Contacts of the strand formed by residues 132 - 137 (chain A) in PDB entry 6N8Q


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 132 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     78A  GLN*     4.9     0.9    +      -       -      -
     91A  LEU*     3.8    21.1    -      -       +      +
     95A  ASN*     2.5    40.6    +      -       -      +
     97A  LEU*     3.9    30.1    -      -       +      -
    119A  LEU*     4.0    19.3    -      -       +      +
    130A  THR      4.0     5.8    -      -       -      +
    131A  GLN*     1.3    73.8    +      -       -      +
    133A  THR*     1.3    63.2    +      -       -      +
    134A  VAL      4.2     5.2    -      -       -      +
    135A  VAL*     3.6    29.2    -      -       +      -
    146A  LEU*     3.9    17.0    -      -       +      -
    147A  GLY      3.5     9.2    -      -       -      +
    148A  THR*     4.3     0.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 133 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     78A  GLN*     2.5    33.0    +      -       -      -
    131A  GLN      3.4     0.2    +      -       -      -
    132A  ILE*     1.3    74.8    -      -       -      +
    134A  VAL*     1.3    65.2    +      -       -      +
    147A  GLY      2.7    23.1    +      -       -      -
    148A  THR      3.7     1.6    +      -       -      -
    149A  GLU*     3.7    37.2    -      -       +      +
    190A  MET*     3.9    17.5    -      -       +      -
    191A  VAL*     2.8    27.4    +      -       -      +
    192A  GLU*     6.0     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 134 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     78A  GLN*     4.6     1.1    -      -       -      +
     80A  HIS*     6.3     0.2    -      -       +      -
    132A  ILE*     4.2     0.8    -      -       -      +
    133A  THR*     1.3    84.6    +      -       -      +
    135A  VAL*     1.3    71.4    +      -       -      +
    145A  TYR      3.8     0.9    -      -       -      +
    146A  LEU*     3.7     3.8    -      -       -      -
    147A  GLY      2.9    26.2    +      -       -      +
    191A  VAL*     3.9    10.8    -      -       +      +
    192A  GLU*     3.5    33.2    -      -       -      +
    193A  ALA*     4.1     2.9    -      -       -      +
    194A  LEU*     3.7    38.7    -      -       +      +
    195A  GLN*     6.2     0.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 135 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     78A  GLN*     3.5    16.1    +      -       -      +
     80A  HIS*     3.4    43.9    -      -       +      +
     89A  VAL*     5.0     3.6    -      -       +      -
     91A  LEU*     4.1     9.6    -      -       +      -
     97A  LEU*     4.2    13.2    -      -       +      -
    132A  ILE*     3.6    25.8    -      -       +      -
    134A  VAL*     1.3    77.6    -      -       -      +
    136A  LEU*     1.3    63.7    +      -       -      +
    137A  PRO*     3.7     3.8    -      -       +      +
    144A  LEU*     4.2    23.3    -      -       +      -
    145A  TYR      3.8     2.5    -      -       -      -
    146A  LEU*     3.9    17.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 136 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    135A  VAL*     1.3    74.8    -      -       -      +
    137A  PRO*     1.3    78.4    -      -       +      +
    138A  HIS*     3.4     4.0    +      -       +      +
    144A  LEU*     3.7     2.8    -      -       -      -
    145A  TYR*     2.9    53.0    +      -       +      +
    194A  LEU*     3.5    41.3    -      -       +      +
    195A  GLN*     3.6    27.8    -      -       +      +
    196A  GLU*     3.8    16.8    -      -       +      +
    204A  ILE*     4.6    10.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with PRO 137 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     80A  HIS*     3.9    30.3    -      -       +      +
     81A  LEU      5.4     2.7    -      -       -      +
     82A  LEU*     3.9    20.9    -      -       +      -
     83A  PRO*     4.7     9.9    -      -       +      +
     89A  VAL*     5.9     0.2    -      -       +      -
    135A  VAL*     3.7     8.7    -      -       +      +
    136A  LEU*     1.3    96.6    -      -       +      +
    138A  HIS*     1.3    68.0    +      -       -      +
    139A  SER*     3.7     1.0    +      -       -      -
    141A  CYS*     6.3     0.4    -      -       -      -
    143A  LEU      3.9     0.9    -      -       -      +
    144A  LEU*     3.6    26.2    -      -       +      -
    196A  GLU*     4.5     1.4    -      -       -      +
----------------------------------------------------------
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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