Contacts of the strand formed by residues 69 - 74 (chain A) in PDB entry 3RTC


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 ASP 69 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     41A  TYR      3.9     1.2    +      -       -      -
     42A  ARG*     3.4    20.1    -      -       +      +
     43A  PHE      2.8    30.1    +      -       -      -
     67A  VAL*     3.4     4.9    -      -       -      +
     68A  LYS*     1.3    84.4    -      -       +      +
     70A  VAL*     1.3    75.2    +      -       -      +
     71A  LEU*     5.1     1.1    -      -       -      +
    108A  GLU*     5.0     1.7    -      -       -      +
    109A  PHE*     3.3    25.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 70 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     43A  PHE*     3.3    11.2    -      -       +      +
     45A  VAL*     4.2    11.0    -      -       +      -
     60A  ALA*     4.0    27.8    -      -       +      +
     63A  LEU*     3.9    23.8    -      -       +      +
     64A  LEU*     4.2    17.6    -      -       +      +
     65A  GLY      5.7     0.2    -      -       -      +
     67A  VAL*     3.6    19.3    -      -       +      -
     69A  ASP*     1.3    90.1    +      -       -      +
     71A  LEU*     1.3    65.8    +      -       -      +
     90A  TYR*     3.8    19.9    +      -       -      +
     96A  LYS*     4.7     7.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 71 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     43A  PHE      2.9     7.3    +      -       -      +
     44A  LEU*     3.5    19.5    -      -       +      +
     45A  VAL*     2.9    26.5    +      -       -      +
     69A  ASP*     5.1     1.3    -      -       -      +
     70A  VAL*     1.3    75.5    -      -       -      +
     72A  VAL*     1.3    73.3    +      -       -      +
     73A  VAL*     4.8     0.2    -      -       +      -
     96A  LYS*     3.5    49.1    -      -       +      +
     98A  VAL*     4.3    22.4    -      -       +      -
    105A  ILE*     4.0    15.3    -      -       +      -
    109A  PHE*     3.5    31.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 72 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     45A  VAL*     3.2    17.0    -      -       +      +
     47A  CYS*     3.9    11.0    -      -       +      -
     57A  PHE*     3.7    26.7    -      -       +      -
     60A  ALA*     3.5    22.4    -      -       +      -
     71A  LEU*     1.3    74.1    -      -       -      +
     73A  VAL*     1.3    75.9    +      -       -      +
     74A  PHE      3.9     2.5    -      -       -      +
     90A  TYR*     3.5    31.8    +      -       +      +
     96A  LYS      3.0    11.7    +      -       -      +
     97A  VAL*     3.3     6.3    -      -       +      -
     98A  VAL*     2.8    28.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 73 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     44A  LEU*     3.9    25.1    -      -       +      -
     45A  VAL      2.9     8.1    +      -       -      -
     46A  LEU*     3.6    19.5    -      -       +      -
     47A  CYS      3.0    24.4    +      -       -      +
     71A  LEU*     4.1     2.4    +      -       +      -
     72A  VAL*     1.3    73.5    -      -       -      +
     74A  PHE*     1.3    63.0    +      -       -      +
     75A  LEU*     3.6    28.3    +      -       +      +
     98A  VAL*     3.3    21.1    -      -       +      +
     99A  GLU      4.7     1.1    -      -       -      -
    100A  GLN      4.4     7.6    -      -       -      +
    101A  PHE*     4.1    26.0    -      -       +      -
    105A  ILE*     5.2     3.8    -      -       +      -
    132A  ILE*     6.3     0.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 74 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     47A  CYS      3.5    11.2    -      -       -      -
     48A  GLY      3.5    22.7    -      -       -      -
     49A  GLY*     3.7     6.7    -      -       -      -
     57A  PHE*     4.1    18.4    -      +       +      -
     72A  VAL*     3.9     3.2    -      -       -      -
     73A  VAL*     1.3    71.2    -      -       -      +
     75A  LEU*     1.3    58.0    +      -       -      +
     76A  GLY*     3.2    34.6    -      -       -      +
     77A  LYS      4.3     5.6    -      -       -      -
     78A  LYS      4.0     7.0    -      -       -      -
     79A  LYS*     3.6    47.8    -      -       +      -
     87A  TYR*     6.0     0.4    -      +       -      -
     97A  VAL*     3.7    21.5    -      -       +      -
     98A  VAL      2.8     9.6    +      -       -      +
     99A  GLU*     3.5    46.5    -      -       +      +
----------------------------------------------------------
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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