Contacts of the strand formed by residues 202 - 206 (chain B) in PDB entry 6DU3


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 VAL 202 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     91B  ILE*     4.0     0.6    -      -       -      +
     92B  CYS*     3.3    13.2    -      -       +      +
     94B  VAL*     5.2     0.4    -      -       +      -
    192B  LEU*     4.3    13.0    -      -       +      -
    195B  LEU*     4.1    20.6    -      -       +      -
    197B  ARG*     3.6    25.4    -      -       +      -
    198B  ASP      3.4    15.3    -      -       -      +
    199B  LEU*     3.3    30.9    +      -       +      +
    200B  ARG      3.6     0.8    -      -       -      -
    201B  ARG*     1.3    82.6    -      -       -      +
    203B  LEU*     1.3    73.5    +      -       -      +
    218B  ASN*     2.7    26.6    +      -       -      +
    250B  VAL*     3.5     9.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 203 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     91B  ILE*     4.1     9.8    -      -       +      +
     92B  CYS      3.0     7.9    +      -       -      +
     93B  VAL*     3.9    28.3    -      -       +      -
     94B  VAL*     2.8    26.5    +      -       -      +
    146B  PHE*     4.4     2.7    -      -       +      -
    202B  VAL*     1.3    82.3    -      -       -      +
    204B  ILE*     1.3    61.5    +      -       -      +
    218B  ASN*     3.3     6.3    -      -       -      +
    220B  VAL*     4.2     8.3    -      -       +      -
    241B  PHE*     4.0    18.8    -      -       +      -
    244B  LEU*     3.5    42.4    -      -       +      -
    250B  VAL*     3.5    26.9    -      -       +      -
    254B  LEU*     3.7    15.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 204 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     93B  VAL*     5.2     0.7    -      -       -      -
     94B  VAL*     3.3    21.1    -      -       +      +
    190B  LYS*     4.0    34.5    -      -       +      -
    192B  LEU*     3.9    23.3    -      -       +      -
    203B  LEU*     1.3    75.7    -      -       -      +
    205B  LEU*     1.3    60.8    +      -       -      +
    206B  ASP*     3.9    20.9    +      -       +      +
    211B  SER      4.8     0.2    -      -       -      +
    212B  TYR*     3.9    25.1    -      -       +      -
    215B  HIS      4.9     0.4    -      -       -      +
    218B  ASN*     2.9    20.1    +      -       +      +
    219B  ALA*     3.4    17.7    -      -       +      +
    220B  VAL*     2.8    30.9    +      -       -      +
    241B  PHE*     6.2     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 205 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     93B  VAL*     4.9     2.5    -      -       +      -
     94B  VAL      2.8    13.1    +      -       -      +
     95B  ILE*     3.6    12.0    -      -       +      -
     96B  ASN*     3.0    26.3    +      -       -      +
    100B  THR*     4.1    16.2    -      -       +      +
    138B  PHE*     3.5    36.8    -      -       +      -
    204B  ILE*     1.3    72.3    -      -       -      +
    206B  ASP*     1.3    61.3    +      -       -      +
    220B  VAL*     3.2    23.6    -      -       +      +
    222B  VAL*     3.6    24.9    -      -       +      -
    234B  LEU*     4.7     6.3    -      -       +      -
    237B  LEU*     3.9    15.0    -      -       +      -
    241B  PHE*     3.9    21.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 206 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     96B  ASN*     3.4    16.6    -      -       +      +
    100B  THR*     3.9     1.6    -      -       -      -
    190B  LYS*     2.8    36.2    +      -       -      +
    204B  ILE*     3.9    16.0    +      -       +      -
    205B  LEU*     1.3    78.7    -      -       -      +
    207B  ASN*     1.3    86.8    +      -       -      +
    208B  SER*     2.9    18.5    +      -       -      +
    211B  SER*     3.1    16.2    +      -       -      -
    212B  TYR*     3.6    24.1    +      -       +      -
    220B  VAL      4.2     2.0    +      -       -      -
    221B  PRO*     4.6     1.4    -      -       -      +
    222B  VAL*     3.9    15.6    +      -       -      +
    301B   MG      4.1     0.3    -      -       -      -
    861D  SEP      4.8     0.2    +      -       -      -
----------------------------------------------------------
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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