Contacts of the strand formed by residues 113 - 118 (chain B) in PDB entry 3STJ


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 ILE 113 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     78B  LEU*     3.7    24.0    -      -       +      -
     79B  THR      3.6     8.3    -      -       -      +
     80B  ASN*     5.0     0.7    -      -       -      +
     81B  ASN*     4.1     1.3    -      -       -      -
    107B  SER*     3.3     1.7    -      -       -      -
    108B  ASP*     2.7    36.0    +      -       +      +
    111B  SER*     3.6     8.9    +      -       -      +
    112B  ASP*     1.3    81.9    -      -       -      +
    114B  ALA*     1.3    60.6    +      -       -      +
    201B  ILE*     5.1     4.5    -      -       +      -
    219B  ILE*     3.5    41.1    -      -       +      -
    224B  ALA*     3.8    22.4    -      -       +      +
    227B  LEU*     4.0    28.7    -      -       +      -
    228B  ALA      4.9     0.9    -      -       -      +
    231B  LEU*     4.3    11.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 114 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     78B  LEU*     3.7     5.4    -      -       -      +
     79B  THR*     2.9    37.2    +      -       +      +
     80B  ASN      3.8     9.4    -      -       -      +
     81B  ASN*     3.9     2.4    -      -       -      +
     84B  ILE*     3.5    39.3    -      -       +      -
    104B  LEU*     4.1     3.1    -      -       +      -
    106B  GLY      3.5     5.8    -      -       -      +
    107B  SER*     3.8     7.9    -      -       -      +
    113B  ILE*     1.3    78.1    -      -       -      +
    115B  LEU*     1.3    60.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 115 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     70B  ILE*     4.3     7.2    -      -       +      -
     76B  TYR*     4.2    22.7    -      -       +      -
     77B  VAL      3.5    19.3    -      -       -      +
     78B  LEU*     4.4     6.3    -      -       +      +
    104B  LEU*     3.5     4.0    -      -       -      +
    105B  ILE*     2.8    53.3    +      -       +      -
    106B  GLY      2.8    13.5    +      -       -      +
    114B  ALA*     1.3    72.6    -      -       -      +
    116B  LEU*     1.3    60.1    +      -       -      +
    228B  ALA*     4.2    24.7    -      -       +      +
    231B  LEU*     3.9    19.0    -      -       +      +
    232B  ILE*     3.4    31.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 116 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29B  VAL*     4.2     7.4    -      -       +      -
     76B  TYR*     3.4     8.5    -      -       -      -
     77B  VAL*     2.8    48.0    +      -       +      +
     79B  THR*     3.8    23.3    -      -       +      -
     84B  ILE*     3.9    15.9    -      -       +      -
     90B  ILE*     3.9    21.3    -      -       +      -
     92B  ILE*     3.8    25.6    -      -       +      -
    102B  ALA*     4.4     8.3    -      -       +      -
    103B  LYS      3.3     5.8    -      -       -      +
    104B  LEU*     3.8    33.0    -      -       +      -
    105B  ILE*     4.1     3.6    -      -       -      -
    115B  LEU*     1.3    75.1    -      -       -      +
    117B  GLN*     1.3    60.7    +      -       -      +
    118B  ILE      4.2     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLN 117 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     74B  LYS*     2.9    36.3    +      -       -      +
     75B  GLY      3.3     2.5    -      -       -      -
     76B  TYR*     3.6    26.1    +      -       +      -
    102B  ALA*     3.3     3.6    -      -       -      -
    103B  LYS      2.8    33.6    +      -       -      +
    105B  ILE*     3.5    29.1    -      -       +      +
    116B  LEU*     1.3    74.7    -      -       -      +
    118B  ILE*     1.3    64.8    +      -       -      +
    119B  GLN*     3.1    17.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 118 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     69B  ILE*     4.5     7.0    -      -       +      -
     74B  LYS      4.2     0.2    -      -       -      +
     75B  GLY*     2.7    19.1    +      -       -      +
     77B  VAL*     3.7    27.4    -      -       +      -
     92B  ILE*     4.1    30.1    -      -       +      -
     94B  LEU*     5.2     0.4    -      -       +      -
    100B  PHE*     3.5    35.9    -      -       +      -
    101B  ASP      3.5     4.9    -      -       -      +
    102B  ALA*     4.4     2.2    -      -       +      +
    116B  LEU      4.2     0.2    -      -       -      -
    117B  GLN*     1.3    80.6    -      -       -      +
    119B  GLN*     1.3    64.2    +      -       -      +
    120B  ASN      3.5     0.2    +      -       -      -
    121B  PRO*     3.3    33.3    -      -       +      +
    124B  LEU*     3.7    26.7    -      -       +      -
----------------------------------------------------------
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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