Contacts of the strand formed by residues 66 - 69 (chain B) in PDB entry 1SN8


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 GLY 66 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     57B  PHE*     3.3     9.7    -      -       -      -
     58B  VAL      2.7    34.9    +      -       -      -
     60B  TYR*     3.7    10.9    -      -       -      -
     64B  ARG      3.6     2.0    +      -       -      -
     65B  HIS*     1.3    75.1    -      -       -      +
     67B  PHE*     1.3    61.2    +      -       -      -
     68B  LEU      4.0     0.2    +      -       -      -
    114B  ALA      3.3    13.5    -      -       -      -
    116B  LEU*     3.8    15.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 67 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     53B  LEU*     4.2    21.5    -      -       +      -
     55B  ALA*     3.4    29.4    -      -       +      -
     56B  ALA      3.8     1.8    -      -       -      -
     57B  PHE*     3.8    31.2    -      +       +      -
     66B  GLY*     1.3    72.4    -      -       -      -
     68B  LEU*     1.3    57.6    +      -       -      +
     69B  PRO*     3.5    30.4    -      -       +      +
    109B  ARG*     6.3     0.4    -      -       -      -
    113B  GLY*     5.2     4.9    -      -       -      +
    114B  ALA      2.9    15.3    +      -       -      +
    115B  ALA*     3.8    10.3    -      -       +      -
    116B  LEU*     2.8    28.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 68 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     55B  ALA*     3.4     1.7    -      -       -      -
     56B  ALA*     2.8    37.3    +      -       +      +
     58B  VAL*     3.7    27.8    -      -       +      -
     67B  PHE*     1.3    74.4    -      -       -      +
     69B  PRO*     1.3    61.9    -      -       -      +
     70B  LEU      3.9     0.2    +      -       -      -
     72B  GLU*     3.9    25.6    -      -       +      +
     73B  ILE*     3.9    23.1    -      -       +      -
     90B  ILE*     4.5     2.3    -      -       -      +
     94B  LEU*     4.3    11.9    -      -       +      -
    100B  VAL*     4.2    20.6    -      -       +      -
    102B  VAL*     4.5     2.0    -      -       +      -
    116B  LEU*     3.6    23.8    -      -       +      +
    117B  THR*     3.9     9.0    -      -       -      +
    118B  THR*     4.2     9.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with PRO 69 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     53B  LEU      5.4     1.6    -      -       -      +
     54B  GLU      3.6     9.9    -      -       -      +
     55B  ALA*     3.7     4.9    -      -       +      -
     67B  PHE*     3.5    33.0    -      -       +      +
     68B  LEU*     1.3    88.3    -      -       -      +
     70B  LEU*     1.3    65.9    +      -       -      +
     71B  LYS*     3.8    34.3    -      -       +      +
     72B  GLU*     2.9    24.8    +      -       +      +
     73B  ILE*     3.5     7.5    -      -       -      +
    115B  ALA*     6.1     1.3    -      -       +      -
    116B  LEU      3.8    12.1    -      -       -      +
----------------------------------------------------------
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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