Contacts of the strand formed by residues 65 - 69 (chain A) in PDB entry 1ADI


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 THR 65 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     28A  LYS*     3.2    24.3    +      -       -      -
     29A  TYR*     3.4    24.0    -      -       +      +
     30A  VAL      3.1    22.3    +      -       -      +
     64A  VAL*     1.3    77.5    +      -       -      +
     66A  SER*     1.3    66.7    +      -       -      +
     67A  ILE*     3.9     8.2    +      -       +      +
     96A  ARG*     3.8    12.9    -      -       -      +
     98A  LEU*     3.7    32.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 66 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     30A  VAL*     3.7     6.8    -      -       -      +
     56A  PRO*     3.7    21.2    -      -       -      +
     58A  GLY*     3.6     7.1    -      -       -      -
     59A  ILE*     3.2    37.2    +      -       -      -
     64A  VAL*     4.2     0.9    +      -       -      +
     65A  THR*     1.3    72.5    -      -       -      +
     67A  ILE*     1.3    55.4    +      -       -      +
     96A  ARG      3.1     7.1    +      -       -      +
     97A  LEU*     3.3    24.1    -      -       -      +
     98A  LEU*     2.8    32.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 67 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29A  TYR*     3.7    24.9    -      -       +      -
     30A  VAL      3.1     6.9    +      -       -      +
     31A  VAL*     3.6    24.9    -      -       +      -
     32A  ARG*     3.2    23.6    +      -       -      +
     56A  PRO*     4.4     2.4    -      -       -      +
     65A  THR*     4.2    15.7    -      -       +      +
     66A  SER*     1.3    77.9    -      -       -      +
     68A  ILE*     1.3    70.2    +      -       -      +
     69A  GLY      3.6     1.5    +      -       -      +
     98A  LEU*     3.1    15.7    -      -       +      +
    202A  VAL*     5.4     0.2    -      -       +      -
    204A  VAL*     3.8    38.1    -      -       +      -
    207A  LEU*     3.9    21.1    -      -       +      -
    208A  LEU*     4.6     9.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 68 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     32A  ARG*     4.3     7.2    -      -       +      -
     54A  LEU*     3.7    39.5    -      -       +      +
     55A  ILE*     4.8     1.3    -      -       -      -
     56A  PRO*     4.1    16.8    -      -       +      -
     67A  ILE*     1.3    78.7    -      -       -      +
     69A  GLY*     1.3    60.1    +      -       -      +
     72A  VAL*     3.4    34.5    -      -       +      -
     74A  LEU*     4.4    13.0    -      -       +      -
     79A  LEU*     4.7    10.1    -      -       +      -
     97A  LEU*     4.9     9.2    -      -       +      -
     98A  LEU      2.8    15.1    +      -       -      +
     99A  LEU*     3.7     8.6    -      -       +      -
    100A  SER*     3.2    26.0    +      -       -      -
    103A  CYS*     3.8    10.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 69 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     31A  VAL*     4.5     4.7    -      -       -      +
     32A  ARG      2.8    22.7    +      -       -      -
     67A  ILE*     3.6     3.2    +      -       -      +
     68A  ILE*     1.3    75.9    -      -       -      +
     70A  ASN*     1.3    57.0    +      -       -      -
     71A  GLY      3.1     5.6    -      -       -      -
     72A  VAL*     2.9    26.9    +      -       -      +
    100A  SER*     4.5     2.7    -      -       -      -
    103A  CYS*     3.5     4.7    -      -       -      -
    204A  VAL*     4.7    13.9    -      -       -      -
    251A  GLY      3.4     7.0    -      -       -      -
    252A  SER*     4.9     0.4    -      -       -      -
----------------------------------------------------------
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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