Contacts of the strand formed by residues 55 - 60 (chain B) in PDB entry 3GJ9


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 55 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33B  ILE*     4.0    25.6    -      -       +      -
     34B  GLY      3.6     2.9    -      -       -      +
     35B  GLY*     3.7    27.6    -      -       -      +
     36B  GLY*     3.7     9.4    -      -       -      +
     54B  GLY*     1.3    72.6    -      -       -      -
     56B  TYR*     1.3    63.0    +      -       -      +
     76B  LYS*     3.2    11.5    -      -       -      +
     77B  ILE*     2.9    57.0    +      -       +      +
     85B  MET*     3.6    24.4    +      -       +      +
     88B  VAL*     4.2     6.1    -      -       +      +
     89B  THR      4.5     2.7    -      -       -      +
     90B  HIS*     4.7     2.5    -      -       -      -
     93B  ALA*     3.6    28.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 56 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33B  ILE*     3.2     7.3    -      -       -      +
     34B  GLY      2.8    36.8    +      -       -      +
     35B  GLY*     5.5     0.9    -      -       -      -
     45B  PRO*     4.6     9.4    -      -       +      -
     46B  PHE*     4.4    19.7    -      +       +      -
     47B  SER*     2.8    44.2    -      -       -      -
     52B  ASP*     2.9    29.3    +      -       -      -
     54B  GLY      3.7    14.8    -      -       -      -
     55B  ILE*     1.3    80.3    -      -       -      +
     57B  VAL*     1.3    65.0    +      -       -      +
     58B  THR*     3.4     2.8    +      -       +      +
     74B  GLY      3.4    25.1    -      -       -      -
     75B  ASP      3.2     7.0    -      -       -      -
     76B  LYS*     3.6    30.0    -      -       +      +
     77B  ILE*     4.7     0.4    -      -       -      +
    440D  ARG*     5.8     3.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 57 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     31B  PHE*     4.0     7.6    -      -       +      -
     32B  SER      3.4     7.2    -      -       -      +
     33B  ILE*     4.7     0.4    -      -       -      +
     46B  PHE*     4.1     2.1    -      -       -      -
     56B  TYR*     1.3    71.7    -      -       -      +
     58B  THR*     1.3    59.0    +      -       -      +
     59B  ARG      3.5    23.6    -      -       -      +
     60B  VAL*     3.5    20.0    -      -       +      -
     71B  LEU*     3.5    38.1    -      -       +      -
     72B  GLN      3.7    12.3    -      -       -      +
     73B  ILE*     3.6     1.0    -      -       -      +
     74B  GLY*     2.6    31.2    +      -       -      -
     75B  ASP*     2.8    21.7    +      -       +      +
     77B  ILE*     4.2    14.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 58 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     32B  SER*     2.8    18.6    +      -       -      -
     33B  ILE      4.1     0.2    -      -       -      -
     34B  GLY*     3.7    16.4    -      -       -      +
     44B  ASN*     5.9     1.6    -      -       -      +
     46B  PHE*     4.6    17.3    -      -       +      -
     56B  TYR*     3.9     4.5    -      -       +      +
     57B  VAL*     1.3    74.7    -      -       -      +
     59B  ARG*     1.3    68.1    +      -       -      +
     73B  ILE*     3.7    18.1    -      -       -      +
    440D  ARG*     3.7    27.1    -      -       -      +
    442D  GLU*     3.0    34.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 59 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     31B  PHE*     3.1     9.1    -      -       -      +
     32B  SER*     2.9    43.9    +      -       -      +
     57B  VAL*     3.5     3.5    -      -       -      +
     58B  THR*     1.3    89.9    +      -       -      +
     60B  VAL*     1.3    67.0    +      -       -      +
     61B  SER*     5.4     0.7    -      -       -      +
     73B  ILE*     4.4     6.7    -      -       +      -
    442D  GLU*     3.2    32.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 60 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     30B  GLY      3.8     6.5    -      -       -      +
     31B  PHE*     4.4     3.4    -      -       +      -
     57B  VAL*     3.5    20.4    -      -       +      -
     59B  ARG*     1.3    82.8    -      -       -      +
     61B  SER*     1.3    62.2    +      -       -      +
     62B  GLU*     3.5     2.1    +      -       -      +
     66B  ALA*     4.4     2.7    -      -       +      -
     67B  GLU*     3.6    44.1    -      -       +      +
     71B  LEU*     3.9    13.5    -      -       +      +
     72B  GLN*     4.0     3.8    -      -       -      -
     73B  ILE*     3.8    32.8    -      -       +      +
----------------------------------------------------------
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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