Contacts of the strand formed by residues 206 - 211 (chain B) in PDB entry 3GSB


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 206 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    140B  ARG*     3.4    21.1    +      -       -      +
    142B  LYS*     3.4    25.4    -      -       +      +
    144B  ILE*     3.6    21.5    -      -       +      -
    185B  LEU*     3.6    14.4    -      -       +      -
    198B  LEU      4.6     1.8    -      -       -      +
    199B  PHE*     3.6    45.0    -      -       +      -
    202B  ASN*     3.4    39.3    -      -       +      +
    204B  GLY      5.8     0.2    -      -       -      +
    205B  GLU*     1.3    77.7    -      -       -      +
    207B  ALA*     1.3    64.8    +      -       -      +
    208B  GLY      3.8    10.3    -      -       -      +
    240B  ALA*     4.2     4.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 207 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    134B  MET*     4.1    12.3    -      -       +      +
    135B  ARG*     4.1     2.0    -      -       -      -
    138B  THR*     3.4    34.8    -      -       -      +
    140B  ARG*     3.6    18.0    -      -       -      +
    142B  LYS      2.6    16.8    +      -       -      +
    143B  ILE*     3.5    18.4    -      -       +      -
    205B  GLU      3.9     2.2    +      -       -      -
    206B  ILE*     1.3    71.5    -      -       -      +
    208B  GLY*     1.3    55.2    +      -       -      +
    240B  ALA*     3.5     5.1    -      -       -      -
    241B  LEU*     3.0    20.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 208 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    134B  MET*     3.4    11.7    -      -       -      +
    142B  LYS      3.9     0.6    +      -       -      -
    143B  ILE*     3.9     3.0    -      -       -      +
    144B  ILE*     3.1    25.8    +      -       -      +
    206B  ILE*     3.4     7.9    -      -       -      +
    207B  ALA*     1.3    82.8    -      -       -      +
    209B  VAL*     1.3    64.3    -      -       -      +
    240B  ALA*     4.0     9.0    -      -       -      -
    241B  LEU      3.0    15.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 209 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    134B  MET*     3.8     2.6    -      -       -      +
    144B  ILE*     3.6    22.4    -      -       +      +
    146B  PHE*     4.1    27.8    -      -       +      -
    195B  VAL*     5.2     1.3    -      -       +      -
    199B  PHE*     4.2    17.5    -      -       +      -
    208B  GLY*     1.3    79.0    -      -       -      +
    210B  ILE*     1.3    65.1    -      -       -      +
    211B  LEU*     5.3     0.4    -      -       +      -
    231B  LEU*     4.4    16.4    -      -       +      -
    235B  THR*     3.4    28.0    -      -       +      -
    241B  LEU      2.8     6.5    +      -       -      -
    242B  LEU*     3.6    12.2    -      -       +      +
    243B  VAL*     2.8    29.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 210 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    127B  CYS*     5.1     4.7    -      -       +      -
    130B  VAL*     4.2    19.3    -      -       +      -
    131B  LEU*     4.1    13.7    -      -       +      -
    134B  MET*     4.7     4.0    -      -       -      -
    143B  ILE*     4.0     6.7    -      -       +      -
    144B  ILE      3.2    14.7    +      -       -      +
    145B  LYS*     3.9     7.0    -      -       +      -
    146B  PHE*     4.3     3.3    -      -       -      -
    151B  HIS*     3.9    32.8    +      -       +      -
    157B  PHE*     3.2    40.6    -      -       +      -
    209B  VAL*     1.3    76.2    -      -       -      +
    211B  LEU*     1.3    66.4    +      -       -      +
    243B  VAL*     3.4    22.7    -      -       +      +
    245B  ASP*     4.7     8.5    -      -       +      -
    270B  THR*     5.6     0.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 211 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    146B  PHE*     3.5    33.2    -      -       +      -
    149B  CYS*     4.7     0.9    -      -       -      -
    151B  HIS*     3.3    14.6    -      -       -      -
    189B  TYR*     3.8    20.4    -      -       +      +
    209B  VAL      4.9     0.4    -      -       -      +
    210B  ILE*     1.3    80.7    -      -       -      +
    212B  GLU*     1.3    67.5    +      -       -      +
    213B  PRO*     3.6     2.2    -      -       +      +
    227B  PHE*     4.1     2.7    -      -       +      -
    228B  LEU*     3.9    21.3    -      -       +      -
    231B  LEU*     3.9    10.8    -      -       +      -
    242B  LEU*     4.1    11.4    -      -       +      -
    243B  VAL      3.3    14.1    +      -       -      +
    244B  PHE*     3.7    22.8    -      -       +      -
    245B  ASP      2.9    22.8    +      -       -      -
----------------------------------------------------------
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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