Contacts of the strand formed by residues 113 - 118 (chain F) 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 F).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     78F  LEU*     3.8    23.8    -      -       +      -
     79F  THR      3.6     7.0    -      -       -      +
     80F  ASN*     5.2     0.4    -      -       -      +
     81F  ASN*     4.1     1.7    -      -       -      +
    107F  SER*     3.3     2.8    -      -       -      -
    108F  ASP*     2.7    37.0    +      -       +      +
    111F  SER*     3.5     7.8    +      -       -      +
    112F  ASP*     1.3    80.1    -      -       -      +
    114F  ALA*     1.3    61.3    +      -       -      +
    201F  ILE*     5.3     4.7    -      -       +      -
    219F  ILE*     3.5    40.6    -      -       +      -
    224F  ALA*     3.7    23.1    -      -       +      +
    227F  LEU*     3.8    30.3    -      -       +      -
    228F  ALA      4.8     0.7    -      -       -      +
    231F  LEU*     4.2    13.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 114 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     77F  VAL      3.9     0.2    -      -       -      +
     78F  LEU*     3.6     7.6    -      -       -      +
     79F  THR*     2.9    40.1    +      -       +      +
     80F  ASN      3.9    19.7    -      -       -      +
     81F  ASN*     3.9     9.0    -      -       -      -
     84F  ILE*     3.9    15.9    -      -       +      -
    104F  LEU*     4.1     4.0    -      -       +      -
    106F  GLY      3.5     5.6    -      -       -      +
    107F  SER*     4.0     7.4    -      -       -      +
    113F  ILE*     1.3    77.7    -      -       -      +
    115F  LEU*     1.3    60.7    +      -       -      +
    116F  LEU      4.3     0.2    -      -       -      -
    231F  LEU*     4.7     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 115 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     70F  ILE*     4.3     7.6    -      -       +      -
     76F  TYR*     4.2    23.6    -      -       +      -
     77F  VAL      3.5    18.6    -      -       -      +
     78F  LEU*     4.4     6.5    -      -       +      +
    104F  LEU*     3.5     4.0    -      -       -      +
    105F  ILE*     2.8    54.2    +      -       +      -
    106F  GLY      2.8    13.8    +      -       -      +
    114F  ALA*     1.3    74.8    -      -       -      +
    116F  LEU*     1.3    60.5    +      -       -      +
    228F  ALA*     4.2    24.2    -      -       +      +
    231F  LEU*     3.9    16.8    -      -       +      +
    232F  ILE*     3.4    31.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 116 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29F  VAL*     4.3     3.8    -      -       +      -
     76F  TYR*     3.4     8.0    -      -       -      -
     77F  VAL*     2.8    50.4    +      -       +      +
     79F  THR*     4.0    15.7    -      -       +      -
     84F  ILE*     3.7    41.1    -      -       +      -
     90F  ILE*     3.9    12.6    -      -       +      -
     92F  ILE*     3.9    25.6    -      -       +      -
    102F  ALA*     4.4     7.9    -      -       +      -
    103F  LYS      3.3     5.8    -      -       -      +
    104F  LEU*     3.8    26.9    -      -       +      -
    105F  ILE*     4.1     3.4    -      -       -      -
    115F  LEU*     1.3    75.2    -      -       -      +
    117F  GLN*     1.3    59.9    +      -       -      +
    118F  ILE      4.2     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLN 117 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     74F  LYS*     2.9    36.5    +      -       -      +
     75F  GLY      3.5     2.2    -      -       -      -
     76F  TYR*     3.5    25.3    +      -       +      -
    102F  ALA*     3.3     3.2    -      -       -      -
    103F  LYS      2.9    33.5    +      -       -      +
    105F  ILE*     3.5    30.4    -      -       +      +
    116F  LEU*     1.3    73.7    -      -       -      +
    118F  ILE*     1.3    65.6    +      -       -      +
    119F  GLN*     3.1    17.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 118 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     69F  ILE*     4.7     6.1    -      -       +      -
     75F  GLY*     2.8    20.2    +      -       -      +
     77F  VAL*     3.6    27.1    -      -       +      -
     92F  ILE*     4.0    29.2    -      -       +      -
     94F  LEU*     5.2     0.2    -      -       +      -
    100F  PHE*     3.5    36.3    -      -       +      -
    101F  ASP      3.5     5.4    -      -       -      +
    102F  ALA*     4.4     2.2    -      -       +      +
    117F  GLN*     1.3    81.0    -      -       -      +
    119F  GLN*     1.3    62.1    +      -       -      +
    121F  PRO*     3.3    31.4    -      -       +      +
    124F  LEU*     3.7    28.0    -      -       +      -
----------------------------------------------------------
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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