Contacts of the strand formed by residues 362 - 366 (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 MET 362 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    214B  ILE*     4.2    11.0    -      -       +      +
    215B  VAL      4.1     1.6    -      -       -      +
    216B  GLY*     3.6    34.5    -      -       -      +
    220B  PHE*     3.9    20.1    -      -       +      -
    248B  MET*     4.1    20.2    -      -       +      +
    249B  THR*     4.9     4.7    -      -       +      -
    252B  ARG*     4.4     9.0    -      -       -      -
    253B  ILE*     4.1    23.6    -      -       +      -
    336B  THR*     3.9     0.6    -      -       -      +
    358B  GLN*     3.1     4.8    -      -       -      +
    359B  VAL      3.1    33.0    +      -       -      +
    360B  SER      3.0     3.0    +      -       -      -
    361B  GLY*     1.3    79.0    -      -       -      +
    363B  PHE*     1.3    64.2    +      -       -      +
    407B  ALA*     4.0     8.7    -      -       +      -
    408B  GLY      3.6    11.4    -      -       -      +
    409B  PHE*     4.1    15.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 363 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     63B  TYR*     4.4    17.3    -      +       +      -
    220B  PHE*     3.5     9.0    -      -       -      -
    336B  THR*     4.1    12.3    -      -       +      -
    339B  LEU*     4.0    28.3    -      -       +      -
    340B  SER*     4.8     8.1    -      -       -      -
    343B  LEU*     4.3    15.9    -      -       +      -
    357B  GLY      3.1    14.4    -      -       -      +
    358B  GLN*     3.6    11.0    -      -       +      +
    362B  MET*     1.3    78.7    -      -       -      +
    364B  GLY*     1.3    71.9    +      -       -      +
    365B  PHE*     5.0     4.3    -      -       +      -
    400B  LEU*     4.8    10.5    -      -       +      -
    407B  ALA*     3.3    10.6    -      -       -      +
    408B  GLY*     3.0    57.7    +      -       -      -
    409B  PHE*     3.6    12.3    -      -       -      -
    410B  THR*     5.2     2.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 364 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    220B  PHE*     3.5    21.9    -      -       -      +
    340B  SER*     5.6     1.7    +      -       -      -
    356B  GLY*     3.2    22.7    -      -       -      -
    357B  GLY      2.9    10.9    +      -       -      +
    363B  PHE*     1.3    84.7    -      -       -      +
    365B  PHE*     1.3    63.9    +      -       -      +
    366B  PHE*     4.3     4.0    -      -       -      -
    406B  GLU      5.7     1.1    -      -       -      -
    407B  ALA*     5.1     2.5    -      -       -      -
    408B  GLY      5.1     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 365 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    340B  SER      5.1     0.7    -      -       -      -
    343B  LEU*     3.7    41.7    -      -       +      -
    344B  LEU*     3.2    36.1    -      -       +      -
    347B  ALA*     4.4     2.7    -      -       +      -
    354B  ALA*     3.9    16.8    -      -       +      -
    355B  CYS      3.6     2.9    -      -       -      -
    363B  PHE*     5.0     5.8    -      -       +      -
    364B  GLY*     1.3    76.4    -      -       -      +
    366B  PHE*     1.3    58.0    +      -       -      +
    367B  PHE*     4.2    26.9    -      +       -      -
    386B  PHE*     4.6     7.6    -      +       -      -
    389B  PHE*     4.9    16.6    -      +       -      -
    404B  GLN*     2.8    24.8    +      -       -      -
    430B  MET*     3.9    26.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 366 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    218B  SER      3.7     8.5    -      -       -      -
    219B  GLY*     3.5    29.8    -      -       -      -
    220B  PHE*     3.4    29.2    -      +       -      -
    354B  ALA*     3.3     5.3    -      -       -      +
    355B  CYS*     2.8    42.4    +      -       -      +
    356B  GLY*     4.7     3.8    -      -       -      -
    364B  GLY*     4.8     2.7    -      -       -      -
    365B  PHE*     1.3    83.3    -      -       -      +
    367B  PHE*     1.3    60.2    +      -       -      +
    368B  THR*     2.8    21.0    +      -       +      -
    372B  VAL*     3.9    36.3    -      -       +      -
    378B  ALA*     4.3    11.4    -      -       +      -
    381B  SER*     3.6    16.2    -      -       -      +
    404B  GLN*     3.4    22.2    -      -       +      +
    405B  PHE*     4.8     1.3    -      +       -      -
----------------------------------------------------------
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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