Contacts of the strand formed by residues 334 - 339 (chain G) in PDB entry 5U07


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 ILE 334 (chain G).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    287G  ALA*     3.5     1.6    -      -       -      -
    288G  VAL*     2.9    44.5    +      -       +      +
    290G  PHE*     3.4    36.1    -      -       +      -
    332G  ASP      4.1     5.6    -      -       -      +
    333G  ALA*     1.3    69.4    -      -       -      +
    335G  ARG*     1.3    69.9    +      -       -      +
    353G  TYR*     6.0     1.6    -      -       -      +
    363G  MET*     3.9    13.4    -      -       +      +
    366G  ALA*     4.9    25.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 335 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    285G  HIS*     4.1    15.7    +      -       -      +
    286G  ILE      3.7     4.7    -      -       -      -
    287G  ALA*     4.2    10.8    -      -       +      +
    296G  PHE*     6.1     2.6    -      -       -      -
    322G  ALA*     5.4     6.2    +      -       -      +
    326G  ARG*     2.9    59.6    -      -       -      +
    331G  ASP*     3.0    38.5    +      -       -      -
    333G  ALA*     3.2    27.2    +      -       +      +
    334G  ILE*     1.3    77.0    -      -       -      +
    336G  GLY*     1.3    59.3    +      -       -      +
    348G  ALA      3.9    16.0    +      -       -      -
    349G  LEU      4.0     8.3    -      -       -      +
    350G  GLY*     4.1     8.9    -      -       -      +
    351G  GLU*     4.1    11.6    +      -       -      +
    353G  TYR*     5.0     0.5    -      -       -      -
    363G  MET*     3.0    16.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 336 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    285G  HIS*     3.5     4.4    +      -       -      -
    286G  ILE      2.8    31.3    +      -       -      +
    335G  ARG*     1.3    79.1    -      -       -      +
    337G  TYR*     1.3    60.0    +      -       -      -
    349G  LEU      3.3     8.9    +      -       -      -
    351G  GLU      3.4    14.6    -      -       -      -
    353G  TYR*     4.5     0.4    -      -       -      -
    359G  LEU*     4.0     7.5    -      -       -      +
    363G  MET*     3.3    11.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 337 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    283G  LEU*     5.3     0.4    -      -       +      -
    284G  VAL      3.1    13.9    -      -       -      +
    285G  HIS*     4.1     4.5    -      -       -      -
    336G  GLY*     1.3    74.2    -      -       -      +
    338G  ALA*     1.3    61.2    +      -       -      +
    339G  THR*     3.1    28.0    -      -       -      -
    345G  ASP*     2.2    34.4    +      -       -      -
    346G  LEU*     3.5    25.3    +      -       +      -
    349G  LEU*     3.2    38.4    -      -       +      -
    350G  GLY      3.4    20.4    -      -       -      -
    351G  GLU      3.4     2.8    +      -       -      -
    352G  ARG*     3.3    45.7    +      -       +      +
    353G  TYR*     2.9    27.2    +      -       -      +
    359G  LEU*     4.0     7.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 338 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    328F  VAL*     5.2     1.3    -      -       +      -
    283G  LEU*     3.7     0.2    -      -       -      -
    284G  VAL      2.9    30.3    +      -       -      -
    337G  TYR*     1.3    75.8    -      -       -      +
    339G  THR*     1.3    62.8    +      -       -      +
    352G  ARG*     5.0     0.4    -      -       -      -
    353G  TYR      3.5    19.5    -      -       -      +
    354G  ASP      5.0     1.1    -      -       -      +
    355G  SER*     4.3     9.6    -      -       -      +
    356G  TYR*     3.5    34.3    -      -       +      -
    359G  LEU*     3.9    12.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with THR 339 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    324F  ARG*     3.6     4.2    +      -       -      -
    328F  VAL*     3.9    13.6    -      -       -      +
    282G  ASP      3.6    10.8    -      -       -      +
    283G  LEU*     3.4    15.5    -      -       +      +
    337G  TYR*     3.1    30.6    -      -       -      -
    338G  ALA*     1.3    74.8    +      -       -      +
    340G  VAL*     1.3    64.3    +      -       -      +
    341G  GLU*     3.1    47.3    -      -       +      +
    346G  LEU*     3.9     4.1    -      -       +      +
    352G  ARG*     3.2    25.4    +      -       -      +
    353G  TYR      4.9     0.6    +      -       -      -
    354G  ASP      5.6     0.2    -      -       -      +
    356G  TYR*     5.0     1.1    -      -       -      -
----------------------------------------------------------
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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