Contacts of the strand formed by residues 77 - 82 (chain C) in PDB entry 2UZC


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 LEU 77 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6C  VAL*     3.7     2.3    -      -       -      +
      7C  SER*     3.4     1.4    -      -       -      -
      8C  LEU*     2.8    43.1    +      -       +      +
     14C  TRP*     3.7    51.1    -      -       +      -
     16C  PHE*     3.7    25.6    -      -       +      -
     53C  ILE*     4.0    26.0    -      -       +      -
     54C  ASP*     4.1     9.2    -      -       -      +
     70C  ILE*     4.1    13.0    -      -       +      -
     73C  CYS*     3.7    14.0    -      -       +      -
     76C  SER*     1.3    70.3    -      -       -      +
     78C  ASN*     1.3    64.1    +      -       -      +
     79C  MET*     4.1    16.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 78 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6C  VAL      3.4     5.6    -      -       -      +
      7C  SER*     2.6    32.7    +      -       -      -
     53C  ILE*     3.5     0.7    -      -       -      +
     54C  ASP*     2.7    59.3    +      -       -      +
     55C  GLY      5.2     2.0    -      -       -      +
     76C  SER*     3.6    14.2    +      -       -      -
     77C  LEU*     1.3    74.6    -      -       -      +
     79C  MET*     1.3    65.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with MET 79 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5C  SER*     3.3     5.2    -      -       -      -
      6C  VAL*     2.9    49.9    +      -       +      +
      8C  LEU*     4.9     4.0    -      -       +      -
     16C  PHE*     3.8    39.0    -      -       +      -
     30C  ILE*     4.8     8.1    -      -       +      -
     39C  ALA*     5.9     0.4    -      -       +      -
     44C  VAL*     5.2     5.6    -      -       +      -
     50C  VAL*     4.3    21.5    -      -       +      -
     52C  SER*     3.2    14.1    -      -       -      +
     53C  ILE*     4.4    10.3    -      -       +      -
     70C  ILE*     4.7     4.3    -      -       -      -
     77C  LEU*     4.1    19.0    +      -       +      -
     78C  ASN*     1.3    80.7    -      -       -      +
     80C  THR*     1.3    65.0    +      -       -      +
     81C  LEU*     3.9    18.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with THR 80 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      3C  ASN*     6.1     1.8    -      -       -      -
      4C  TYR      3.4     7.9    -      -       -      -
      5C  SER*     3.3    20.0    -      -       -      +
     50C  VAL*     3.8     0.7    -      -       -      +
     51C  LEU*     2.8    40.9    +      -       -      +
     52C  SER*     2.5    38.1    +      -       -      +
     79C  MET*     1.3    76.9    -      -       -      +
     81C  LEU*     1.3    60.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 81 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      3C  ASN*     3.2     6.2    -      -       -      +
      4C  TYR*     2.8    76.4    +      -       +      +
      6C  VAL*     4.3    10.3    -      -       +      -
     30C  ILE*     3.8    31.2    -      -       +      -
     44C  VAL*     4.3     4.9    -      -       +      -
     48C  ASP*     4.1     4.5    -      -       +      -
     49C  VAL      3.1    11.2    -      -       -      +
     50C  VAL*     4.0    17.3    -      -       +      -
     51C  LEU*     4.1     6.3    -      -       -      +
     79C  MET*     3.9    26.9    -      -       +      +
     80C  THR*     1.3    80.9    -      -       -      +
     82C  GLN*     1.3    62.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 82 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      0C  SER*     5.7     3.4    -      -       -      +
      2C  SER*     4.2     3.8    -      -       -      +
      3C  ASN*     3.5    22.1    +      -       -      +
      4C  TYR*     4.5     2.0    -      -       -      -
     48C  ASP*     3.5     2.8    -      -       -      +
     49C  VAL*     2.8    44.1    +      -       +      +
     51C  LEU*     4.0    23.2    -      -       +      +
     81C  LEU*     1.3    73.6    -      -       -      +
     83C  ARG*     1.3    68.8    +      -       -      +
     84C  GLU*     2.5    34.6    +      -       -      +
----------------------------------------------------------
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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