9    +      -       -      -
    349A  PHE*     4.1     3.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLN 283 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    179A  ARG*     4.2    14.3    +      -       -      +
    185A  ASP*     5.0     1.1    -      -       -      +
    234A  LEU      2.9    14.8    +      -       -      +
    235A  LEU*     3.8    17.7    -      -       +      -
    236A  SER      3.1    26.4    +      -       -      +
    282A  ILE*     1.3    73.7    -      -       -      +
    284A  ALA*     1.3    59.2    +      -       -      +
    285A  ALA*     4.2     9.5    -      -       -      +
    332A  SER*     2.8    34.5    +      -       -      -
    334A  VAL      2.9    26.0    +      -       -      +
    347A  SER*     4.3    21.2    -      -       -      +
    349A  PHE*     3.7    16.7    -      -       +      +
    350A  VAL*     4.7     3.8    -      -       +      -
   1403A  SO4      4.7     7.2    +      -       -      +
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Residues in contact with ALA 284 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    236A  SER      3.1     6.5    -      -       -      +
    238A  GLY*     3.2    22.2    -      -       -      -
    242A  VAL      5.1     0.9    -      -       -      +
    243A  ILE*     3.4    29.6    -      -       +      -
    258A  ILE*     6.2     0.7    -      -       +      -
    282A  ILE*     3.9     9.1    -      -       +      +
    283A  GLN*     1.3    73.8    -      -       -      +
    285A  ALA*     1.3    61.7    +      -       -      +
    331A  TYR*     3.5    24.1    +      -       +      +
    332A  SER      3.1    13.7    +      -       -      +
    333A  THR*     4.2     4.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 285 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    236A  SER      3.7     3.4    +      -       -      -
    237A  HIS*     3.3     9.7    +      -       -      +
    238A  GLY      2.6    23.9    +      -       -      -
    283A  GLN*     4.0     3.9    -      -       -      +
    284A  ALA*     1.3    75.1    -      -       -      +
    286A  ARG*     1.3    63.5    +      -       -      +
    332A  SER      4.2     1.0    +      -       -      -
    333A  THR*     3.4    29.6    -      -       -      +
    334A  VAL      4.1     2.7    -      -       -      +
    335A  PRO*     3.8    27.8    -      -       +      -
   1403A  SO4      3.9    14.1    +      -       -      +
----------------------------------------------------------
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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