Contacts of the strand formed by residues 113 - 118 (chain A) 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 A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     78A  LEU*     3.8    23.1    -      -       +      -
     79A  THR      3.7     7.6    -      -       -      +
     80A  ASN*     5.1     0.4    -      -       -      +
     81A  ASN*     4.1     1.5    -      -       -      +
    107A  SER*     3.3     2.1    -      -       -      -
    108A  ASP*     2.7    37.0    +      -       +      +
    111A  SER*     3.9     8.7    +      -       -      +
    112A  ASP*     1.3    81.8    -      -       -      +
    114A  ALA*     1.3    60.7    +      -       -      +
    201A  ILE*     5.2     3.8    -      -       +      -
    219A  ILE*     3.5    39.7    -      -       +      -
    224A  ALA*     3.7    23.1    -      -       +      +
    227A  LEU*     3.8    30.7    -      -       +      -
    228A  ALA      4.7     0.9    -      -       -      +
    231A  LEU*     4.2    12.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 114 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     78A  LEU*     3.6     7.6    -      -       -      +
     79A  THR*     3.0    49.5    +      -       +      +
     81A  ASN*     3.9    11.0    -      -       -      +
     84A  ILE*     3.8    24.5    -      -       +      -
    104A  LEU*     4.2     3.4    -      -       +      -
    106A  GLY      3.5     6.5    -      -       -      +
    107A  SER*     4.0     7.2    -      -       -      +
    113A  ILE*     1.3    77.8    -      -       -      +
    115A  LEU*     1.3    60.8    +      -       -      +
    231A  LEU*     4.7     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 115 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     70A  ILE*     4.3     8.7    -      -       +      -
     76A  TYR*     4.2    22.7    -      -       +      -
     77A  VAL      3.6    18.4    -      -       -      +
     78A  LEU*     4.4     5.4    -      -       +      +
    104A  LEU*     3.5     4.0    -      -       -      +
    105A  ILE*     2.8    53.4    +      -       +      -
    106A  GLY      2.8    13.8    +      -       -      +
    114A  ALA*     1.3    74.3    -      -       -      +
    116A  LEU*     1.3    60.8    +      -       -      +
    228A  ALA*     4.2    25.6    -      -       +      +
    231A  LEU*     3.9    17.7    -      -       +      +
    232A  ILE*     3.4    30.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 116 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29A  VAL*     4.3     4.3    -      -       +      -
     75A  GLY      4.2     0.2    -      -       -      -
     76A  TYR*     3.3     9.7    -      -       -      -
     77A  VAL*     2.8    49.9    +      -       +      +
     79A  THR*     3.8    22.7    -      -       +      -
     84A  ILE*     3.7    31.6    -      -       +      -
     90A  ILE*     3.8    20.2    -      -       +      -
     92A  ILE*     3.8    26.9    -      -       +      -
    102A  ALA*     4.4     6.7    -      -       +      -
    103A  LYS      3.4    10.3    -      -       -      +
    104A  LEU*     4.2    10.5    -      -       +      -
    105A  ILE*     4.1     3.4    -      -       -      -
    115A  LEU*     1.3    77.5    -      -       -      +
    117A  GLN*     1.3    61.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 117 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     74A  LYS*     2.9    37.1    +      -       -      +
     75A  GLY      3.3     1.8    -      -       -      -
     76A  TYR*     3.5    25.1    +      -       +      -
    102A  ALA*     3.3     3.6    -      -       -      -
    103A  LYS      2.9    32.1    +      -       -      +
    105A  ILE*     3.5    29.7    -      -       +      +
    116A  LEU*     1.3    74.1    -      -       -      +
    118A  ILE*     1.3    66.2    +      -       -      +
    119A  GLN*     3.1    17.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 118 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     69A  ILE*     4.4     7.2    -      -       +      -
     74A  LYS      4.2     0.2    -      -       -      +
     75A  GLY*     2.7    19.1    +      -       -      +
     77A  VAL*     3.6    28.3    -      -       +      -
     92A  ILE*     4.0    28.3    -      -       +      -
     94A  LEU*     5.2     0.2    -      -       +      -
    100A  PHE*     3.5    36.6    -      -       +      -
    101A  ASP      3.5     5.2    -      -       -      +
    102A  ALA*     4.4     2.2    -      -       +      +
    116A  LEU      4.2     0.2    -      -       -      -
    117A  GLN*     1.3    81.7    -      -       -      +
    119A  GLN*     1.3    61.8    +      -       -      +
    121A  PRO*     3.3    33.3    -      -       +      +
    124A  LEU*     3.7    27.1    -      -       +      -
----------------------------------------------------------
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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