Contacts of the strand formed by residues 50 - 56 (chain B) in PDB entry 3GYQ


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 PHE 50 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     34B  ILE*     3.9    12.1    -      -       +      -
     40B  LEU*     3.4    33.0    -      -       +      -
     43B  SER*     3.7    24.0    -      -       -      -
     44B  ILE*     3.5    28.5    -      -       +      -
     48B  VAL*     3.3    28.9    +      -       +      -
     49B  GLU*     1.3    74.6    -      -       -      +
     51B  ILE*     1.3    62.2    +      -       -      +
     52B  GLU      4.5     1.3    -      -       -      +
     53B  VAL*     4.3     9.4    -      -       +      -
     74B  ILE*     3.9    36.2    -      -       +      +
     75B  PRO*     5.1     2.1    -      -       -      +
     98B  GLY      4.1    11.4    -      -       -      -
     99B  ILE      3.4    16.6    -      -       -      +
    100B  ALA*     3.5    12.8    -      -       +      -
    101B  ARG*     3.6    11.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 51 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     18B  ILE*     5.7    13.0    -      -       +      -
     31B  THR*     3.7    30.7    -      -       +      -
     50B  PHE*     1.3    74.1    -      -       -      +
     52B  GLU*     1.3    65.9    +      -       +      +
     75B  PRO*     3.5    21.5    -      -       -      +
     99B  ILE*     2.7    35.5    +      -       +      +
    101B  ARG*     4.2    25.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 52 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     50B  PHE*     3.6     0.6    -      -       -      -
     51B  ILE*     1.3    88.3    -      -       +      +
     53B  VAL*     1.3    72.6    +      -       -      +
     54B  TYR*     2.8    44.6    +      -       +      +
     74B  ILE*     4.5     2.7    -      -       -      -
     75B  PRO*     3.3    29.0    -      -       +      +
     77B  ARG*     3.0    41.4    +      -       -      +
     98B  GLY*     3.4     1.2    -      -       -      -
     99B  ILE*     2.9    27.6    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 53 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     40B  LEU*     4.2    19.1    -      -       +      -
     44B  ILE*     5.1     2.9    -      -       +      -
     50B  PHE*     4.3    18.8    -      -       +      -
     52B  GLU*     1.3    77.9    -      -       -      +
     54B  TYR*     1.3    70.9    +      -       -      +
     61B  PHE*     4.3    18.2    -      -       +      -
     65B  LEU*     4.6     3.4    -      -       +      -
     69B  CYS*     3.8    20.4    -      -       -      -
     74B  ILE*     3.7    20.6    -      -       +      -
     75B  PRO      2.9    10.7    +      -       -      +
     76B  VAL*     3.0    27.3    -      -       +      +
     77B  ARG      3.1     4.9    +      -       -      -
     97B  PHE      3.6    11.2    -      -       -      +
     98B  GLY*     4.3     3.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 54 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      9B  ASN*     5.4     2.0    -      -       -      -
     16B  GLN*     5.3    10.1    -      -       +      -
     18B  ILE*     5.5     4.5    -      -       -      +
     19B  ILE*     3.5    24.4    -      -       +      +
     52B  GLU*     2.8    52.8    +      -       +      +
     53B  VAL*     1.3    79.5    -      -       -      +
     55B  GLY*     1.3    59.4    +      -       -      +
     61B  PHE*     3.7     6.1    -      -       -      -
     77B  ARG*     3.3    26.9    -      -       +      +
     79B  ILE*     3.7    19.1    -      -       +      -
     96B  THR*     3.5    10.2    -      -       -      +
     97B  PHE*     2.7    70.2    +      +       +      +
     98B  GLY*     4.6     1.1    -      -       -      -
     99B  ILE*     3.8    22.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 55 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     54B  TYR*     1.3    77.8    -      -       -      +
     56B  SER*     1.3    58.9    +      -       -      -
     61B  PHE*     4.0    18.3    -      -       -      -
     77B  ARG      3.3     5.1    +      -       -      -
     78B  LEU*     3.4     7.2    -      -       -      -
     79B  ILE*     2.7    35.5    +      -       -      +
     84B  VAL*     5.1     1.6    -      -       -      -
     95B  LYS      3.7    11.4    -      -       -      -
     96B  THR*     4.4     1.3    -      -       -      -
     97B  PHE*     4.8     3.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 56 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     55B  GLY*     1.3    72.3    -      -       -      -
     57B  ASP*     1.3    58.3    +      -       -      +
     58B  SER*     2.8    27.0    +      -       -      -
     59B  SER*     3.1    24.2    -      -       -      +
     61B  PHE*     5.7     0.7    -      -       -      +
     78B  LEU*     4.6     4.4    -      -       -      +
     79B  ILE      3.2     8.2    +      -       -      -
     81B  SER*     4.1     7.1    -      -       -      -
     84B  VAL*     4.1    23.3    -      -       -      +
     95B  LYS*     3.2    37.8    +      -       -      +
     97B  PHE*     5.5     0.4    -      -       -      -
----------------------------------------------------------
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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