Contacts of the strand formed by residues 19 - 23 (chain K) in PDB entry 4ZZ7


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 SER 19 (chain K).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     18H  ARG*     3.5     4.1    -      -       -      +
     19H  SER*     2.7    49.6    +      -       -      +
     33H  GLN*     5.3     1.6    +      -       -      -
      3K  THR*     5.5     3.8    -      -       -      -
     18K  ARG*     1.3    77.9    -      -       -      +
     20K  GLN*     1.3    60.4    +      -       -      +
     33K  GLN*     2.7    32.5    +      -       -      +
     34K  LEU      3.2    16.6    -      -       -      -
     35K  ASP*     4.3     2.7    -      -       -      -
     36K  LEU*     4.2     2.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLN 20 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     17H  THR*     3.2    18.1    +      -       -      +
     18H  ARG*     3.0    32.4    +      -       -      +
     19K  SER*     1.3    75.4    -      -       -      +
     21K  ASN*     1.3    75.1    +      -       -      +
     22K  VAL      3.5     0.2    +      -       -      -
     33K  GLN*     3.4     6.5    -      -       -      -
     34K  LEU*     2.7    48.5    +      -       +      +
     36K  LEU*     4.0    13.5    -      -       +      +
    175K  GLU*     3.8    34.2    +      -       -      +
    176K  ARG*     5.3     6.1    -      -       -      +
    204K  ASP*     5.0     3.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASN 21 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16H  ASN*     2.7    34.8    +      -       -      +
     17H  THR*     2.8    19.6    +      -       -      +
     18H  ARG*     5.4     0.7    -      -       -      -
     19H  SER*     5.7     0.3    +      -       -      -
     20K  GLN*     1.3    85.2    +      -       -      +
     22K  VAL*     1.3    61.9    +      -       -      +
     23K  PHE*     3.5    25.9    -      -       +      -
     30K  ILE*     3.1    31.5    -      -       +      +
     32K  LYS      3.8     4.3    -      -       -      -
     33K  GLN*     2.5    32.1    +      -       -      +
    175K  GLU      4.8     2.4    -      -       -      +
    176K  ARG*     5.8     0.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 22 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4K  ILE*     4.8     1.8    -      -       +      -
     20K  GLN*     4.1     0.4    -      -       +      +
     21K  ASN*     1.3    76.7    -      -       -      +
     23K  PHE*     1.3    61.6    +      -       -      +
     30K  ILE*     3.7     3.5    -      -       -      +
     31K  GLY*     2.9    22.7    +      -       -      -
     32K  LYS*     3.0    43.8    +      -       +      +
     33K  GLN      4.6     0.9    -      -       -      -
     34K  LEU*     3.7    29.2    -      -       +      +
     89K  GLU*     3.9    20.0    -      -       +      +
    175K  GLU      3.9    13.2    -      -       -      +
    176K  ARG*     4.4    13.9    -      -       -      +
    178K  PRO*     4.3    10.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 23 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16H  ASN      4.6     6.1    -      -       -      -
     17H  THR*     4.8    15.5    -      -       +      -
     21K  ASN*     3.5    36.8    -      -       +      -
     22K  VAL*     1.3    81.0    -      -       -      +
     24K  ASN*     1.3    60.2    +      -       -      +
     25K  PRO*     3.4    10.9    -      -       +      +
     28K  GLY      3.4    27.8    -      -       -      -
     29K  GLU      3.4     8.7    -      -       -      -
     30K  ILE*     4.0    14.1    -      -       +      -
     31K  GLY*     4.5     2.7    -      -       -      -
     88K  GLU      3.7     5.9    -      -       -      +
     89K  GLU*     3.8    14.2    -      -       -      +
    176K  ARG      4.9     3.9    +      -       -      +
    324K  ILE      5.4     3.1    -      -       -      +
    325K  THR*     5.9     7.2    -      -       +      -
    362K  PHE*     4.0    28.0    -      +       +      -
----------------------------------------------------------
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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