Contacts of the strand formed by residues 192 - 201 (chain F) in PDB entry 3CB4


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 GLN 192 (chain F).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    190F  PRO*     3.3     5.3    +      -       -      +
    191F  LEU*     1.3    79.2    -      -       -      +
    193F  ALA*     1.3    54.1    +      -       -      +
    194F  LEU      4.2     0.2    -      -       -      -
    212F  ILE      3.8     0.3    -      -       -      -
    213F  LYS*     2.8    36.0    +      -       +      +
    214F  ASN*     2.8    41.0    +      -       +      +
    273F  THR*     4.8     7.2    -      -       -      +
    274F  LEU      3.5     2.2    -      -       -      -
    281F  ALA*     3.7    15.2    -      -       +      +
    283F  LYS      3.0    27.1    +      -       -      +
    284F  ALA      4.6     0.2    -      -       -      -
    285F  LEU*     4.2    34.2    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA 193 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    191F  LEU*     4.2     6.5    -      -       +      -
    192F  GLN*     1.3    74.5    -      -       -      +
    194F  LEU*     1.3    60.7    +      -       -      +
    195F  ILE*     3.6     1.7    +      -       -      +
    210F  ILE*     3.4    29.4    -      -       +      -
    211F  ARG      3.3     4.9    -      -       -      +
    212F  ILE*     4.1    11.0    -      -       +      -
    217F  LEU*     5.6     1.3    -      -       +      -
    273F  THR*     3.1     5.7    -      -       -      -
    274F  LEU*     2.6    56.5    +      -       +      +
    285F  LEU*     4.3     1.7    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 194 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     90F  ARG*     3.5    36.3    -      -       -      +
     93F  ALA*     3.9    27.4    -      -       +      +
     94F  ALA*     4.0    11.4    -      -       +      +
    193F  ALA*     1.3    70.5    -      -       -      +
    195F  ILE*     1.3    65.3    +      -       -      +
    196F  ILE*     3.1     8.7    +      -       +      +
    210F  ILE*     3.6     3.5    -      -       -      -
    211F  ARG*     2.8    37.1    +      -       +      +
    213F  LYS*     4.5     8.7    -      -       +      -
    271F  GLY*     3.6    32.3    -      -       -      +
    272F  ASP      3.7     2.7    -      -       -      +
    285F  LEU*     3.9    25.7    -      -       +      +
    286F  PRO      5.6     1.6    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 195 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     90F  ARG*     4.8     1.0    -      -       -      +
    193F  ALA      4.2     0.7    -      -       -      +
    194F  LEU*     1.3    70.4    -      -       -      +
    196F  ILE*     1.3    61.9    +      -       -      +
    197F  ASP      4.0     8.5    -      -       -      +
    198F  SER*     3.6    22.9    -      -       -      +
    208F  SER*     4.6    15.0    -      -       -      +
    209F  LEU      3.9     3.4    -      -       -      +
    210F  ILE*     5.1     2.7    -      -       +      +
    225F  VAL*     4.8     4.3    -      -       +      -
    268F  ALA*     3.9     7.2    -      -       +      +
    269F  PRO      3.2    21.3    -      -       -      +
    270F  VAL*     3.9     7.6    -      -       -      +
    271F  GLY*     2.9    28.8    +      -       -      -
    272F  ASP*     2.9    44.4    +      -       +      +
    273F  THR      4.0     2.9    -      -       -      +
    274F  LEU*     3.7    37.0    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 196 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     76F  ILE*     4.7     8.3    -      -       +      -
     87F  GLU*     5.1     3.3    -      -       -      +
     90F  ARG*     4.6     8.9    -      -       -      +
     91F  SER*     3.2    38.1    +      -       -      +
     94F  ALA*     3.9    18.8    -      -       +      -
    194F  LEU*     3.6    10.8    -      -       +      +
    195F  ILE*     1.3    73.7    -      -       -      +
    197F  ASP*     1.3    66.0    +      -       +      +
    209F  LEU*     2.9    34.0    +      -       +      +
    210F  ILE      3.7    28.3    -      -       -      +
    211F  ARG*     3.7    10.8    -      -       +      +
    255F  VAL*     4.3     7.4    -      -       +      -
    270F  VAL*     3.4    19.1    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ASP 197 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     57F  GLN*     2.9    29.5    +      -       -      +
     87F  GLU*     5.2    10.8    -      -       -      +
    195F  ILE*     3.6     4.3    -      -       -      +
    196F  ILE*     1.3    85.7    -      -       +      +
    198F  SER*     1.3    79.8    +      -       -      +
    199F  TRP*     3.9    15.1    -      -       +      +
    208F  SER*     3.1     5.5    -      -       -      -
    209F  LEU*     2.8    31.4    +      -       +      +
    270F  VAL*     4.9     7.0    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with SER 198 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    195F  ILE*     3.6     4.4    -      -       -      +
    197F  ASP*     1.3    85.8    +      -       -      +
    199F  TRP*     1.3    62.3    +      -       -      +
    206F  VAL*     4.7     1.8    -      -       -      -
    207F  VAL      3.2     7.2    -      -       -      -
    208F  SER*     2.8    24.4    +      -       -      -
    265F  ILE*     3.9    32.5    -      -       -      +
    268F  ALA*     2.8    29.7    +      -       -      -
    270F  VAL*     5.5     2.7    -      -       -      +
    320F  ASN      5.0     2.6    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with TRP 199 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     57F  GLN*     4.0    24.2    -      -       -      -
    197F  ASP*     3.9    13.0    -      -       +      +
    198F  SER*     1.3    80.8    -      -       -      +
    200F  PHE*     1.3    73.7    +      -       -      +
    201F  ASP*     4.2     8.9    +      -       -      +
    206F  VAL*     3.5     3.8    -      -       -      -
    207F  VAL*     2.9    70.0    +      -       +      +
    208F  SER      4.5     0.2    -      -       -      -
    209F  LEU*     3.8    31.9    -      -       +      -
    240F  PHE*     4.0    31.6    -      +       -      -
    244F  GLN*     6.1     0.4    -      -       -      -
    257F  TRP*     4.9     0.4    -      -       +      -
    265F  ILE*     3.6    10.7    -      -       -      +
    320F  ASN*     3.4    16.2    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 200 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    202E  ASN      5.0     5.8    -      -       -      -
    199F  TRP*     1.3    79.2    -      -       -      +
    201F  ASP*     1.3    76.1    +      -       -      +
    202F  ASN*     4.0    24.5    +      -       -      +
    205F  GLY*     3.8    17.5    -      -       -      -
    206F  VAL*     4.0    21.8    -      -       +      -
    262F  ILE      5.8     0.2    -      -       -      -
    263F  LYS      4.6     9.2    -      -       -      -
    264F  ASP*     5.6     1.3    -      -       -      -
    265F  ILE*     4.0     1.4    -      -       +      +
    319F  LEU*     3.6    50.0    -      -       +      +
    320F  ASN*     2.8    26.8    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ASP 201 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    316E  LYS*     4.9     5.9    +      -       -      -
    199F  TRP*     4.0     8.1    +      -       -      +
    200F  PHE*     1.3    77.8    -      -       -      +
    202F  ASN*     1.3    60.9    +      -       -      +
    203F  TYR*     2.8    20.3    +      -       -      +
    204F  LEU*     2.8    50.1    +      -       +      +
    205F  GLY*     2.8    45.3    +      -       -      +
    207F  VAL*     3.9    10.2    -      -       +      +
    244F  GLN*     5.3     2.3    +      -       -      -
----------------------------------------------------------
 Back to top of page


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