Contacts of the strand formed by residues 216 - 220 (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 GLY 216 (chain G).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    176G  ILE      3.6     0.2    -      -       -      +
    177G  GLN*     3.2     8.3    -      -       -      +
    178G  THR*     2.9    43.3    +      -       -      +
    180G  ALA      5.4     0.8    +      -       -      -
    182G  ILE*     4.2    13.2    -      -       -      -
    204G  ALA      3.7     6.1    -      -       -      -
    205G  ILE*     4.0     9.4    -      -       -      -
    214G  GLY      3.9     0.2    -      -       -      -
    215G  ILE*     1.3    74.1    -      -       -      +
    217G  PHE*     1.3    64.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 217 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    164G  ARG*     4.4     5.8    -      -       +      -
    167G  LEU*     3.7    29.4    -      -       +      -
    169G  LEU*     4.2    10.5    -      -       +      -
    175G  PHE*     3.7    32.3    -      -       +      -
    176G  ILE      3.3     4.9    -      -       -      -
    177G  GLN*     3.5    30.3    -      -       +      -
    178G  THR*     5.7     0.4    -      -       -      -
    182G  ILE*     4.8     2.2    -      -       -      +
    202G  ASN*     3.8     5.1    +      -       -      +
    203G  THR*     2.9    29.3    +      -       -      -
    204G  ALA*     2.7    35.5    +      -       +      +
    205G  ILE*     4.2     0.9    -      -       -      -
    206G  LEU*     3.8    33.2    -      -       +      -
    215G  ILE*     3.6    25.1    -      -       +      -
    216G  GLY*     1.3    77.2    -      -       -      -
    218G  ALA*     1.3    54.5    +      -       -      +
    150I  LEU*     4.3     8.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 218 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    175G  PHE*     3.4     8.2    -      -       -      -
    176G  ILE*     2.9    36.2    +      -       +      +
    178G  THR*     5.5     1.1    -      -       +      -
    191G  LEU*     3.8    21.1    -      -       +      -
    200G  GLY*     4.3     3.4    -      -       -      -
    201G  ILE      3.2    17.3    -      -       -      +
    202G  ASN*     3.6    22.4    -      -       -      +
    217G  PHE*     1.3    76.0    -      -       -      +
    219G  ILE*     1.3    63.9    +      -       -      +
    220G  PRO      3.4     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 219 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     80G  ASN*     3.6    16.2    -      -       -      +
    111G  SER*     3.2    26.7    -      -       -      +
    112G  ASP      3.8     5.6    -      -       -      +
    113G  ILE*     3.5    28.9    -      -       +      -
    172G  LEU      6.0     0.7    -      -       -      +
    175G  PHE*     3.8    17.0    -      -       +      -
    200G  GLY*     3.1     1.9    -      -       -      -
    201G  ILE*     2.8    36.5    +      -       +      +
    203G  THR*     3.2    24.0    +      -       +      +
    218G  ALA*     1.3    69.7    -      -       -      +
    220G  PRO*     1.3    81.0    -      -       +      +
    223G  MET*     4.0    19.5    -      -       +      -
    224G  ALA*     4.3     1.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with PRO 220 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    132G  SER*     3.5    21.8    -      -       -      +
    174G  ASN*     3.1    44.9    -      -       +      +
    175G  PHE*     4.4     0.2    -      -       -      -
    176G  ILE*     3.6    20.6    -      -       +      +
    218G  ALA      3.4     4.9    -      -       -      +
    219G  ILE*     1.3    90.4    -      -       +      +
    221G  SER*     1.4    58.9    +      -       -      +
    222G  ASN*     3.3     1.3    -      -       +      +
    223G  MET*     3.1    20.9    +      -       +      +
    224G  ALA*     2.9    23.7    +      -       -      +
----------------------------------------------------------
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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