Contacts of the strand formed by residues 113 - 118 (chain G) 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 G).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     78G  LEU*     3.8    22.2    -      -       +      -
     79G  THR      3.8     8.5    -      -       -      +
     80G  ASN*     5.1     0.2    -      -       -      +
     81G  ASN*     4.1     1.7    -      -       -      +
    107G  SER*     3.3     2.9    -      -       -      -
    108G  ASP*     2.7    36.8    +      -       +      +
    111G  SER*     3.5     9.1    +      -       -      +
    112G  ASP*     1.3    80.9    -      -       -      +
    114G  ALA*     1.3    62.1    +      -       -      +
    201G  ILE*     5.3     4.3    -      -       +      -
    219G  ILE*     3.5    39.9    -      -       +      -
    224G  ALA*     3.7    23.6    -      -       +      +
    227G  LEU*     3.8    31.0    -      -       +      -
    228G  ALA      4.8     0.7    -      -       -      +
    231G  LEU*     4.3    12.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 114 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     78G  LEU*     3.5     9.4    -      -       -      +
     79G  THR*     3.2    38.9    +      -       +      +
     80G  ASN      3.8    20.9    -      -       -      +
     81G  ASN*     3.9     9.8    -      -       -      +
     84G  ILE*     4.0    16.6    -      -       +      -
    104G  LEU*     4.2     3.4    -      -       +      -
    106G  GLY      3.6     6.1    -      -       -      +
    107G  SER*     4.1     7.4    -      -       -      -
    113G  ILE*     1.3    77.2    -      -       -      +
    115G  LEU*     1.3    61.1    +      -       -      +
    116G  LEU*     5.1     0.2    -      -       +      -
    231G  LEU*     4.7     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 115 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     70G  ILE*     4.3     7.2    -      -       +      -
     76G  TYR*     4.2    22.2    -      -       +      -
     77G  VAL      3.5    18.6    -      -       -      +
     78G  LEU*     4.4     6.5    -      -       +      +
    104G  LEU*     3.5     4.2    -      -       -      +
    105G  ILE*     2.8    53.9    +      -       +      -
    106G  GLY      2.8    14.5    +      -       -      +
    114G  ALA*     1.3    76.0    -      -       -      +
    116G  LEU*     1.3    60.3    -      -       -      +
    228G  ALA*     4.2    24.7    -      -       +      +
    231G  LEU*     3.9    18.1    -      -       +      +
    232G  ILE*     3.4    32.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 116 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29G  VAL*     4.3     6.3    -      -       +      -
     76G  TYR*     3.4     8.3    -      -       -      -
     77G  VAL*     2.8    45.4    +      -       +      +
     79G  THR*     3.7    24.5    -      -       +      -
     84G  ILE*     3.7    32.8    -      -       +      -
     90G  ILE*     4.0    12.8    -      -       +      -
     92G  ILE*     3.9    24.5    -      -       +      -
    102G  ALA*     4.4     8.5    -      -       +      -
    103G  LYS      3.3     5.4    -      -       -      +
    104G  LEU*     3.8    27.6    -      -       +      -
    105G  ILE*     4.1     3.4    -      -       -      -
    115G  LEU*     1.3    74.5    -      -       -      +
    117G  GLN*     1.3    62.0    +      -       -      +
    118G  ILE*     4.2     0.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 117 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     74G  LYS*     2.9    37.6    +      -       -      +
     75G  GLY      3.3     2.0    -      -       -      -
     76G  TYR*     3.6    26.2    +      -       +      -
    102G  ALA*     3.3     2.8    -      -       -      -
    103G  LYS      2.9    33.6    +      -       -      +
    105G  ILE*     3.5    28.9    -      -       +      +
    116G  LEU*     1.3    74.9    -      -       -      +
    118G  ILE*     1.3    66.4    +      -       -      +
    119G  GLN*     3.1    17.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 118 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     69G  ILE*     4.5     5.2    -      -       +      -
     74G  LYS      4.2     0.3    -      -       -      +
     75G  GLY*     2.7    20.2    +      -       -      +
     77G  VAL*     3.6    28.0    -      -       +      -
     92G  ILE*     4.1    29.8    -      -       +      -
     94G  LEU*     5.2     0.2    -      -       +      -
    100G  PHE*     3.5    35.4    -      -       +      -
    101G  ASP      3.5     5.6    -      -       -      +
    102G  ALA*     4.4     2.2    -      -       +      +
    116G  LEU      4.2     0.2    -      -       -      -
    117G  GLN*     1.3    82.4    -      -       -      +
    119G  GLN*     1.3    63.4    +      -       -      +
    121G  PRO*     3.3    31.9    -      -       +      +
    124G  LEU*     3.7    27.8    -      -       +      -
----------------------------------------------------------
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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