Contacts of the strand formed by residues 731 - 738 (chain E) in PDB entry 6C3P


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 GLN 731 (chain E).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    405E  SER*     5.6     0.4    +      -       -      -
    687E  THR*     2.6    55.9    +      -       +      +
    688E  TRP      4.4     8.6    +      -       -      +
    690E  PRO*     5.4     9.4    -      -       +      -
    729E  GLU      3.8     2.4    +      -       -      -
    730E  MET*     1.3    68.2    -      -       -      +
    732E  LYS*     1.3    61.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 732 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    685E  TYR      3.0    16.4    -      -       -      +
    686E  PHE*     3.4    25.6    -      -       +      -
    730E  MET      2.9     6.5    +      -       -      +
    731E  GLN*     1.3    72.2    -      -       -      +
    733E  VAL*     1.3    63.1    +      -       -      +
    734E  SER*     4.1     9.3    -      -       -      +
    735E  GLY      3.6    25.5    +      -       -      +
    736E  ALA*     5.8     0.4    -      -       -      +
    737E  VAL*     4.6    13.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 733 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    685E  TYR*     2.8    20.9    +      -       +      -
    686E  PHE      4.6     1.6    -      -       -      -
    687E  THR*     3.7    31.4    -      -       +      -
    690E  PRO*     6.2     0.4    -      -       +      -
    694E  PRO*     4.3    15.9    -      -       +      -
    731E  GLN      3.5     0.8    +      -       -      -
    732E  LYS*     1.3    76.2    +      -       -      +
    734E  SER*     1.3    63.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 734 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    683E  GLY      4.6     0.5    +      -       -      -
    684E  GLY*     3.7     0.5    -      -       -      -
    685E  TYR*     2.6    59.3    +      -       -      +
    686E  PHE*     4.8     0.7    -      -       -      -
    732E  LYS*     3.3    10.6    -      -       -      +
    733E  VAL*     1.3    84.6    -      -       -      +
    735E  GLY*     1.3    66.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 735 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    681E  ILE*     4.6     1.6    -      -       -      -
    682E  MET      3.5    15.7    -      -       -      -
    683E  GLY      3.6     6.9    +      -       -      -
    684E  GLY*     4.1     5.8    -      -       -      -
    686E  PHE*     6.0     0.2    -      -       -      -
    732E  LYS*     3.6    25.7    +      -       -      +
    734E  SER*     1.3    86.0    +      -       -      +
    736E  ALA*     1.3    60.8    +      -       -      -
    737E  VAL*     4.9     1.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 736 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    680E  GLN      3.6     0.7    -      -       -      +
    681E  ILE*     3.2    24.0    -      -       -      +
    682E  MET*     3.2    19.7    +      -       +      +
    732E  LYS*     5.8     0.2    -      -       -      +
    735E  GLY*     1.3    72.7    -      -       -      -
    737E  VAL*     1.3    62.1    -      -       -      +
    738E  PHE*     4.0    29.2    +      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 737 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    679E  VAL*     4.7     1.6    -      -       +      -
    680E  GLN      3.4     9.9    -      -       -      +
    681E  ILE*     3.6    25.1    -      -       +      -
    686E  PHE*     4.3    17.5    -      -       +      -
    725E  ALA      5.9     1.8    -      -       -      +
    726E  ALA*     5.0     7.0    -      -       -      +
    732E  LYS*     4.6    16.5    -      -       +      +
    735E  GLY      4.9     0.2    -      -       -      -
    736E  ALA*     1.3    77.9    -      -       -      +
    738E  PHE*     1.3    64.2    +      -       -      +
    739E  TRP*     3.2    42.8    +      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 738 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    678E  CYS      5.5     0.7    -      -       -      -
    679E  VAL*     3.2    18.5    -      -       -      -
    680E  GLN*     3.3    38.7    +      -       +      +
    682E  MET*     4.9    18.4    -      -       +      -
    736E  ALA*     4.0    29.4    -      -       +      -
    737E  VAL*     1.3    75.7    -      -       -      +
    739E  TRP*     1.3    70.8    +      -       -      +
    740E  SER      5.2     2.7    -      -       -      +
----------------------------------------------------------
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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