Contacts of the strand formed by residues 6 - 11 (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 LYS 6 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    227C  TYR      5.3     4.4    +      -       -      -
    228C  GLY*     5.5     1.2    -      -       -      -
    229C  ASP*     3.2    39.5    +      -       -      +
    241C  TRP*     6.2     1.2    -      -       -      -
      5D  PRO*     1.3    70.7    -      -       -      +
      7D  ILE*     1.3    62.0    +      -       -      +
      8D  GLN*     3.6    27.8    +      -       -      +
     26D  TYR      3.2    15.8    -      -       -      +
     27D  VAL*     3.7     0.6    -      -       -      -
     28D  SER*     2.8    34.1    +      -       -      +
     29D  GLY      4.8     0.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 7 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4D  THR*     5.7     1.3    -      -       +      -
      5D  PRO*     3.7    28.7    -      -       +      +
      6D  LYS*     1.3    75.8    -      -       -      +
      8D  GLN*     1.4    67.6    +      -       -      +
      9D  VAL*     4.4     1.1    -      -       +      -
     25D  CYS*     3.8    26.2    -      -       -      -
     26D  TYR      4.0     2.0    -      -       -      -
     27D  VAL*     4.5     9.0    -      -       +      +
     80D  CYS*     4.4     1.6    -      -       +      -
     82D  VAL*     3.6    33.7    -      -       +      -
     87D  LEU*     5.5     3.1    -      -       +      -
     91D  LYS*     4.7    16.6    -      -       +      -
     93D  VAL*     3.6    39.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLN 8 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    229C  ASP*     3.8    21.1    -      -       -      +
    231C  LEU*     3.7    28.4    -      -       +      +
    241C  TRP*     5.0    12.5    -      -       -      +
      6D  LYS*     3.6    41.3    -      -       +      +
      7D  ILE*     1.4    78.7    -      -       -      +
      9D  VAL*     1.3    62.2    +      -       -      +
     10D  TYR*     3.5    19.2    -      -       +      -
     25D  CYS*     3.5     1.3    -      -       -      -
     26D  TYR*     3.0    38.4    +      -       +      +
     28D  SER*     4.3     4.5    +      -       -      -
     93D  VAL*     5.4     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 9 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7D  ILE*     4.5     0.7    -      -       +      -
      8D  GLN*     1.3    74.6    -      -       -      +
     10D  TYR*     1.3    66.5    +      -       -      +
     23D  LEU*     4.0    16.8    -      -       +      -
     24D  ASN      3.4    10.1    -      -       -      +
     25D  CYS*     4.0     5.2    -      -       +      -
     39D  LEU*     5.5     0.4    -      -       +      -
     79D  ALA      5.0     2.2    -      -       -      -
     80D  CYS*     3.4    25.6    -      -       +      -
     93D  VAL*     3.3    38.3    -      -       +      +
     94D  LYS      4.5     2.4    -      -       -      +
     95D  TRP*     3.7    38.5    -      -       +      +
     96D  ASP      5.0     1.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 10 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    231C  LEU*     3.4    36.1    -      -       +      +
    232C  PRO*     2.7    29.6    +      -       -      +
    239C  GLN*     3.5    34.8    -      -       -      +
      8D  GLN*     3.5    25.6    -      -       +      -
      9D  VAL*     1.3    75.5    -      -       -      +
     11D  SER*     1.4    54.7    +      -       -      +
     23D  LEU*     3.7     5.5    -      -       -      +
     24D  ASN*     2.8    63.1    +      -       +      +
     26D  TYR*     3.6    21.4    -      -       +      +
     65D  LEU*     4.1     3.3    -      -       -      +
     95D  TRP*     3.7    15.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER 11 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    239C  GLN*     3.6    18.9    +      -       -      +
     10D  TYR*     1.4    76.0    -      -       -      +
     12D  ARG*     1.3    64.0    +      -       -      +
     13D  HIS      2.8    24.5    +      -       -      +
     14D  PRO*     4.3     1.2    -      -       -      +
     15D  ALA*     3.9     9.3    +      -       -      +
     21D  ASN*     3.4    11.0    -      -       -      -
     22D  PHE      3.3     8.5    -      -       -      -
     23D  LEU*     4.7     0.2    -      -       -      +
     24D  ASN*     3.9     3.1    -      -       -      -
     70D  PHE*     4.5     6.1    -      -       -      -
     95D  TRP*     3.8    27.0    +      -       -      +
----------------------------------------------------------
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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