Contacts of the strand formed by residues 306 - 311 (chain A) in PDB entry 1TAQ


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 306 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    304A  GLY      4.3     2.2    -      -       -      -
    305A  ALA*     1.3    71.7    -      -       -      +
    307A  VAL*     1.3    61.2    +      -       -      +
    326A  ALA*     3.2     2.1    -      -       -      -
    327A  ALA      2.8    38.2    +      -       -      +
    349A  ARG*     3.0    66.0    -      -       +      +
    350A  GLY*     4.0     6.1    -      -       -      -
    371A  ASP*     4.7     1.6    -      -       +      -
    373A  PRO*     5.3     0.9    -      -       +      -
    406A  ALA*     3.4    22.7    -      -       -      +
    409A  SER*     3.8    13.5    -      -       -      -
    410A  GLU*     3.4    39.3    -      -       +      -
    413A  PHE*     3.7    39.0    -      +       +      -
----------------------------------------------------------
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Residues in contact with VAL 307 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    299A  TRP*     5.7     0.2    -      -       +      -
    305A  ALA      4.5     6.5    -      -       -      +
    306A  PHE*     1.3    75.8    -      -       -      +
    308A  GLY*     1.3    61.4    +      -       -      +
    309A  PHE*     4.9     6.9    -      -       +      -
    324A  LEU*     4.4     7.0    -      -       +      -
    325A  ALA      3.3    11.0    -      -       -      +
    326A  ALA*     4.7     4.5    -      -       +      -
    345A  LEU*     3.6    37.7    -      -       +      -
    347A  GLU      4.8     2.9    -      -       -      +
    348A  ALA*     4.2     4.3    -      -       +      -
    349A  ARG      2.8    37.3    +      -       -      +
    350A  GLY*     4.1    11.0    -      -       -      +
    351A  LEU      4.6     4.2    +      -       -      +
    353A  ALA*     5.8     1.6    -      -       -      -
    356A  LEU*     4.1    19.3    -      -       +      -
    406A  ALA*     3.9     1.3    -      -       -      -
    409A  SER*     4.1     8.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 308 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    307A  VAL*     1.3    74.7    -      -       -      +
    309A  PHE*     1.3    64.9    +      -       -      +
    324A  LEU*     3.5     3.3    -      -       -      +
    325A  ALA      2.9    30.3    +      -       -      +
    402A  ALA      3.2    23.8    -      -       -      -
    405A  ARG*     4.2     6.3    -      -       -      -
    406A  ALA*     3.5    13.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 309 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    307A  VAL*     4.9     5.6    -      -       +      -
    308A  GLY*     1.3    80.4    -      -       -      +
    310A  VAL*     1.3    62.3    +      -       -      +
    311A  LEU*     3.5    42.2    -      -       +      -
    321A  LEU*     3.7     8.3    -      -       +      -
    323A  ALA      3.2    13.7    -      -       -      +
    324A  LEU*     3.9     8.5    -      -       +      -
    351A  LEU      3.8    13.7    -      -       -      -
    352A  LEU*     3.4    33.4    -      -       +      -
    353A  ALA*     5.0     1.1    -      -       -      -
    355A  ASP*     4.2     6.7    -      -       +      -
    356A  LEU*     3.7    39.9    -      -       +      -
    398A  TRP*     5.4     3.8    -      +       -      -
    402A  ALA*     4.0     5.2    -      -       -      +
    405A  ARG*     2.9    28.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 310 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    283A  HIS*     3.8    30.3    -      -       +      +
    309A  PHE*     1.3    77.8    -      -       -      +
    311A  LEU*     1.3    67.1    +      -       -      +
    321A  LEU*     3.5     2.8    -      -       -      -
    322A  LEU*     2.6    34.8    +      -       +      +
    323A  ALA*     2.9    24.8    +      -       +      +
    400A  GLU*     3.2    33.4    -      -       -      +
    401A  GLU*     4.0     0.7    -      -       -      -
    402A  ALA*     3.3    24.7    -      -       +      +
    405A  ARG*     3.9    11.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 311 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    309A  PHE*     3.5    39.3    -      -       +      -
    310A  VAL*     1.3    81.6    -      -       -      +
    312A  SER*     1.3    65.1    +      -       -      +
    313A  ARG*     3.3    23.6    +      -       -      +
    314A  LYS*     4.2    14.1    -      -       -      +
    316A  PRO*     4.2    16.4    -      -       +      -
    319A  ALA*     3.9     7.9    -      -       +      -
    320A  ASP      3.1     6.7    -      -       -      +
    321A  LEU*     3.9    23.6    -      -       +      -
    322A  LEU*     3.9     5.6    -      -       -      +
    355A  ASP*     5.0     1.3    -      -       +      +
    359A  LEU*     4.2    20.0    -      -       +      -
    405A  ARG*     4.7     3.0    -      -       -      +
----------------------------------------------------------
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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