Contacts of the strand formed by residues 274 - 289 (chain A) in PDB entry 1QFG


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 THR 274 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    239A  PRO      4.7     1.9    +      -       -      -
    240A  GLU*     2.7    27.3    +      -       -      -
    272A  ASN      4.0     5.8    -      -       -      +
    273A  ASN*     1.3    77.1    -      -       -      +
    275A  TYR*     1.3    61.2    +      -       -      +
    276A  SER*     5.5     1.6    -      -       -      -
    308A  SER*     6.4     0.7    -      -       -      -
    309A  GLN*     2.9     9.3    -      -       -      +
    310A  ASN*     2.7    71.0    +      -       +      +
    311A  SER*     4.0     1.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 275 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     86A  THR*     4.1    11.2    -      -       +      -
     87A  TYR*     2.9    29.6    +      -       -      -
    116A  TYR*     3.1    13.0    -      -       +      -
    239A  PRO      3.1     8.0    -      -       -      +
    240A  GLU*     3.1     9.5    +      -       -      +
    241A  THR*     2.8    46.2    +      -       +      +
    242A  GLY      4.4    12.6    -      -       -      +
    244A  TYR*     3.9    30.5    -      +       +      -
    274A  THR*     1.3    74.6    +      -       -      +
    276A  SER*     1.3    65.7    +      -       -      +
    277A  ARG*     6.2     1.1    -      -       +      -
    307A  THR*     3.9    16.8    -      -       -      -
    308A  SER      3.6     6.3    -      -       -      -
    309A  GLN*     3.0    44.3    +      -       +      -
    311A  SER*     4.0     6.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER 276 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    238A  GLU      3.2     8.3    -      -       -      -
    239A  PRO*     2.9    25.1    -      -       -      -
    241A  THR*     4.3     3.6    -      -       -      -
    274A  THR*     5.5     1.6    -      -       -      -
    275A  TYR*     1.3    74.4    -      -       -      +
    277A  ARG*     1.3    58.4    +      -       -      +
    307A  THR*     2.6    28.2    +      -       -      -
    308A  SER*     2.8    42.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 277 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     85A  ASN      4.9     0.6    +      -       -      -
     86A  THR*     2.9    38.0    +      -       -      +
     87A  TYR*     3.3    18.3    +      -       -      -
    116A  TYR      5.9     0.2    -      -       -      -
    117A  ASN*     5.4     2.5    -      -       -      +
    118A  ASP      2.9    27.8    +      -       -      -
    119A  ALA*     4.4     0.2    -      -       -      +
    120A  VAL*     3.2    24.4    -      -       -      +
    212A  ARG*     4.2     1.2    -      -       -      +
    236A  GLN      4.3     0.2    -      -       -      +
    237A  ASN*     3.9     2.0    -      -       -      +
    238A  GLU*     2.7    74.7    +      -       -      +
    241A  THR*     4.2    10.5    +      -       -      +
    275A  TYR*     6.2     1.1    -      -       +      -
    276A  SER*     1.3    73.8    -      -       -      +
    278A  ASN*     1.3    66.7    +      -       -      +
    279A  GLU*     3.2    24.6    +      -       +      +
    305A  ASN*     5.7     0.9    -      -       +      -
    306A  LYS      3.2    10.5    -      -       -      +
    307A  THR*     4.5     8.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASN 278 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    236A  GLN      3.6    10.5    +      -       -      -
    237A  ASN*     3.1    29.2    +      -       -      +
    277A  ARG*     1.3    74.6    -      -       -      +
    279A  GLU*     1.3    64.2    +      -       -      +
    280A  LYS*     3.6    33.1    +      -       -      +
    304A  GLU      5.1     1.0    -      -       -      +
    305A  ASN*     3.1     6.8    -      -       -      +
    306A  LYS*     2.6    63.6    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 279 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    119A  ALA*     3.2    14.2    -      -       +      +
    120A  VAL      2.5    46.6    +      -       -      +
    234A  TYR*     3.7    11.1    -      -       +      -
    235A  PHE*     3.3     1.4    -      -       -      +
    236A  GLN*     2.6    65.6    +      -       +      +
    277A  ARG*     3.2    28.9    +      -       +      -
    278A  ASN*     1.3    76.8    -      -       -      +
    280A  LYS*     1.3    65.0    +      -       -      +
    281A  MET*     4.3     8.4    -      -       +      +
    305A  ASN*     3.2    17.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with LYS 280 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    234A  TYR      3.3     6.3    -      -       -      -
    235A  PHE*     3.5    23.1    -      -       +      -
    278A  ASN*     3.6    21.9    +      -       -      +
    279A  GLU*     1.3    76.4    -      -       -      +
    281A  MET*     1.3    62.6    +      -       -      +
    303A  ALA*     3.3     4.7    -      -       -      +
    304A  GLU*     2.9    46.6    +      -       +      +
    305A  ASN*     3.4     1.0    +      -       -      -
    306A  LYS*     4.3    16.6    -      -       -      +
   1014A  MYR      4.1    34.0    +      -       +      +
----------------------------------------------------------
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Residues in contact with MET 281 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    106A  LEU*     4.2    10.3    -      -       -      -
    111A  LEU*     3.4    33.4    -      -       +      -
    119A  ALA*     4.5     3.8    -      -       +      -
    121A  ILE*     4.0    14.6    -      -       +      -
    232A  LEU      4.6     0.7    -      -       -      +
    233A  SER*     3.3     5.9    -      -       -      -
    234A  TYR*     2.9    58.5    +      -       +      +
    235A  PHE*     3.9     3.1    -      -       -      -
    279A  GLU*     4.3    11.7    -      -       +      +
    280A  LYS*     1.3    78.4    -      -       -      +
    282A  VAL*     1.3    69.2    +      -       -      +
    301A  ARG*     4.0    22.4    -      -       -      -
    302A  PHE      3.2    11.4    -      -       -      +
    303A  ALA*     4.2     6.3    -      -       +      -
    305A  ASN*     4.4    13.7    -      -       -      +
   1014A  MYR      5.9     1.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 282 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    231A  PHE*     4.3    11.9    -      -       +      -
    232A  LEU      3.7     5.6    -      -       -      -
    233A  SER*     4.3     5.6    -      -       -      -
    235A  PHE*     4.2    10.8    -      -       +      -
    281A  MET*     1.3    81.1    -      -       -      +
    283A  GLY*     1.3    54.8    +      -       -      +
    301A  ARG*     3.6     3.0    -      -       -      -
    302A  PHE*     2.7    43.5    +      -       +      +
   1011A  FTT      3.9    18.1    -      -       +      +
   1013A  FTT      3.6    27.6    -      -       +      -
   1014A  MYR      3.9    38.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 283 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    231A  PHE*     3.2    13.9    -      -       -      -
    232A  LEU*     3.0    29.3    +      -       -      -
    282A  VAL*     1.3    75.0    -      -       -      +
    284A  TYR*     1.3    68.9    -      -       -      +
    300A  LEU*     3.0    22.2    -      -       -      -
    301A  ARG*     4.0     4.5    -      -       -      -
   1011A  FTT      4.3     4.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 284 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    229A  PHE*     3.4    28.3    -      +       +      -
    230A  THR      3.1    15.9    -      -       -      +
    231A  PHE*     4.0     0.2    -      -       -      -
    232A  LEU*     4.0    10.5    -      -       -      +
    283A  GLY*     1.3    74.1    -      -       -      +
    285A  SER*     1.3    62.2    +      -       -      +
    286A  PHE*     4.1    15.5    -      +       +      -
    298A  GLN*     2.7    36.9    +      -       -      -
    299A  ASN*     3.7     1.9    -      -       -      +
    300A  LEU*     3.0    71.6    +      -       +      +
   1009A  FTT      3.9     3.6    -      -       -      +
   1011A  FTT      3.5    21.3    -      -       +      -
   1012A  DAO      3.8    34.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with SER 285 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    107A  ASN*     6.0     1.1    -      -       -      -
    155A  ARG*     4.0    33.5    +      -       -      -
    228A  ASN*     3.6     2.5    -      -       -      +
    229A  PHE*     3.5     1.9    -      -       -      -
    230A  THR*     2.7    37.2    +      -       -      +
    232A  LEU*     4.2     6.4    -      -       -      +
    284A  TYR*     1.3    76.5    -      -       -      +
    286A  PHE*     1.3    62.9    +      -       -      +
    287A  ASP*     4.5     8.2    +      -       -      -
    299A  ASN*     3.3    19.1    +      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 286 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    221A  TRP*     6.2     2.7    -      +       -      -
    227A  THR*     4.2    16.2    -      -       +      -
    228A  ASN      3.2    17.3    -      -       -      -
    229A  PHE*     3.9    18.8    -      +       +      -
    284A  TYR*     4.1    15.3    -      +       +      -
    285A  SER*     1.3    78.5    +      -       -      +
    287A  ASP*     1.3    72.0    +      -       -      +
    288A  HIS*     3.8    31.2    -      -       +      -
    296A  VAL*     4.5    12.1    -      -       +      -
    297A  ARG*     3.0    23.1    -      -       -      +
    298A  GLN*     3.0    38.1    +      -       +      +
    299A  ASN*     4.3     0.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 287 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    226A  LYS      4.4     2.0    -      -       -      +
    227A  THR*     3.6     2.1    +      -       -      -
    228A  ASN*     2.9    64.1    +      -       -      +
    285A  SER*     4.5     7.3    +      -       -      -
    286A  PHE*     1.3    83.8    -      -       -      +
    288A  HIS*     1.3    62.4    +      -       -      +
    295A  THR*     5.2     5.2    -      -       +      -
    296A  VAL      3.4     5.2    -      -       -      +
    297A  ARG*     4.0    17.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with HIS 288 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    226A  LYS*     3.1    11.6    -      -       -      +
    227A  THR*     3.7    16.9    +      -       -      +
    286A  PHE*     3.8    20.4    -      -       +      -
    287A  ASP*     1.3    77.5    -      -       -      +
    289A  GLU*     1.3    83.8    +      -       -      +
    290A  PHE*     3.4    39.4    +      +       -      -
    295A  THR*     3.2     5.1    -      -       -      +
    296A  VAL*     2.6    49.4    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 289 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    225A  ASP      5.4     1.2    -      -       -      +
    226A  LYS*     2.8    50.6    +      -       +      +
    287A  ASP      4.4     0.2    -      -       -      -
    288A  HIS*     1.3    82.2    +      -       -      +
    290A  PHE*     1.3    59.0    +      -       -      +
    291A  ASN*     3.6    24.6    -      -       -      +
    292A  ASP*     5.0     3.6    -      -       -      +
    294A  PHE      3.9     0.2    -      -       -      -
    295A  THR*     3.7    24.7    +      -       +      +
----------------------------------------------------------
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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