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


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
----------------------------------------------------------
     23D  LEU*     3.8    24.9    -      -       +      -
     40D  LEU      3.4    13.9    -      -       -      -
     41D  LYS*     3.6    24.5    -      -       +      +
     46D  ILE*     4.4     7.0    -      -       +      -
     70D  PHE*     3.5    44.3    -      +       +      +
     71D  THR      3.9     8.0    +      -       -      -
     72D  PRO*     4.7     5.8    -      -       +      -
     76D  ASP*     2.7    46.5    +      -       +      -
     77D  GLU*     1.4    73.1    -      -       -      +
     79D  ALA*     1.4    56.4    +      -       -      +
     94D  LYS*     3.3    10.9    -      -       -      +
     95D  TRP*     2.8    52.3    +      +       +      +
----------------------------------------------------------
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Residues in contact with ALA 79 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      9D  VAL*     5.0     3.6    -      -       -      -
     23D  LEU*     4.7     2.0    -      -       -      +
     39D  LEU*     3.8     6.8    -      -       -      +
     40D  LEU*     2.8    42.1    +      -       +      +
     77D  GLU      5.6     0.2    -      -       -      +
     78D  TYR*     1.4    75.6    -      -       -      +
     80D  CYS*     1.4    59.8    +      -       -      +
     92D  ILE*     3.8    20.2    -      -       +      -
     93D  VAL      3.3    13.2    -      -       -      +
     94D  LYS*     3.7    16.8    -      -       +      -
     95D  TRP*     4.1     2.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with CYS 80 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7D  ILE*     4.5     1.3    -      -       +      -
      9D  VAL*     3.4    18.6    -      -       +      -
     25D  CYS*     2.0    50.3    -      -       +      -
     37D  VAL*     4.0    14.1    -      -       -      -
     38D  ASP      3.6    13.0    -      -       -      -
     39D  LEU*     4.2     6.1    -      -       +      -
     79D  ALA*     1.4    73.7    -      -       -      +
     81D  ARG*     1.3    59.8    +      -       -      +
     82D  VAL*     4.0     7.3    +      -       -      +
     91D  LYS      3.4     3.3    -      -       -      +
     92D  ILE*     3.3     3.5    -      -       -      -
     93D  VAL*     2.8    36.9    +      -       -      +
----------------------------------------------------------
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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
----------------------------------------------------------
     37D  VAL*     3.8     1.2    -      -       -      +
     38D  ASP*     3.0    72.3    +      -       +      +
     40D  LEU*     3.9    31.7    -      -       +      +
     43D  GLY      5.0     3.0    +      -       -      -
     45D  ARG*     4.4    12.5    -      -       -      +
     80D  CYS*     1.3    70.4    -      -       -      +
     82D  VAL*     1.3    67.8    +      -       -      +
     83D  ASN*     6.2     0.4    -      -       -      -
     90D  PRO*     3.8    28.3    -      -       +      +
     91D  LYS      3.3     4.5    -      -       -      -
     92D  ILE*     3.8    21.5    -      -       +      +
----------------------------------------------------------
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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
----------------------------------------------------------
      5D  PRO*     4.4     4.0    -      -       +      -
      7D  ILE*     3.6    50.0    -      -       +      -
     27D  VAL*     4.2    10.3    -      -       +      -
     35D  ILE*     3.7    29.2    -      -       +      -
     36D  GLU      3.6     7.2    -      -       -      +
     37D  VAL*     4.2     6.1    -      -       +      -
     80D  CYS*     4.0    12.8    -      -       -      +
     81D  ARG*     1.3    81.2    -      -       -      +
     83D  ASN*     1.3    63.1    +      -       -      +
     87D  LEU*     3.6     7.1    -      -       +      +
     90D  PRO*     3.3     4.6    -      -       -      +
     91D  LYS      2.8    35.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASN 83 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     35D  ILE*     3.7     3.8    -      -       -      +
     36D  GLU*     2.8    46.2    +      -       +      +
     81D  ARG*     5.9     0.9    -      -       -      +
     82D  VAL*     1.3    75.7    -      -       -      +
     84D  HIS*     1.3    71.7    +      -       -      +
     87D  LEU*     3.0    35.4    +      -       -      +
     88D  SER      4.5     2.2    +      -       -      -
     89D  GLN      4.0     1.2    -      -       -      +
     90D  PRO*     3.8    28.6    -      -       +      +
----------------------------------------------------------
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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