Contacts of the strand formed by residues 314 - 318 (chain F) in PDB entry 6Q2J


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 TYR 314 (chain F).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    266F  ASP*     4.5     0.2    +      -       -      -
    300F  ASP*     3.8    11.4    +      -       -      -
    302F  ASP*     5.1     1.9    -      -       -      +
    303F  VAL      5.3     0.7    +      -       -      -
    305F  PRO*     3.3    44.7    +      -       +      +
    310F  LEU*     3.0    45.4    +      -       +      +
    311F  VAL*     4.1     6.6    -      -       -      +
    313F  ARG*     1.3    81.7    -      -       -      +
    315F  THR*     1.3    64.3    +      -       -      +
    316F  SER      3.7     1.6    +      -       -      -
    333F  HIS*     4.2    23.8    -      -       +      +
    350F  THR*     4.7     7.9    +      -       +      +
    352F  HIS*     3.3    34.2    +      +       -      -
    354F  TYR*     5.1     6.5    -      -       -      +
    376F  VAL*     6.4     1.6    -      -       +      -
    377F  ASN      3.3     3.8    -      -       -      -
    378F  ASP*     3.2    38.1    +      -       +      -
    379F  SER      4.6     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with THR 315 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    311F  VAL      4.4    11.7    -      -       -      +
    312F  ARG*     4.5     6.7    -      -       -      +
    313F  ARG      3.7     2.0    -      -       -      +
    314F  TYR*     1.3    79.5    -      -       -      +
    316F  SER*     1.3    59.0    +      -       -      +
    317F  THR*     4.0     9.9    +      -       -      -
    354F  TYR*     5.5     0.9    -      -       -      -
    375F  LEU      3.5     3.1    -      -       -      +
    376F  VAL*     4.8     0.7    -      -       -      -
    377F  ASN*     2.9    52.3    +      -       -      +
    703F  NAG      3.7    27.9    +      -       +      +
----------------------------------------------------------
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Residues in contact with SER 316 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    314F  TYR      3.7     3.6    +      -       -      -
    315F  THR*     1.3    70.8    -      -       -      +
    317F  THR*     1.3    61.4    +      -       -      +
    318F  LEU      4.1     1.2    +      -       -      -
    331F  VAL*     4.4    15.1    +      -       -      +
    333F  HIS*     4.1    14.2    -      -       -      +
    354F  TYR*     3.5    33.4    -      -       -      -
    374F  VAL*     4.6     7.9    -      -       -      -
    375F  LEU      3.2     7.9    -      -       -      -
    376F  VAL*     4.8     0.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with THR 317 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    315F  THR*     4.0    12.0    +      -       -      -
    316F  SER*     1.3    73.2    +      -       -      +
    318F  LEU*     1.3    73.2    +      -       -      +
    319F  LEU*     3.4    13.8    +      -       +      -
    320F  PRO*     5.9     1.3    -      -       +      -
    374F  VAL*     3.7     3.0    -      -       -      -
    375F  LEU*     2.9    52.6    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 318 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    316F  SER      4.1     2.4    +      -       -      -
    317F  THR*     1.3    79.0    -      -       -      +
    319F  LEU*     1.3    75.0    +      -       -      +
    320F  PRO*     3.7     2.6    -      -       -      +
    325F  ALA*     5.4     2.0    -      -       +      -
    326F  GLN*     3.8    29.2    +      -       +      +
    329F  PHE*     4.0    26.5    -      -       +      +
    330F  ARG*     5.0     0.9    -      -       -      -
    331F  VAL*     3.7    35.7    -      -       +      +
    356F  LEU*     5.3     0.9    -      -       +      -
    372F  LEU*     4.7    24.2    -      -       +      -
    373F  ALA      3.9    11.9    -      -       -      +
    374F  VAL*     4.0     7.9    -      -       +      +
----------------------------------------------------------
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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