Contacts of the strand formed by residues 4 - 12 (chain C) 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 SER 4 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      2C  THR      4.9     0.9    -      -       -      -
      3C  HIS*     1.4    76.5    -      -       -      +
      5C  LEU*     1.4    58.0    +      -       -      +
      6C  ARG*     3.8    24.0    +      -       -      -
     27C  TYR      3.6     0.3    -      -       -      +
     28C  VAL*     3.3     4.5    -      -       -      +
     29C  ASP*     2.7    49.7    +      -       -      -
     98C  CYS      3.3    13.9    -      -       -      -
     99C  GLU*     3.6    18.8    -      -       -      +
    165C  LEU*     3.6     7.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 5 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4C  SER*     1.4    71.3    -      -       -      +
      6C  ARG*     1.4    68.1    +      -       -      +
      7C  TYR*     3.9    32.8    -      -       +      -
     27C  TYR      3.4    12.3    -      -       -      +
     28C  VAL*     3.8    14.8    -      -       +      -
     33C  ILE*     5.3     1.8    -      -       +      -
     97C  GLY*     2.9    24.1    -      -       -      -
     98C  CYS      2.9    14.3    +      -       -      +
    156C  TRP*     4.7     2.5    -      -       +      -
    161C  CYS*     3.8    31.0    -      -       -      +
    164C  TRP*     4.0     6.7    -      -       +      -
    165C  LEU*     3.7    27.8    -      -       +      +
    168C  PHE*     4.0    23.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 6 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4C  SER*     3.8    18.7    +      -       -      +
      5C  LEU*     1.4    81.8    -      -       -      +
      7C  TYR*     1.4    63.9    +      -       -      +
      8C  PHE*     4.4    19.3    -      -       +      -
     25C  VAL      4.2     0.3    -      -       -      +
     26C  GLY*     3.2     1.9    -      -       -      -
     27C  TYR*     2.8    45.4    +      -       +      +
     29C  ASP      5.4     7.2    -      -       -      -
     95C  MET*     3.7    20.0    -      -       +      +
     96C  ILE      3.4     9.4    -      -       -      +
     97C  GLY*     4.1     0.9    -      -       -      -
     98C  CYS      5.1     0.2    -      -       -      +
     99C  GLU*     3.6    22.6    +      -       -      -
    109C  PHE*     3.4    37.3    -      -       +      -
     58D  LYS*     4.8    13.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 7 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5C  LEU*     3.9    20.8    -      -       +      +
      6C  ARG*     1.4    73.2    -      -       -      +
      8C  PHE*     1.3    63.4    +      -       -      +
      9C  ARG*     5.8     0.2    -      -       -      +
     24C  SER*     5.2     2.7    -      -       -      +
     25C  VAL      3.5     4.0    -      -       -      -
     26C  GLY*     3.5    19.3    -      -       -      -
     33C  ILE*     4.7     4.0    -      -       +      +
     34C  THR*     3.7    15.8    -      -       -      +
     43C  LYS*     4.0     1.6    +      -       -      -
     58C  HIS*     5.6     2.9    +      -       -      -
     94C  ARG*     4.7     1.9    +      -       -      -
     95C  MET*     3.6     2.4    -      -       -      -
     96C  ILE*     3.2    55.1    +      -       +      +
    156C  TRP*     4.0    22.2    -      +       -      -
    164C  TRP*     5.8     1.7    -      -       -      +
    168C  PHE*     3.6    27.4    -      -       -      -
    301C  6FP      3.5    56.9    -      +       +      +
----------------------------------------------------------
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Residues in contact with PHE 8 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6C  ARG*     4.4    17.3    -      -       +      -
      7C  TYR*     1.3    74.2    -      -       -      +
      9C  ARG*     1.3    64.1    +      -       -      +
     23C  ILE      4.5     0.2    -      -       -      -
     24C  SER*     2.8    34.1    +      -       -      -
     25C  VAL*     2.9    22.4    +      -       +      -
     27C  TYR*     3.3    35.7    -      +       -      -
     93C  GLN*     6.3     0.9    -      -       +      -
     94C  ARG*     3.2    11.0    -      -       -      +
     95C  MET*     3.3    44.0    -      -       +      -
     55D  SER*     4.0     5.2    -      -       -      -
     56D  PHE*     3.4    36.8    -      -       +      -
     57D  SER      5.3     3.1    -      -       -      -
     60D  TRP*     6.0     1.6    -      +       +      -
----------------------------------------------------------
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Residues in contact with ARG 9 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7C  TYR      5.8     0.2    -      -       -      +
      8C  PHE*     1.3    81.4    -      -       -      +
     10C  LEU*     1.3    59.7    +      -       -      +
     22C  PHE*     4.0    24.5    -      -       +      -
     23C  ILE      3.4     6.1    -      -       -      -
     24C  SER*     4.1     6.1    -      -       -      +
     66C  LEU*     5.4     0.4    -      -       -      +
     69C  TRP*     3.1    58.0    +      -       -      +
     72C  MET*     6.1     1.8    -      -       -      +
     73C  PHE*     3.8    29.3    -      -       +      -
     93C  GLN*     3.3     7.4    -      -       -      +
     94C  ARG*     3.1    80.9    +      -       +      +
    112C  TYR*     5.2     3.2    +      -       -      -
    149C  GLU*     5.5     3.6    +      -       -      -
    153C  GLN*     5.3     0.2    +      -       -      -
    301C  6FP      3.4    15.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 10 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      9C  ARG*     1.3    75.4    -      -       -      +
     11C  GLY*     1.3    64.8    +      -       -      +
     12C  VAL*     4.0    13.0    -      -       +      -
     21C  GLU      4.2     0.4    -      -       -      -
     22C  PHE*     3.3    10.6    -      -       -      -
     23C  ILE*     2.9    57.5    +      -       +      +
     73C  PHE*     3.8     4.0    -      -       -      -
     91C  THR*     3.9    26.0    -      -       +      -
     92C  TYR      3.4    10.3    -      -       -      +
     93C  GLN*     3.8    18.4    -      -       +      -
     33D  SER*     4.6     8.1    -      -       -      -
     54D  LEU*     4.8    10.1    -      -       +      -
     62D  PHE*     4.0    24.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 11 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10C  LEU*     1.3    74.8    -      -       -      +
     12C  VAL*     1.4    62.3    +      -       -      +
     21C  GLU      3.0    10.3    -      -       -      -
     22C  PHE*     5.1     0.4    -      -       -      -
     73C  PHE*     3.5    14.3    -      -       -      -
     77C  LEU*     3.5    12.6    -      -       -      +
     91C  THR*     3.4     5.0    -      -       -      -
     92C  TYR      2.8    34.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 12 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10C  LEU*     4.0    15.7    -      -       +      -
     11C  GLY*     1.4    78.6    -      -       -      +
     13C  SER*     1.3    68.4    +      -       -      +
     15C  PRO*     4.1    26.3    -      -       +      +
     20C  PRO      4.8     6.7    -      -       -      +
     21C  GLU*     3.1    29.5    +      -       -      +
     23C  ILE*     5.6     0.4    -      -       +      -
     77C  LEU*     4.3     3.8    -      -       -      +
     89C  SER*     3.3    17.5    -      -       -      +
     90C  HIS      3.5     7.0    -      -       -      +
     91C  THR*     3.7    21.5    -      -       +      -
     33D  SER*     4.2    14.4    -      -       -      +
----------------------------------------------------------
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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