Contacts of the strand formed by residues 67 - 71 (chain B) in PDB entry 3SDI


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 67 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     48B  LEU*     4.1    16.6    -      -       +      +
     50B  ALA*     4.4    14.8    -      -       +      -
     64B  THR*     3.3    20.4    -      -       -      +
     66B  LYS*     1.3    87.8    -      -       -      +
     68B  TYR*     1.3    63.4    +      -       -      +
     69B  LYS      4.4     0.2    +      -       -      -
     75B  ALA*     6.4     0.9    -      -       +      -
     76B  VAL      3.4     3.4    -      -       -      +
     77B  ALA*     3.6    23.6    -      -       +      +
    211B  GLU*     3.3    19.8    +      -       +      +
    212B  PHE*     3.5    45.1    -      -       -      +
    213B  ALA*     3.7    15.0    -      -       +      +
    223B  ILE*     4.7    20.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 68 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     64B  THR*     2.8    38.8    +      -       +      -
     65B  GLU*     3.6    22.5    -      -       -      -
     66B  LYS      4.0     0.7    -      -       -      -
     67B  LEU*     1.3    75.5    -      -       -      +
     69B  LYS*     1.3    63.5    +      -       -      +
     70B  LEU*     3.5     0.7    +      -       +      -
     75B  ALA*     3.3     6.2    -      -       -      +
     76B  VAL*     3.0    39.3    +      -       +      +
     78B  VAL*     3.8    19.3    -      -       +      -
     82B  THR*     3.4    19.2    -      -       +      +
     85B  ALA*     5.6     1.1    -      -       +      -
     86B  GLU*     3.2    32.3    +      -       +      -
     89B  ILE*     3.4    36.1    -      -       +      -
     93B  ARG*     4.2    18.2    -      -       -      +
    223B  ILE*     5.3     1.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 69 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     67B  LEU      4.4     0.4    +      -       -      -
     68B  TYR*     1.3    70.8    -      -       -      +
     70B  LEU*     1.3    62.5    +      -       -      +
     71B  ASN      3.4    16.4    -      -       -      +
     72B  ASP*     5.0     7.9    -      -       -      +
     74B  ILE      4.1     2.5    -      -       -      -
     75B  ALA*     4.5     1.3    -      -       -      -
     93B  ARG*     2.8    34.9    +      -       -      +
    221B  GLN*     3.0    39.6    +      -       -      +
    223B  ILE*     3.8    28.3    -      -       +      +
     68I  LEU*     3.9    23.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 70 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     68B  TYR*     3.5     1.0    +      -       +      -
     69B  LYS*     1.3    75.7    -      -       -      +
     71B  ASN*     1.3    64.4    +      -       +      +
     74B  ILE*     2.9    29.4    +      -       +      +
     76B  VAL*     3.8    34.5    -      -       +      +
     89B  ILE*     4.1    45.5    -      -       +      +
     92B  ALA*     4.1    11.4    -      -       +      -
     93B  ARG*     3.4    27.0    -      -       +      +
     96B  ALA*     4.5     3.3    -      -       -      +
     97B  GLN*     5.7     0.2    -      -       -      +
    112B  LEU*     3.6    36.6    -      -       +      -
    116B  LEU*     5.0     1.1    -      -       +      -
    138B  TYR*     4.4     2.7    -      -       +      -
     68I  LEU*     3.7     6.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASN 71 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     69B  LYS*     3.4    12.6    -      -       -      +
     70B  LEU*     1.3    81.7    -      -       +      +
     72B  ASP*     1.3    84.3    +      -       -      +
     73B  LYS*     3.1    18.3    +      -       -      +
     74B  ILE*     3.2    28.5    +      -       +      +
     96B  ALA*     4.5    16.6    -      -       +      -
     97B  GLN*     5.3     8.2    +      -       -      +
    106B  ASP*     4.8    17.3    +      -       -      +
    107B  ILE*     4.9     6.1    -      -       -      +
    112B  LEU*     5.5     0.2    -      -       +      -
    221B  GLN*     2.9    22.2    +      -       -      -
     68I  LEU*     4.3    13.2    -      -       +      +
----------------------------------------------------------
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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