Contacts of the strand formed by residues 191 - 196 (chain C) 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 SER 191 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    149C  LYS      3.9     0.9    -      -       -      +
    150C  ILE      3.6     1.2    -      -       -      -
    151C  ASP*     2.7    67.7    +      -       -      -
    152C  GLY      3.9     1.7    +      -       -      -
    189C  HIS      4.0     0.2    -      -       -      -
    190C  ASN*     1.3    81.7    -      -       -      +
    192C  TYR*     1.3    67.8    +      -       -      +
    193C  THR*     5.5     4.3    -      -       -      -
    209C  PHE      3.5     6.5    -      -       -      -
    210C  ASN*     5.0     4.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 192 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    117C  ILE*     4.1     8.1    -      -       +      +
    132C  VAL*     5.0    12.3    -      -       +      -
    148C  TRP*     5.8     6.1    -      +       +      -
    149C  LYS      3.8     1.8    -      -       -      -
    150C  ILE*     4.0    27.5    -      -       +      +
    179C  LEU*     5.4    12.3    -      -       +      -
    185C  GLU      4.1     1.7    +      -       -      -
    186C  TYR*     2.7    60.0    +      +       -      -
    189C  HIS*     4.0    23.4    -      -       +      +
    190C  ASN      4.6     4.0    -      -       -      -
    191C  SER*     1.3    80.3    -      -       -      +
    193C  THR*     1.3    61.9    +      -       -      +
    208C  SER*     2.8    27.7    -      -       -      -
    209C  PHE*     3.0    46.6    +      +       +      -
    211C  ARG*     5.2     3.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 193 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    117C  ILE*     4.8     0.4    -      -       -      -
    148C  TRP*     3.6    14.4    -      -       -      -
    149C  LYS*     2.7    59.0    +      -       -      +
    152C  GLY*     4.9     4.7    +      -       -      +
    191C  SER*     5.2     3.5    +      -       -      -
    192C  TYR*     1.3    74.7    -      -       -      +
    194C  CYS*     1.3    61.0    +      -       -      +
    195C  GLU*     3.8     5.6    -      -       -      -
    206C  VAL*     4.4    12.3    -      -       +      -
    208C  SER*     3.1    26.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with CYS 194 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    115C  VAL*     4.3     5.9    -      -       +      +
    117C  ILE*     4.0    14.8    -      -       +      +
    134C  CYS*     2.0    51.6    -      -       +      -
    136C  LEU*     4.4     3.4    -      -       -      -
    146C  VAL*     4.9    11.4    -      -       -      -
    147C  LYS      4.0     2.2    -      -       -      -
    148C  TRP*     4.3    13.0    -      -       +      -
    192C  TYR      4.3     0.2    +      -       -      -
    193C  THR*     1.3    72.4    -      -       -      +
    195C  GLU*     1.3    59.8    +      -       -      +
    196C  ALA*     3.7     3.6    +      -       -      +
    205C  ILE      3.9     0.5    -      -       -      +
    206C  VAL*     3.8     4.1    -      -       -      -
    207C  LYS      3.0    32.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 195 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    145C  ASN      4.1     0.5    -      -       -      +
    146C  VAL*     3.4     2.9    -      -       -      -
    147C  LYS*     2.6    69.1    +      -       +      +
    149C  LYS*     2.7    40.0    +      -       -      +
    193C  THR*     3.8     6.7    +      -       -      +
    194C  CYS*     1.3    71.3    -      -       -      +
    196C  ALA*     1.3    60.5    +      -       -      +
    197C  THR*     4.1     3.6    +      -       -      +
    204C  PRO*     4.3    21.9    -      -       +      +
    205C  ILE      4.0     1.8    -      -       -      -
    206C  VAL*     3.9    19.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 196 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    113C  PRO*     6.0     2.0    -      -       +      -
    115C  VAL*     5.0     3.6    -      -       +      -
    136C  LEU*     4.2    28.0    -      -       +      -
    144C  ILE*     5.4     6.3    -      -       +      -
    145C  ASN      3.6     5.4    -      -       -      +
    146C  VAL*     4.2     4.0    -      -       +      +
    194C  CYS*     4.8     3.4    -      -       -      +
    195C  GLU*     1.3    72.9    -      -       -      +
    197C  THR*     1.3    61.0    +      -       -      +
    198C  HIS*     4.0     2.6    +      -       +      +
    204C  PRO*     4.8     1.3    -      -       -      -
    205C  ILE*     2.8    58.2    +      -       +      +
----------------------------------------------------------
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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