Contacts of the strand formed by residues 106 - 111 (chain C) in PDB entry 4BPW


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 LEU 106 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    104C  LYS      3.7     1.0    +      -       -      -
    105C  GLU*     1.3    72.3    -      -       -      +
    107C  VAL*     1.3    66.1    +      -       -      +
    108C  PHE*     4.0    29.2    -      -       +      -
    152C  PHE*     3.5    33.4    -      -       +      -
    167C  CYS      3.5     1.9    -      -       -      +
    168C  TRP*     3.7     0.7    -      -       -      -
    169C  VAL*     2.8    39.0    +      -       +      +
    174C  VAL*     3.4    20.9    -      -       +      +
    177C  LEU*     4.6     2.5    -      -       +      -
    182C  ARG*     3.7    40.8    -      -       +      +
    185C  ILE*     3.7    16.4    -      -       +      -
    186C  VAL*     6.0     0.2    -      -       +      -
    310C  SER*     4.4    10.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 107 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    104C  LYS*     3.7    28.9    -      -       -      +
    105C  GLU      3.8     4.5    -      -       -      +
    106C  LEU*     1.3    81.4    -      -       -      +
    108C  PHE*     1.3    59.0    +      -       -      +
    167C  CYS      3.2     3.8    -      -       -      +
    168C  TRP*     3.7    32.8    -      -       +      -
    309C  VAL*     3.6    30.9    -      -       +      +
    310C  SER*     2.4    34.7    +      -       -      +
    315C  HIS*     4.7     1.8    -      -       +      -
    317C  LEU*     3.6    21.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 108 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    106C  LEU*     4.0    27.8    -      -       +      -
    107C  VAL*     1.3    74.9    -      -       -      +
    109C  ASP*     1.3    59.8    +      -       -      +
    110C  ILE*     4.2     8.2    -      -       +      +
    142C  ILE*     4.8     6.1    -      -       +      -
    146C  LEU*     3.6    33.2    -      -       +      -
    157C  TRP*     5.3     1.6    -      -       +      -
    165C  VAL      4.0     0.2    -      -       -      +
    166C  HIS*     3.3     9.0    -      -       -      +
    167C  CYS*     3.0    51.9    +      -       +      -
    169C  VAL*     4.3     1.6    -      -       +      -
    185C  ILE*     4.2     6.1    -      -       +      -
    186C  VAL*     4.4    13.9    -      -       +      -
    189C  LEU*     3.6    30.7    -      -       +      -
    305C  LEU*     4.3    25.6    -      -       +      -
    309C  VAL*     4.8     1.1    -      -       -      -
    310C  SER*     3.8    17.3    -      -       -      -
    317C  LEU*     4.7     1.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 109 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    108C  PHE*     1.3    73.4    -      -       -      +
    110C  ILE*     1.3    63.3    +      -       -      +
    111C  ASP*     3.9     4.5    +      -       -      +
    114C  ASP*     5.8     0.2    -      -       -      +
    165C  VAL      4.0     1.6    -      -       -      -
    166C  HIS*     3.0    34.2    +      -       +      -
    304C  ARG      4.5     1.0    -      -       -      +
    305C  LEU*     4.3     4.5    -      -       -      +
    306C  ASP*     4.2    19.6    +      -       -      +
    309C  VAL*     3.9    30.0    -      -       +      +
    310C  SER*     5.0     0.4    +      -       -      -
    317C  LEU*     4.6     3.6    -      -       +      -
   1410C   MG      2.8    23.2    -      -       -      -
   1411C   MG      3.3     5.0    -      -       -      -
   1412C  UTP      3.0    34.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 110 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    108C  PHE*     4.9     3.8    -      -       +      -
    109C  ASP*     1.3    79.6    -      -       -      +
    111C  ASP*     1.3    61.7    +      -       -      +
    115C  TYR*     3.9    20.2    -      -       +      +
    135C  MET*     3.6    21.9    -      -       +      +
    138C  ALA*     4.0    15.7    -      -       +      -
    142C  ILE*     3.8    26.9    -      -       +      -
    157C  TRP*     3.9    26.5    -      -       +      -
    164C  GLY*     3.2    25.3    -      -       -      -
    165C  VAL*     3.1    19.0    +      -       +      +
    303C  PRO*     5.1     0.4    -      -       +      -
    304C  ARG      4.0    12.8    -      -       -      +
    305C  LEU*     3.8    12.3    -      -       +      -
   1411C   MG      3.8     4.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with ASP 111 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    109C  ASP*     3.9     5.6    +      -       -      +
    110C  ILE*     1.3    73.9    -      -       -      +
    112C  MET*     1.3    64.8    +      -       -      +
    113C  THR*     3.5    10.3    +      -       -      -
    114C  ASP*     3.1    40.2    +      -       -      +
    115C  TYR*     3.6     8.3    -      -       -      -
    135C  MET*     3.7     3.1    -      -       -      -
    163C  ARG*     2.6    42.5    +      -       -      +
    304C  ARG      4.9     1.6    +      -       -      +
   1410C   MG      4.5     2.9    -      -       -      -
   1411C   MG      2.5    24.2    -      -       -      -
   1412C  UTP      2.8    25.5    +      -       -      +
----------------------------------------------------------
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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