Contacts of the strand formed by residues 190 - 195 (chain D) in PDB entry 2QC8


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 190 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     46C  THR*     2.7    27.7    +      -       -      +
    179D  HIS*     4.0    22.2    -      -       +      +
    180D  TYR*     3.6    32.8    -      -       +      -
    183D  CYS*     4.0    18.2    -      -       +      -
    184D  LEU*     3.6    30.3    -      -       +      +
    188D  VAL      3.0     9.7    +      -       -      +
    189D  LYS*     1.3    72.0    -      -       -      +
    191D  ALA*     1.3    55.5    +      -       -      +
    192D  GLY      4.0    10.8    -      -       -      +
    193D  THR*     4.2     4.0    -      -       +      -
    204D  PHE*     3.8    26.2    -      -       +      -
    205D  GLN      3.5    11.2    -      -       -      +
    206D  ILE*     3.6     8.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 191 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     45C  ARG*     3.3     8.5    -      -       -      +
     46C  THR*     2.8    32.1    +      -       -      +
     60C  TRP*     5.8     0.2    -      -       -      -
    189D  LYS      3.5     1.6    +      -       -      -
    190D  ILE*     1.3    69.3    -      -       -      +
    192D  GLY*     1.3    58.2    +      -       -      +
    205D  GLN*     2.9    24.9    +      -       +      +
    207D  GLY      3.6    20.2    -      -       -      +
    501D  ADP      3.7    18.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 192 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     44C  THR      3.1    14.1    -      -       -      -
     45C  ARG*     4.1     0.2    -      -       -      -
    180D  TYR*     3.4    12.9    +      -       -      -
    190D  ILE*     3.5     4.4    -      -       -      +
    191D  ALA*     1.3    81.9    -      -       -      +
    193D  THR*     1.3    63.7    +      -       -      +
    204D  PHE*     3.2     5.0    -      -       -      +
    205D  GLN*     2.8    37.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 193 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     43C  LYS*     3.7     1.9    -      -       -      +
     44C  THR*     3.0    30.1    +      -       -      +
     60C  TRP*     5.4     0.2    -      -       -      -
     90C  ARG*     4.6     0.9    +      -       -      -
    702C   CL      3.2    18.2    -      -       -      +
    176D  VAL*     4.1    22.0    -      -       +      +
    179D  HIS*     5.6     1.6    -      -       -      +
    180D  TYR*     3.1    38.5    -      -       +      -
    190D  ILE*     4.2     3.6    -      -       +      -
    192D  GLY*     1.3    77.8    -      -       -      +
    194D  ASN*     1.3    68.8    +      -       -      +
    203D  GLU      3.2    15.5    -      -       -      +
    204D  PHE*     3.8    12.6    -      -       +      +
    205D  GLN*     3.7     2.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASN 194 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     43C  LYS*     3.7    27.8    -      -       +      +
    702C   CL      4.4     5.4    -      -       -      -
    162D  TYR*     4.2     9.6    -      -       -      -
    163D  CYS*     4.0     5.8    -      -       -      -
    193D  THR*     1.3    77.7    -      -       -      +
    195D  ALA*     1.3    82.6    +      -       -      +
    196D  GLU*     3.5    12.5    +      -       -      +
    202D  TRP*     3.6     6.9    -      -       -      -
    203D  GLU*     3.0    50.4    +      -       -      -
    205D  GLN*     3.0    28.8    +      -       -      -
    403D   MN      4.2     1.9    +      -       -      -
    601D  P3S      4.9     1.4    +      -       -      -
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Residues in contact with ALA 195 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     42C  CYS      5.2     1.0    +      -       -      -
    161D  TYR      3.5    11.4    -      -       -      +
    162D  TYR*     3.9     2.3    -      -       -      -
    163D  CYS*     3.0    35.1    +      -       -      +
    164D  GLY*     3.7    11.7    -      -       -      +
    170D  ALA*     5.3     3.1    -      -       +      -
    173D  ARG*     5.6     0.4    -      -       -      +
    194D  ASN*     1.3    85.6    +      -       -      +
    196D  GLU*     1.3    60.7    +      -       -      +
    201D  GLN      4.9     0.7    -      -       -      +
    202D  TRP*     3.3    40.0    -      -       +      -
----------------------------------------------------------
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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