Contacts of the strand formed by residues 348 - 353 (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 VAL 348 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    253A  HIS*     2.9    37.7    +      -       +      +
    256A  ILE*     3.9    23.3    -      -       +      -
    261A  VAL*     4.0    25.8    -      -       +      -
    346A  ASP      3.3    12.1    +      -       -      +
    347A  VAL*     1.3    77.0    -      -       -      +
    349A  MET*     1.3    66.6    +      -       -      +
    367A  PRO*     4.1     8.5    -      -       +      -
    368A  THR      3.5    19.5    -      -       -      +
    369A  SER*     4.2    10.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with MET 349 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    250A  LEU*     3.7    22.4    -      -       +      -
    251A  VAL      3.3    14.8    -      -       -      +
    252A  VAL*     4.0     6.7    -      -       +      -
    253A  HIS*     3.7     7.4    -      -       -      -
    347A  VAL*     4.6     2.0    -      -       +      +
    348A  VAL*     1.3    78.6    -      -       -      +
    350A  SER*     1.3    73.0    +      -       -      +
    351A  LEU*     3.9     9.0    -      -       +      -
    364A  PHE*     3.9    32.1    -      -       +      -
    366A  CYS*     4.1     3.0    -      -       -      -
    367A  PRO*     3.3     2.1    -      -       -      +
    368A  THR*     2.9    56.9    +      -       +      +
    369A  SER      4.8     1.3    -      -       -      +
    370A  TYR*     3.7    44.0    -      -       +      +
    373A  ALA*     5.2     0.2    -      -       +      -
    448A  CYS*     5.8     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 350 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    249A  GLU      3.6     1.4    -      -       -      +
    250A  LEU*     3.7     3.3    -      -       -      +
    251A  VAL*     2.9    31.7    +      -       -      +
    253A  HIS*     2.8    28.9    -      -       -      -
    349A  MET*     1.3    77.5    -      -       -      +
    351A  LEU*     1.3    59.8    +      -       -      +
    352A  ASN*     3.5    22.0    -      -       -      -
    362A  HIS*     4.6     2.0    +      -       -      -
    366A  CYS*     3.5    13.3    -      -       -      +
    367A  PRO*     3.3    18.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 351 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    246A  ARG*     3.7    24.2    -      -       -      +
    248A  TYR*     3.9    13.9    -      -       +      -
    249A  GLU      3.4    11.2    -      -       -      +
    250A  LEU*     4.0    17.7    -      -       +      -
    349A  MET*     3.9    12.8    -      -       -      -
    350A  SER*     1.3    74.6    -      -       -      +
    352A  ASN*     1.3    58.7    -      -       -      +
    362A  HIS*     2.9    20.1    -      -       -      -
    363A  PRO*     3.4    39.6    -      -       +      +
    364A  PHE*     4.0    15.9    -      -       +      -
    366A  CYS*     3.7     7.0    -      -       -      -
    445A  ASP*     3.7    20.2    -      -       +      +
    448A  CYS*     4.1     8.1    -      -       +      -
    449A  GLU*     4.5     6.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with ASN 352 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    248A  TYR*     3.2     3.1    -      -       -      -
    249A  GLU*     2.8    47.2    +      -       +      +
    251A  VAL*     3.2    34.1    -      -       -      +
    350A  SER*     3.5    12.2    -      -       -      -
    351A  LEU*     1.3    74.1    -      -       -      +
    353A  ASN*     1.3    67.4    +      -       -      +
    354A  LEU      3.3     0.2    +      -       -      -
    361A  LYS      3.4     3.8    -      -       -      +
    362A  HIS*     3.0    28.5    +      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 353 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    247A  GLN*     2.7    43.9    +      -       -      +
    248A  TYR*     3.3    11.5    +      -       +      -
    249A  GLU*     5.7     0.7    -      -       -      +
    352A  ASN*     1.3    74.0    -      -       -      +
    354A  LEU*     1.3    65.0    +      -       -      +
    355A  ASP*     2.8    42.8    +      -       -      +
    356A  GLU*     3.9     8.3    +      -       -      +
    358A  SER*     3.3    14.3    +      -       -      -
    360A  LYS*     2.9    30.9    -      -       -      +
    361A  LYS*     2.9    14.4    +      -       -      +
----------------------------------------------------------
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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