Contacts of the strand formed by residues 236 - 239 (chain E) in PDB entry 1ZMC


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 LYS 236 (chain E).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    180E  LYS*     5.0     2.6    -      -       -      +
    203E  ASP*     2.6    39.8    +      -       -      -
    204E  VAL      3.1    27.5    +      -       -      +
    205E  THR*     3.3    18.6    +      -       +      +
    206E  ALA      2.9    24.3    +      -       -      -
    231E  GLN*     4.8     4.7    -      -       +      +
    234E  GLY*     3.7    14.6    -      -       -      +
    235E  PHE*     1.3    79.9    -      -       -      +
    237E  PHE*     1.3    65.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 237 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    186E  ALA*     4.4     8.5    -      -       +      -
    191E  VAL*     4.6     5.4    -      -       +      -
    205E  THR*     4.9     1.6    -      -       -      -
    206E  ALA*     3.4    31.6    -      -       +      -
    213E  VAL*     3.7    28.3    -      -       +      -
    227E  GLN*     4.0    12.2    +      -       +      +
    230E  LEU*     3.8    32.3    -      -       +      -
    231E  GLN*     3.6    26.7    +      -       +      +
    235E  PHE*     3.7    43.5    -      +       -      -
    236E  LYS*     1.3    76.9    -      -       -      +
    238E  LYS*     1.3    65.0    +      -       -      +
    239E  LEU*     3.8    17.5    +      -       +      +
----------------------------------------------------------
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Residues in contact with LYS 238 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    205E  THR*     4.6    12.6    -      -       +      -
    206E  ALA      2.9    13.1    +      -       -      +
    207E  VAL*     4.2    11.2    -      -       +      -
    208E  GLU      3.0    19.1    +      -       -      -
    237E  PHE*     1.3    74.9    -      -       -      +
    239E  LEU*     1.3    62.4    +      -       -      +
    241E  THR*     2.7    31.3    +      -       +      +
    258E  ILE*     4.1    15.7    -      -       +      -
    265E  LYS*     3.6    15.6    -      -       -      +
    267E  GLU*     2.7    38.3    +      -       -      -
    269E  ILE*     5.3     4.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 239 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    208E  GLU*     3.4    27.8    -      -       +      -
    210E  LEU      3.7     5.2    -      -       -      +
    211E  GLY*     3.4    22.7    -      -       -      +
    212E  HIS*     3.9     6.1    -      -       -      +
    213E  VAL*     3.7    21.8    -      -       +      -
    224E  LYS*     4.4     2.7    -      -       -      +
    227E  GLN*     3.2    32.5    -      -       -      +
    237E  PHE*     3.8    18.0    -      -       +      -
    238E  LYS*     1.3    73.2    -      -       -      +
    240E  ASN*     1.3    83.1    +      -       -      +
    241E  THR*     3.1    11.2    +      -       -      +
----------------------------------------------------------
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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