Contacts of the strand formed by residues 65 - 70 (chain A) in PDB entry 1TUB


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 ALA 65 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6A  SER*     2.3    18.9    +      -       -      -
      8A  HIS*     6.1     0.4    -      -       -      -
     21A  TRP*     3.7     8.2    -      -       -      -
     63A  PRO*     3.8     4.3    -      -       +      -
     64A  ARG*     1.2    84.3    -      -       -      +
     66A  VAL*     1.3    72.6    +      -       -      +
     67A  PHE*     6.3     0.4    -      -       -      -
     87A  PHE*     5.4     4.0    -      -       -      -
     91A  GLN*     2.2    50.2    -      -       +      +
    125A  LEU*     3.8     4.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 66 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5A  ILE*     5.2     7.0    -      -       +      -
      6A  SER*     2.5    23.1    +      -       -      +
      7A  ILE*     3.2    10.4    -      -       +      +
      8A  HIS*     2.9    31.4    +      -       -      -
     64A  ARG      4.6     1.6    -      -       -      +
     65A  ALA*     1.3    84.3    -      -       -      +
     67A  PHE*     1.3    66.9    +      -       -      +
     68A  VAL*     4.0    10.0    +      -       +      -
     87A  PHE*     5.7     0.4    -      -       -      -
     91A  GLN*     3.2    14.3    -      -       -      +
     93A  ILE*     4.8    10.3    -      -       +      -
    118A  VAL*     4.9     6.7    -      -       +      -
    121A  ARG*     5.0     6.7    -      -       +      -
    122A  ILE*     5.0     7.2    -      -       +      +
    125A  LEU*     2.6    35.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 67 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8A  HIS*     1.3   116.0    -      +       +      -
     14A  VAL*     3.3    36.8    -      -       +      -
     17A  GLY*     3.8     3.8    -      -       -      -
     18A  ASN*     5.5     0.4    -      -       -      -
     21A  TRP*     4.5    10.5    -      +       +      -
     65A  ALA*     6.4     0.2    -      -       -      -
     66A  VAL*     1.3    71.0    -      -       -      +
     68A  VAL*     1.4    57.3    -      -       -      +
     69A  ASP*     4.1     6.3    -      -       -      +
     78A  VAL*     4.8     4.5    -      -       +      -
     87A  PHE*     3.4    35.0    -      +       -      -
     91A  GLN      2.9     6.9    +      -       -      +
     92A  LEU*     3.0    24.0    -      -       +      -
     93A  ILE*     2.8    34.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 68 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7A  ILE*     4.5     4.3    -      -       +      -
      8A  HIS*     3.7    22.9    -      -       -      +
      9A  VAL*     3.3    22.2    -      -       -      +
     10A  GLY*     4.4     0.3    -      -       -      -
     14A  VAL*     3.7     4.9    -      -       -      +
     66A  VAL*     4.7     3.8    -      -       +      -
     67A  PHE*     1.4    71.2    -      -       -      +
     69A  ASP*     1.3    69.6    +      -       -      +
     70A  LEU*     4.2     8.5    -      -       +      -
     93A  ILE*     4.0    13.0    -      -       +      -
    118A  VAL*     4.1    22.7    -      -       +      -
    149A  PHE*     2.5    50.9    -      -       +      -
    153A  LEU*     4.4     5.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 69 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      9A  VAL      5.2     0.2    -      -       -      -
     10A  GLY*     5.9     1.1    -      -       -      -
     14A  VAL*     2.5    37.2    -      -       -      +
     67A  PHE*     4.1     3.3    -      -       -      +
     68A  VAL*     1.3    79.2    +      -       -      +
     70A  LEU*     1.0    72.0    +      -       -      +
     71A  GLU      3.0    20.4    -      -       -      +
     74A  VAL*     4.0     2.5    -      -       +      -
     75A  ILE*     1.6    53.7    -      -       +      +
     92A  LEU*     5.1     0.2    -      -       -      +
     93A  ILE*     3.1    19.9    +      -       -      +
     94A  THR*     4.2     1.1    -      -       -      -
     95A  GLY      3.3    14.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 70 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     68A  VAL*     4.2     4.7    -      -       +      -
     69A  ASP*     1.0    83.8    -      -       -      +
     71A  GLU*     1.3    67.3    +      -       +      +
     93A  ILE*     6.0     0.7    -      -       +      -
     95A  GLY*     2.9    20.6    -      -       -      +
     97A  GLU*     4.4     2.2    +      -       +      +
     98A  ASP      3.7     4.8    +      -       -      +
     99A  ALA*     3.3    17.5    +      -       -      -
    100A  ALA      5.4     1.8    -      -       -      +
    106A  GLY*     4.5    13.5    -      -       -      -
    110A  ILE*     5.5    10.3    -      -       +      -
    111A  GLY*     5.1     6.7    -      -       -      +
    114A  ILE*     5.4     9.2    -      -       +      +
    145A  THR*     1.9    63.2    -      -       +      +
    149A  PHE*     3.6    34.3    -      -       +      -
----------------------------------------------------------
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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