Contacts of the strand formed by residues 78 - 83 (chain D) in PDB entry 4UN7


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 TYR 78 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     41D  THR*     3.2     8.5    -      -       -      -
     42D  GLN      2.8    35.5    +      -       -      +
     43D  LYS      3.1    25.1    -      -       -      -
     45D  GLU*     3.2    56.8    +      -       +      -
     48D  ILE*     3.5    16.8    -      -       +      +
     49D  LYS*     5.1     1.8    -      -       -      -
     71D  ILE*     4.2    17.0    -      -       +      -
     72D  VAL      3.5     4.9    -      -       -      -
     73D  LYS*     3.3    58.1    +      -       +      +
     77D  ARG*     1.3    75.7    -      -       -      +
     79D  GLU*     1.3    60.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 79 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37D  ARG*     4.6     1.6    +      -       -      -
     39D  VAL*     3.4    28.1    -      -       +      +
     40D  ILE      3.6     2.9    -      -       -      -
     41D  THR*     3.9     4.9    -      -       +      -
     48D  ILE*     4.4     2.2    -      -       -      -
     70D  GLN      3.6     0.5    -      -       -      +
     71D  ILE*     3.3     7.0    -      -       -      +
     72D  VAL*     2.9    36.3    +      -       +      +
     77D  ARG*     2.9    31.6    +      -       -      +
     78D  TYR*     1.3    74.1    -      -       -      +
     80D  LEU*     1.3    71.1    +      -       -      +
     81D  ARG*     2.6    53.7    +      -       -      +
     16E    T      5.0     3.4    -      -       -      -
     17E    T      4.9     1.1    -      -       -      +
      9F    A      3.2     7.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 80 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38D  VAL      4.9     2.9    -      -       -      +
     39D  VAL*     3.3     5.0    -      -       -      -
     40D  ILE*     2.7    53.6    +      -       +      +
     48D  ILE*     4.1    20.5    -      -       +      +
     52D  ILE*     3.8    25.4    -      -       +      +
     53D  ALA*     3.8    27.6    -      -       +      +
     56D  MET*     4.3    30.1    -      -       +      -
     69D  ILE*     3.9    14.6    -      -       +      -
     70D  GLN      3.4     4.5    -      -       -      +
     71D  ILE*     4.2     4.9    -      -       +      -
     79D  GLU*     1.3    74.2    -      -       -      +
     81D  ARG*     1.3    66.3    +      -       -      +
     82D  VAL*     4.3     8.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 81 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     35D  GLU*     4.9     1.8    -      -       -      -
     37D  ARG*     3.4    38.4    -      -       -      +
     38D  VAL      3.4     6.3    -      -       -      +
     39D  VAL*     4.4     1.1    -      -       +      -
     68D  LYS      3.7     0.3    -      -       -      +
     69D  ILE      3.8     0.3    -      -       -      -
     70D  GLN*     2.8    68.0    +      -       +      +
     72D  VAL*     4.1    11.4    -      -       +      +
     79D  GLU*     2.6    49.9    +      -       +      +
     80D  LEU*     1.3    74.1    -      -       -      +
     82D  VAL*     1.3    73.2    +      -       -      +
     83D  SER      4.4     0.7    -      -       -      +
      7F    G      3.2    32.5    +      -       -      -
      8F    G      3.2    25.0    +      -       -      -
      9F    A      3.2    12.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 82 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37D  ARG*     3.5     0.7    -      -       -      -
     38D  VAL*     2.8    42.5    +      -       +      +
     56D  MET*     3.8    30.3    -      -       +      -
     60D  ILE*     4.1    10.5    -      -       +      -
     65D  VAL*     5.0     0.4    -      -       +      -
     67D  SER*     4.0    21.8    -      -       -      -
     68D  LYS      4.0     7.0    -      -       -      +
     69D  ILE*     4.2    14.1    -      -       +      -
     80D  LEU*     4.3     6.3    -      -       +      -
     81D  ARG*     1.3    78.4    -      -       -      +
     83D  SER*     1.3    60.6    +      -       -      +
     84D  SER*     3.3    12.3    +      -       -      -
     87D  LEU*     3.8    25.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 83 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     35D  GLU*     2.8    39.5    +      -       -      +
     36D  TYR      3.4     5.6    +      -       -      -
     37D  ARG*     4.7     3.1    -      -       -      +
     67D  SER*     2.6    27.3    +      -       -      -
     68D  LYS      4.4     4.2    +      -       -      -
     70D  GLN*     4.0    16.0    -      -       -      +
     81D  ARG*     4.0     4.3    +      -       -      +
     82D  VAL*     1.3    71.6    -      -       -      +
     84D  SER*     1.3    53.4    +      -       -      +
      5F    C      3.4    34.6    +      -       -      +
      6F    C      4.7     1.3    -      -       -      -
----------------------------------------------------------
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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