Contacts of the strand formed by residues 104 - 108 (chain B) in PDB entry 1DSU


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 LEU 104 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     52B  VAL      3.6     1.4    -      -       -      +
     53B  LEU*     3.4     6.1    -      -       -      +
     54B  SER*     2.9    42.3    +      -       -      +
     55B  ALA      3.7     5.8    -      -       -      +
     56B  ALA*     3.6    22.0    -      -       +      +
     59B  LEU*     3.9    29.6    -      -       +      -
     88B  ALA*     4.0    16.8    -      -       +      -
     89B  VAL      3.8     2.7    -      -       -      -
     90B  PRO*     3.8    30.3    -      -       +      -
    103B  LEU*     1.3    76.3    -      -       -      +
    105B  LEU*     1.3    67.0    +      -       -      +
    106B  LEU*     3.7    32.8    -      -       +      -
    237B  TRP*     4.8     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 105 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     47B  VAL*     4.3    12.3    -      -       +      -
     51B  TRP*     3.9    18.6    -      -       +      -
     52B  VAL      3.5    17.5    -      -       -      +
     53B  LEU*     4.3    12.8    -      -       +      -
     87B  ARG      3.9     0.7    -      -       -      +
     88B  ALA*     3.4     3.1    -      -       -      +
     89B  VAL*     2.7    43.4    +      -       +      +
    104B  LEU*     1.3    74.5    -      -       -      +
    106B  LEU*     1.3    61.0    +      -       -      +
    237B  TRP*     4.0    21.5    -      -       +      -
    238B  ILE*     4.2    15.0    -      -       +      -
    241B  VAL*     3.7    32.3    -      -       +      -
    242B  LEU*     4.0    24.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 106 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33B  VAL*     4.1    35.2    -      -       +      -
     51B  TRP*     3.4     7.8    -      -       -      -
     52B  VAL*     2.9    44.4    +      -       +      +
     54B  SER*     4.8     4.9    -      -       -      -
     59B  LEU*     4.6     8.3    -      -       +      -
     64B  VAL*     4.9     2.7    -      -       +      -
     66B  VAL*     4.6     7.4    -      -       +      -
     85B  VAL*     3.7    31.9    -      -       +      -
     87B  ARG      3.5     1.1    -      -       -      -
     88B  ALA*     3.6    28.3    -      -       +      -
    104B  LEU*     3.7    26.5    -      -       +      -
    105B  LEU*     1.3    72.7    -      -       -      +
    107B  GLN*     1.3    62.1    +      -       -      +
    108B  LEU*     3.8     1.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 107 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     50B  GLN*     3.4    24.8    +      -       +      +
     51B  TRP*     3.7    32.9    +      -       +      -
     85B  VAL*     3.4     4.6    -      -       -      -
     86B  LEU*     2.8    50.3    +      -       +      +
     87B  ARG*     2.9    50.2    +      -       +      +
    106B  LEU*     1.3    71.6    -      -       -      +
    108B  LEU*     1.3    68.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 108 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     46B  LEU*     4.8     2.5    -      -       +      -
     49B  GLU      4.4     5.4    -      -       -      +
     50B  GLN*     2.9    36.5    +      -       -      +
     52B  VAL*     4.0    15.0    -      -       +      -
     66B  VAL*     3.5    37.0    -      -       +      -
     68B  LEU*     3.7    28.7    -      -       +      -
     83B  TYR*     4.0    19.1    -      -       +      -
     84B  ASP      3.5     3.8    -      -       -      +
     85B  VAL*     5.1     0.9    -      -       +      -
     86B  LEU*     3.4     6.8    -      -       -      +
    106B  LEU      4.6     3.1    -      -       -      +
    107B  GLN*     1.3    77.9    -      -       -      +
    109B  SER*     1.3    67.2    +      -       -      +
    110B  GLU      3.0    19.1    -      -       -      +
    112B  ALA*     4.3    11.9    -      -       +      -
----------------------------------------------------------
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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