Contacts of the strand formed by residues 91 - 96 (chain J) in PDB entry 3Q3G


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 VAL 91 (chain J).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     42J  TYR      3.8     0.5    -      -       -      +
     43J  GLN*     3.5     1.9    -      -       -      -
     44J  GLN*     2.7    43.4    +      -       +      +
     90J  ALA*     1.3    74.2    -      -       -      +
     92J  TYR*     1.3    62.9    +      -       -      +
     93J  TYR*     3.6    29.9    +      -       +      +
    107J  GLY*     4.1     0.9    -      -       -      -
    108J  THR      3.4    13.5    -      -       -      +
    109J  LYS*     3.7    29.4    -      -       +      -
    709J  GOL      3.6    37.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 92 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6J  GLN*     2.7    24.1    +      -       -      -
     21J  MET*     3.7    27.1    -      -       -      -
     41J  TRP*     4.6     3.8    -      +       +      -
     42J  TYR      3.3     6.3    -      -       -      +
     43J  GLN*     3.1    32.1    +      -       +      -
     53J  LEU*     3.6    14.8    -      -       +      -
     68J  PHE*     3.4    32.1    -      +       -      -
     79J  LEU*     3.7    21.3    -      -       +      -
     81J  ILE*     4.0     3.3    -      -       +      +
     88J  ASP*     2.5    33.7    +      -       -      +
     90J  ALA*     3.8    11.4    -      -       +      -
     91J  VAL*     1.3    73.6    -      -       -      +
     93J  TYR*     1.3    55.3    +      -       -      +
    107J  GLY*     3.2     1.2    -      -       -      -
    108J  THR      2.9    31.0    +      -       -      +
    110J  LEU*     3.7    16.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 93 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6J  GLN*     3.5     2.7    -      -       -      -
     41J  TRP*     3.3     6.2    -      -       -      -
     42J  TYR*     2.7    47.7    +      -       +      +
     44J  GLN*     3.4    29.9    +      -       +      -
     91J  VAL*     3.6    24.4    -      -       +      +
     92J  TYR*     1.3    75.1    -      -       -      +
     94J  CYS*     1.3    63.6    -      -       -      +
    104J  PHE*     4.6     5.2    -      -       +      -
    105J  GLY      3.3    21.8    -      -       -      -
    106J  ALA      3.6    19.3    -      -       -      -
    107J  GLY*     3.7     6.5    -      -       -      -
    709J  GOL      2.9    20.8    +      -       -      -
     41K  GLN*     3.5     8.5    +      -       -      -
     45K  GLN      3.4    13.3    +      -       -      -
     46K  GLY*     3.9    12.3    -      -       -      -
     47K  LEU*     3.8    28.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with CYS 94 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4J  MET*     3.8    13.6    -      -       -      +
      6J  GLN*     3.3    22.2    +      -       -      -
     23J  CYS*     2.1    53.6    -      -       +      -
     39J  LEU*     4.5     2.2    -      -       +      -
     40J  ALA      3.2     9.9    -      -       -      +
     41J  TRP*     3.9    16.8    -      -       +      -
     93J  TYR*     1.3    74.9    -      -       -      +
     95J  GLN*     1.3    60.8    +      -       -      +
    104J  PHE*     3.4     5.3    -      -       -      +
    105J  GLY      2.9    25.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLN 95 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4J  MET*     3.9     6.7    -      -       -      -
     39J  LEU*     3.4     4.7    -      -       -      +
     40J  ALA*     2.8    39.4    +      -       -      +
     42J  TYR*     2.6    39.4    +      -       +      -
     94J  CYS*     1.3    76.2    -      -       -      +
     96J  GLN*     1.3    78.3    +      -       -      +
     97J  TYR*     3.8    18.5    +      -       -      +
    102J  LEU*     3.9     7.6    -      -       -      +
    103J  THR      3.3    16.4    -      -       -      +
    104J  PHE*     3.6    25.1    -      -       +      -
    111K  MET*     3.4    29.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 96 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      2J  ILE*     3.7    25.1    -      -       +      +
      4J  MET*     3.7    18.6    -      -       +      +
     29J  LEU*     3.7    22.9    -      -       +      -
     38J  TYR      3.3     5.2    -      -       -      +
     95J  GLN*     1.3    85.2    -      -       -      +
     97J  TYR*     1.3    59.4    +      -       -      +
     98J  TYR*     2.9    28.2    +      -       -      +
     99J  SER*     3.0    18.1    +      -       -      -
    101J  PRO      2.9    27.9    +      -       -      -
    102J  LEU*     3.9     2.6    -      -       -      -
    103J  THR*     3.0    41.6    +      -       -      +
----------------------------------------------------------
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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