Contacts of the strand formed by residues 285 - 294 (chain A) in PDB entry 3QFS


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 PHE 285 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    275A  GLN*     3.4    16.4    -      -       +      -
    279A  PHE*     3.4    42.0    -      +       +      +
    283A  ASN      3.7     1.0    +      -       -      -
    284A  PRO*     1.3    72.7    -      -       -      +
    286A  LEU*     1.3    72.8    +      -       -      +
    287A  ALA*     3.2    17.8    +      -       +      -
    309A  ASP      3.5    23.1    -      -       -      -
    310A  ILE*     3.8     9.6    -      -       -      -
    311A  SER      3.6    19.1    -      -       -      -
    312A  ASP*     4.6     2.9    -      -       +      -
    313A  SER*     3.5    22.4    -      -       -      -
    315A  ILE*     3.9    12.1    -      -       +      -
    512A  VAL      3.2     0.2    -      -       -      +
    514A  MET*     2.8    36.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 286 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    272A  TYR*     3.7    55.2    -      -       +      +
    275A  GLN*     2.8    22.5    +      -       -      +
    284A  PRO      3.9     7.4    -      -       -      +
    285A  PHE*     1.3    83.1    -      -       -      +
    287A  ALA*     1.3    63.8    +      -       -      +
    288A  ALA      3.8     1.4    +      -       -      -
    511A  LEU*     3.9    41.4    -      -       +      +
    512A  VAL      3.6     3.8    -      -       -      -
    513A  PRO*     3.8    29.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 287 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    285A  PHE*     3.2     8.8    +      -       +      -
    286A  LEU*     1.3    72.6    -      -       -      +
    288A  ALA*     1.3    64.3    +      -       -      +
    289A  VAL*     3.6     1.2    +      -       -      +
    308A  LEU*     3.8    25.2    -      -       +      +
    309A  ASP      3.4    19.7    -      -       -      +
    310A  ILE*     4.2     3.4    -      -       +      -
    511A  LEU*     3.4     2.4    -      -       -      -
    512A  VAL*     2.8    41.9    +      -       -      +
    514A  MET*     3.9    14.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 288 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    286A  LEU      3.8     3.0    +      -       -      -
    287A  ALA*     1.3    72.3    -      -       -      +
    289A  VAL*     1.3    64.5    +      -       -      +
    290A  THR*     3.3     5.9    +      -       +      -
    308A  LEU*     3.6     1.1    -      -       -      -
    309A  ASP*     2.8    47.9    +      -       +      +
    509A  ARG*     4.4    13.7    -      -       +      -
    510A  ALA      3.3     8.3    -      -       -      +
    511A  LEU*     3.7    13.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 289 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    288A  ALA*     1.3    70.7    -      -       -      +
    290A  THR*     1.3    58.0    +      -       -      +
    291A  THR      3.4    26.9    -      -       -      +
    292A  ASN*     4.1     9.2    -      -       +      -
    306A  LEU*     4.1    11.2    -      -       +      -
    307A  GLU      3.6     6.3    -      -       -      +
    308A  LEU*     3.7     9.4    -      -       +      -
    500A  LYS*     3.9    17.0    -      -       +      +
    502A  PRO*     3.1    33.9    -      -       +      +
    509A  ARG*     5.9     0.7    -      -       -      +
    510A  ALA*     2.8    28.4    +      -       +      +
    512A  VAL*     3.6    31.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 290 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    288A  ALA*     3.9     6.1    -      -       +      +
    289A  VAL*     1.3    76.6    -      -       -      +
    291A  THR*     1.3    65.7    +      -       -      +
    307A  GLU*     2.9    26.3    +      -       -      +
    309A  ASP*     3.8    33.7    +      -       +      +
    471A  SER*     5.0     1.9    +      -       -      -
    502A  PRO*     3.9    12.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with THR 291 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    289A  VAL*     3.4     9.8    -      -       -      +
    290A  THR*     1.3    84.8    +      -       -      +
    292A  ASN*     1.3    63.8    +      -       -      +
    293A  ARG*     4.0    31.2    -      -       +      +
    305A  HIS*     4.2    12.6    -      -       -      +
    306A  LEU*     3.1     4.3    -      -       -      -
    307A  GLU*     3.0    51.0    +      -       +      -
    502A  PRO*     4.2     2.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with ASN 292 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    289A  VAL*     4.1     3.4    -      -       +      -
    291A  THR*     1.3    76.3    -      -       -      +
    293A  ARG*     1.3    62.3    +      -       -      +
    302A  HIS*     5.4     2.1    +      -       -      -
    304A  MET*     4.2    12.0    -      -       -      +
    305A  HIS      3.5     4.3    -      -       -      -
    306A  LEU*     3.8    19.9    -      -       -      +
    497A  LEU      3.0    23.0    +      -       -      -
    498A  ARG*     3.4    14.4    +      -       -      +
    500A  LYS      2.9    28.5    +      -       -      +
    502A  PRO*     4.0    15.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 293 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    291A  THR*     4.0    15.4    -      -       +      +
    292A  ASN*     1.3    76.5    +      -       -      +
    294A  LYS*     1.3    68.6    +      -       -      +
    295A  LEU*     3.6    22.7    +      -       -      +
    302A  HIS*     5.4     0.9    -      -       -      -
    304A  MET*     3.3     5.9    -      -       -      +
    305A  HIS*     2.8    72.8    +      -       +      +
    307A  GLU*     5.2     1.2    +      -       -      -
    578A  TYR*     4.4     3.4    -      -       -      -
    581A  GLU*     2.9    30.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 294 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    293A  ARG*     1.3    82.3    +      -       -      +
    295A  LEU*     1.3    59.8    +      -       -      +
    296A  ASN*     3.2    39.3    -      -       -      +
    297A  GLN      4.7     1.8    +      -       -      -
    298A  GLY      2.8    30.1    +      -       -      -
    299A  THR*     4.0    16.6    -      -       -      +
    301A  ARG      4.4     1.7    +      -       -      -
    302A  HIS*     3.9    31.8    +      -       +      +
    303A  LEU      3.5     6.3    -      -       -      +
----------------------------------------------------------
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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