Contacts of the strand formed by residues 34 - 39 (chain A) in PDB entry 3ANX


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 34 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     28A  GLY      3.7     6.7    -      -       -      +
     29A  LYS*     2.7    45.9    +      -       -      +
     33A  GLN*     1.3    75.3    -      -       -      +
     35A  TYR*     1.4    60.0    +      -       -      +
     36A  PHE*     4.4    19.6    -      -       +      -
     49A  LEU*     3.3     9.5    -      -       -      +
     50A  ASP*     2.6    47.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 35 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26A  ALA*     4.2    11.6    -      -       +      +
     27A  SER*     3.4    17.1    +      -       -      -
     28A  GLY*     3.1    61.7    +      -       -      +
     29A  LYS      3.9     5.4    +      -       -      -
     30A  THR*     4.0    27.4    -      -       +      -
     34A  ASP*     1.4    73.8    -      -       -      +
     36A  PHE*     1.3    81.9    +      -       -      +
     37A  LEU*     5.4     0.4    -      -       +      -
     47A  LEU*     4.2     8.7    -      -       +      -
     48A  ILE      3.2     8.1    -      -       -      +
     49A  LEU*     4.1    12.3    -      -       +      -
    112A  GLU*     5.3     3.7    +      -       -      -
    113A  LEU*     4.3     9.6    -      -       +      -
    116A  VAL*     3.7    37.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 36 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7A  PHE*     3.7    27.8    -      +       +      -
     24A  VAL*     5.8     2.9    -      -       +      -
     26A  ALA      3.5     6.1    -      -       -      -
     27A  SER*     3.5    19.7    -      -       -      -
     28A  GLY      5.5     2.0    -      -       -      -
     34A  ASP*     4.4    19.1    -      -       +      -
     35A  TYR*     1.3    86.5    -      -       -      +
     37A  LEU*     1.3    60.8    +      -       -      +
     38A  PHE*     4.1     9.4    -      -       +      -
     47A  LEU*     3.2     7.1    -      -       -      +
     48A  ILE*     2.7    50.6    +      -       +      -
     50A  ASP      3.8    18.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 37 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     24A  VAL*     3.8     2.7    -      -       -      +
     25A  ILE*     3.3    27.5    +      -       +      -
     26A  ALA*     2.5    39.1    +      -       +      +
     35A  TYR*     5.4     2.0    -      -       +      -
     36A  PHE*     1.3    74.0    -      -       -      +
     38A  PHE*     1.3    63.5    +      -       -      +
     45A  LYS*     4.4     9.0    -      -       +      -
     46A  VAL      2.9    28.9    -      -       -      +
     47A  LEU*     3.8    23.1    -      -       +      -
    116A  VAL*     5.5     3.4    -      -       +      -
    120A  HIS*     3.7    40.2    -      -       +      +
    121A  MET*     4.1    17.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 38 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7A  PHE*     3.9    24.0    -      +       +      -
     19A  ARG*     4.3    16.8    -      -       +      -
     20A  ARG      4.1     9.2    -      -       -      -
     21A  MET*     3.6    39.5    -      -       +      -
     23A  ARG      3.3    12.1    -      -       -      +
     24A  VAL*     4.3     6.3    -      -       +      -
     25A  ILE*     4.3     4.3    -      -       -      +
     36A  PHE*     4.6     9.4    -      -       +      -
     37A  LEU*     1.3    77.9    -      -       -      +
     39A  GLU*     1.3    63.7    +      -       -      +
     40A  SER*     3.4    11.3    +      -       -      -
     45A  LYS*     3.1     4.5    -      -       -      +
     46A  VAL*     2.7    65.4    +      -       +      -
     48A  ILE*     3.8    30.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 39 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22A  GLU*     3.1    30.0    +      -       +      +
     23A  ARG*     2.7    38.7    +      -       +      +
     25A  ILE*     3.5    23.7    -      -       +      +
     38A  PHE*     1.3    75.4    -      -       -      +
     40A  SER*     1.3    79.7    +      -       -      +
     41A  LYS*     5.2     0.9    -      -       -      -
     44A  GLY*     4.0     3.4    -      -       -      -
     45A  LYS*     3.7    27.0    +      -       +      +
     57A  GLU*     4.7     1.9    -      -       -      +
     58A  ARG*     4.9     5.5    +      -       -      -
----------------------------------------------------------
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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