Contacts of the strand formed by residues 299 - 304 (chain A) in PDB entry 1QFM


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 299 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    295A  ASN*     3.2     3.1    -      -       -      -
    296A  GLU*     2.9    43.0    +      -       +      +
    297A  GLY      3.3     0.2    -      -       -      -
    298A  THR*     1.3    78.3    -      -       -      +
    300A  PHE*     1.3    61.5    +      -       -      +
    301A  THR*     4.0     2.6    +      -       -      +
    315A  ASN*     3.8    33.9    -      -       +      +
    316A  ILE      3.8     5.6    -      -       -      +
    317A  ASP*     3.7    24.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 300 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    241A  SER*     4.3     2.9    -      -       -      -
    246A  TYR*     3.4    30.7    -      +       -      -
    248A  LEU*     3.9    14.6    -      -       +      -
    292A  TYR*     3.5    37.5    -      +       -      -
    294A  THR      3.7     2.0    -      -       -      -
    295A  ASN*     3.6    13.7    -      -       +      -
    297A  GLY      3.5    19.1    -      -       -      -
    298A  THR      3.5    11.4    -      -       -      -
    299A  VAL*     1.3    72.0    -      -       -      +
    301A  THR*     1.3    61.0    +      -       -      +
    302A  PHE*     3.5    26.0    -      +       +      -
    314A  ILE      3.6     0.5    -      -       -      +
    315A  ASN*     3.2     4.5    -      -       -      -
    316A  ILE      2.8    41.3    +      -       -      +
    318A  PHE*     3.3    39.7    -      +       +      -
----------------------------------------------------------
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Residues in contact with THR 301 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    292A  TYR*     3.9     1.9    -      -       -      -
    293A  VAL*     2.9    40.7    +      -       +      +
    294A  THR*     2.8    27.8    +      -       -      +
    295A  ASN*     5.3     0.2    -      -       -      -
    299A  VAL*     4.0     3.7    +      -       -      +
    300A  PHE*     1.3    72.2    -      -       -      +
    302A  PHE*     1.3    63.5    +      -       -      +
    313A  LEU*     4.3    15.3    -      -       +      -
    314A  ILE      3.3     6.3    -      -       -      +
    315A  ASN*     2.7    23.6    +      -       -      +
    329A  LEU*     4.0    16.2    -      -       +      -
    349A  LEU*     5.1     0.9    -      -       +      -
    366A  LEU*     3.9    18.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 302 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    248A  LEU*     4.9     1.8    -      -       +      -
    261A  LEU*     4.0    38.4    -      -       +      -
    282A  LEU*     4.6     8.1    -      -       +      -
    290A  TYR*     3.9    18.8    -      +       +      -
    291A  ASP      3.2    23.1    -      -       -      +
    292A  TYR*     3.6    20.2    -      +       +      -
    293A  VAL*     4.3     0.2    -      -       -      -
    300A  PHE*     3.5    42.6    -      +       +      -
    301A  THR*     1.3    73.4    -      -       -      +
    303A  LYS*     1.3    67.5    +      -       -      +
    313A  LEU*     3.4     8.3    -      -       -      -
    314A  ILE*     2.9    42.6    +      -       +      +
    316A  ILE*     3.9    31.4    -      -       +      -
    318A  PHE*     4.7     0.9    -      +       -      -
----------------------------------------------------------
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Residues in contact with LYS 303 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    289A  GLU*     3.6     2.3    -      -       -      +
    290A  TYR*     3.5     2.8    -      -       -      -
    291A  ASP*     2.8    64.5    +      -       +      +
    293A  VAL*     3.9     6.6    -      -       +      +
    302A  PHE*     1.3    72.9    -      -       -      +
    304A  THR*     1.3    62.1    +      -       -      +
    311A  TYR*     3.5    34.7    -      -       +      -
    312A  ARG      3.4     9.6    -      -       -      +
    313A  LEU*     3.7    11.3    -      -       +      +
    338A  LEU*     3.7    29.5    +      -       +      +
    339A  GLU      3.4    22.8    +      -       -      +
    340A  TRP*     4.0    15.0    -      -       -      +
    341A  VAL*     4.3     5.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with THR 304 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    289A  GLU*     2.7    20.6    +      -       -      -
    290A  TYR*     3.4    14.2    -      -       -      -
    302A  PHE      5.0     0.2    -      -       -      -
    303A  LYS*     1.3    75.1    -      -       -      +
    305A  ASN*     1.3    64.9    +      -       -      +
    306A  ARG*     2.9    25.8    +      -       +      +
    308A  SER*     3.5     2.3    +      -       -      +
    311A  TYR*     3.2    10.1    -      -       -      -
    312A  ARG*     2.9    54.4    +      -       +      +
    314A  ILE*     3.8    29.4    -      -       +      -
----------------------------------------------------------
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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