Contacts of the strand formed by residues 334 - 339 (chain E) 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 E).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    286E  ILE      4.3     0.3    -      -       -      +
    287E  ALA*     3.4     1.2    -      -       -      -
    288E  VAL*     2.8    47.5    +      -       +      +
    290E  PHE*     3.5    34.3    -      -       +      -
    332E  ASP      4.0     5.4    -      -       -      +
    333E  ALA*     1.3    68.9    -      -       -      +
    335E  ARG*     1.3    68.2    +      -       -      +
    351E  GLU*     5.4     2.2    -      -       +      +
    363E  MET*     4.3    15.3    -      -       +      +
    366E  ALA*     4.7    26.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 335 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    285E  HIS*     3.6    25.8    -      -       +      +
    286E  ILE      3.7     5.4    -      -       -      -
    287E  ALA*     4.2     7.1    -      -       +      +
    289E  ARG*     3.3    26.7    -      -       -      +
    326E  ARG*     4.0    43.7    -      -       -      +
    329E  TRP      4.9     0.4    +      -       -      -
    331E  ASP*     3.6    18.8    +      -       -      +
    332E  ASP      4.3     0.2    -      -       -      -
    333E  ALA*     2.7    53.3    +      -       -      +
    334E  ILE*     1.3    76.3    -      -       -      +
    336E  GLY*     1.3    59.0    +      -       -      +
    348E  ALA      4.8     9.2    -      -       -      +
    349E  LEU      3.8    11.9    -      -       -      +
    350E  GLY*     4.2     6.9    -      -       -      -
    351E  GLU*     4.2    11.4    +      -       -      +
    363E  MET*     2.9    18.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 336 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    285E  HIS*     3.3     5.1    +      -       -      -
    286E  ILE      2.8    31.8    +      -       -      +
    335E  ARG*     1.3    80.5    -      -       -      +
    337E  TYR*     1.3    61.0    +      -       -      -
    349E  LEU      3.2     9.3    +      -       -      -
    351E  GLU      3.6     9.0    -      -       -      -
    359E  LEU*     3.9     7.1    -      -       -      +
    363E  MET*     3.4    15.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 337 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    283E  LEU*     5.1     0.9    -      -       +      -
    284E  VAL      3.0    14.8    -      -       -      +
    285E  HIS*     4.1     4.7    -      -       +      -
    336E  GLY*     1.3    74.6    -      -       -      +
    338E  ALA*     1.3    61.2    -      -       -      +
    339E  THR*     3.3    27.1    -      -       -      +
    344E  THR      5.9     0.2    -      -       -      -
    345E  ASP*     2.3    35.3    +      -       -      -
    346E  LEU*     3.6    21.8    -      -       +      -
    349E  LEU*     3.3    37.2    -      -       +      -
    350E  GLY      3.3    21.1    -      -       -      -
    351E  GLU      3.6     2.2    +      -       -      -
    352E  ARG*     3.4    46.3    +      -       +      +
    353E  TYR*     3.0    27.2    +      -       -      +
    359E  LEU*     3.9     6.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 338 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    283E  LEU*     3.8     0.5    -      -       -      -
    284E  VAL      2.9    30.0    +      -       -      -
    337E  TYR*     1.3    76.0    -      -       -      +
    339E  THR*     1.3    62.3    +      -       -      +
    352E  ARG*     5.0     0.7    -      -       -      -
    353E  TYR      3.4    18.4    -      -       -      +
    354E  ASP      4.8     1.3    -      -       -      +
    355E  SER*     4.2    12.8    -      -       -      +
    356E  TYR*     3.5    34.9    -      -       +      -
    359E  LEU*     3.9     9.8    -      -       +      +
    328I  VAL*     5.2     0.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 339 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    282E  ASP      3.3    13.7    -      -       -      +
    283E  LEU*     3.6    16.5    -      -       +      +
    337E  TYR*     3.3    24.1    -      -       -      -
    338E  ALA*     1.3    77.5    +      -       -      +
    340E  VAL*     1.3    65.6    +      -       -      +
    341E  GLU*     3.0    46.9    -      -       +      +
    346E  LEU*     4.3     2.8    -      -       +      +
    352E  ARG*     3.1    14.9    +      -       -      +
    353E  TYR      4.7     0.6    +      -       -      -
    354E  ASP      5.2     1.8    +      -       -      +
    356E  TYR*     5.0     1.3    -      -       -      -
    324I  ARG*     3.1    18.9    +      -       -      -
    328I  VAL*     3.9     8.7    -      -       -      +
----------------------------------------------------------
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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