Contacts of the strand formed by residues 135 - 140 (chain Q) in PDB entry 3QUM


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 THR 135 (chain Q).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    133Q  GLY      4.2     0.2    +      -       -      -
    134Q  THR*     1.3    78.5    -      -       -      +
    136Q  CYS*     1.3    59.6    +      -       -      +
    160Q  LEU      3.7     6.7    -      -       -      +
    161Q  HIS*     4.2     0.2    -      -       -      -
    185Q  ARG*     4.2    21.5    -      -       -      +
    201Q  CYS*     3.4    23.9    -      -       -      +
    202Q  ASN*     3.7    21.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with CYS 136 (chain Q). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     97K  TYR*     4.8     3.6    +      -       -      -
    134Q  THR      4.6     5.4    -      -       -      +
    135Q  THR*     1.3    76.5    -      -       -      +
    137Q  TYR*     1.3    66.5    +      -       -      +
    159Q  ASP*     4.0     3.6    -      -       -      +
    160Q  LEU*     2.9    36.9    +      -       +      +
    161Q  HIS*     4.6     2.0    -      -       -      +
    162Q  VAL*     4.6     9.9    -      -       -      -
    183Q  ALA*     6.0     0.9    -      -       +      -
    199Q  LEU*     4.0    22.4    -      -       +      -
    200Q  VAL      3.2     6.5    -      -       -      -
    201Q  CYS*     2.0    51.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 137 (chain Q). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     97K  TYR*     3.6    54.6    -      +       +      +
     27Q  GLN*     3.2    39.0    +      -       -      -
     29Q  TRP*     4.0     8.3    -      -       -      -
    136Q  CYS*     1.3    78.1    -      -       -      +
    138Q  ALA*     1.3    72.3    +      -       -      +
    139Q  SER*     4.5     4.5    -      -       -      -
    157Q  CYS*     4.1     6.7    -      -       +      -
    158Q  VAL      3.5    14.8    -      -       -      +
    160Q  LEU*     4.6     2.7    -      -       -      +
    198Q  PRO      4.0     0.2    -      -       -      +
    199Q  LEU*     3.2    20.7    -      -       -      +
    200Q  VAL*     3.1    60.5    +      -       +      +
    201Q  CYS*     6.0     0.2    -      -       -      -
    202Q  ASN      6.3     0.4    -      -       -      -
    203Q  GLY*     6.0     0.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 138 (chain Q). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    137Q  TYR*     1.3    79.6    -      -       -      +
    139Q  SER*     1.3    60.9    +      -       -      +
    156Q  GLN      3.6     0.2    -      -       -      +
    157Q  CYS*     2.9    27.4    -      -       -      +
    158Q  VAL*     3.2    21.5    +      -       +      +
    160Q  LEU*     4.4    11.7    -      -       +      -
    192Q  SER*     4.9     6.3    -      -       -      +
    197Q  GLY*     6.0     1.3    -      -       -      -
    198Q  PRO      3.7    11.7    -      -       -      +
    199Q  LEU*     4.6     0.9    -      -       +      -
    219Q  PRO*     6.5     0.9    -      -       +      -
    228Q  TYR*     4.1    18.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER 139 (chain Q). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22Q  CYS*     4.5     0.7    -      -       -      -
     27Q  GLN*     4.5     7.1    +      -       -      -
     30Q  GLN*     2.7    43.5    +      -       -      +
    137Q  TYR*     4.5     5.4    -      -       -      -
    138Q  ALA*     1.3    76.9    -      -       -      +
    140Q  GLY*     1.3    59.2    +      -       -      +
    155Q  LEU*     3.8     4.5    -      -       -      -
    156Q  GLN      3.0     4.7    -      -       -      -
    157Q  CYS*     3.5    20.9    -      -       -      -
    192Q  SER      4.7     3.9    -      -       -      +
    194Q  ASP      5.1     0.7    -      -       -      +
    197Q  GLY*     4.0    16.5    -      -       -      -
    198Q  PRO*     3.9    15.0    +      -       -      +
    200Q  VAL*     5.9     1.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 140 (chain Q). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     30Q  GLN*     5.1     0.7    -      -       -      -
    139Q  SER*     1.3    74.7    -      -       -      +
    141Q  TRP*     1.3    59.8    +      -       -      -
    155Q  LEU*     3.1    13.5    -      -       -      +
    156Q  GLN*     2.7    42.8    +      -       -      +
    192Q  SER      4.1     3.0    +      -       -      -
    193Q  GLY*     3.1    25.3    -      -       -      -
    194Q  ASP      4.2     1.6    -      -       -      -
----------------------------------------------------------
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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