Contacts of the strand formed by residues 61 - 65 (chain A) in PDB entry 2ZOT


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 61 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     55A  ARG*     5.6     0.2    -      -       -      -
     59A  THR*     3.1    15.8    -      -       +      +
     60A  GLU*     1.3   103.9    -      -       +      +
     62A  SER*     1.3    60.2    +      -       -      +
     83A  SER      3.3     4.5    -      -       -      +
     84A  ALA*     3.6    30.5    -      -       +      -
     88A  SER*     3.9    12.1    -      -       -      -
     89A  TYR      3.5    22.9    -      -       -      -
     90A  PHE*     3.7    11.4    -      +       +      -
    163A  ILE*     3.5    38.1    -      -       +      -
    165A  GLN*     4.1    12.6    -      -       +      -
    170A  TYR*     4.9    10.1    -      +       +      -
    176A  SER*     2.6    31.2    +      -       -      +
    177A  LEU*     3.9    19.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with SER 62 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     59A  THR      4.4     4.2    +      -       -      -
     60A  GLU      4.6     1.9    +      -       -      -
     61A  PHE*     1.3    80.4    +      -       -      +
     63A  LEU*     1.3    60.5    +      -       -      +
     64A  ARG*     3.5    40.4    +      -       -      +
     81A  THR      3.5     2.1    -      -       -      +
     82A  LEU*     3.4     9.8    -      -       -      +
     83A  SER*     2.8    41.3    +      -       -      -
    176A  SER*     3.4    13.9    -      -       -      -
    177A  LEU*     5.2     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 63 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     62A  SER*     1.3    73.0    -      -       -      +
     64A  ARG*     1.3    63.8    +      -       -      +
     80A  VAL*     3.5    29.8    -      -       +      -
     81A  THR      3.5     9.9    -      -       -      +
     82A  LEU*     4.0    20.6    -      -       +      +
     95A  LEU*     3.7    24.0    -      -       +      -
    159A  LEU*     3.2    40.6    -      -       +      +
    161A  ALA*     4.0     3.1    -      -       +      +
    176A  SER      2.8    19.9    +      -       -      +
    177A  LEU*     3.6    17.5    -      -       -      +
    178A  THR      4.5     2.3    -      -       -      +
    179A  LYS*     4.3    18.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 64 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     62A  SER*     3.5    33.9    +      -       -      +
     63A  LEU*     1.3    77.6    -      -       -      +
     65A  VAL*     1.3    70.8    +      -       -      +
     68A  ASP*     5.8     3.1    -      -       -      +
     80A  VAL*     3.8     5.4    -      -       -      +
     81A  THR*     3.1    41.8    +      -       -      +
     83A  SER*     4.2    18.8    +      -       -      -
    179A  LYS*     4.8    12.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 65 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     64A  ARG*     1.3    84.0    -      -       -      +
     66A  GLU*     1.3    69.0    +      -       -      +
     67A  GLY      3.4     0.2    +      -       -      -
     68A  ASP*     2.9    25.6    +      -       -      +
     69A  PRO*     3.7    25.4    -      -       +      -
     78A  TYR*     3.7    26.5    -      -       +      -
     79A  ARG      3.4    13.0    -      -       -      +
     80A  VAL*     4.6    14.4    -      -       +      -
     81A  THR*     5.7     0.4    -      -       -      -
    147A  TRP*     6.3     0.4    -      -       +      -
    159A  LEU*     4.6     6.1    -      -       +      -
    179A  LYS*     4.5    18.4    -      -       +      +
    181A  LEU*     4.2    21.8    -      -       +      -
----------------------------------------------------------
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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