Contacts of the strand formed by residues 167 - 172 (chain B) in PDB entry 1B0P


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 PHE 167 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    107B  GLY      3.0    10.2    +      -       -      +
    108B  VAL*     3.2     5.2    -      -       +      -
    109B  PHE      3.0    22.0    +      -       -      -
    138B  PHE*     3.4     8.5    -      -       -      -
    139B  ALA*     3.5    33.9    -      -       +      -
    141B  LEU*     4.4    15.3    -      -       +      -
    156B  ALA*     3.7    37.2    -      -       +      +
    159B  ALA*     3.9     7.0    -      -       +      -
    160B  ALA*     3.8    21.3    -      -       +      -
    163B  SER*     4.0     3.6    -      -       -      -
    165B  VAL      3.1    26.0    +      -       -      -
    166B  PRO*     1.3    72.9    -      -       -      +
    168B  MET*     1.3    59.9    +      -       -      +
    169B  HIS      4.1     0.7    -      -       -      -
    239B  VAL*     3.6    16.2    -      -       +      -
    243B  VAL*     3.4    33.2    -      -       +      -
    304B  LEU*     4.2     8.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with MET 168 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     90B  LEU*     4.3    15.7    -      -       -      -
     97B  MET*     4.5     7.0    -      -       +      -
    109B  PHE*     3.4     8.7    -      -       +      -
    111B  VAL*     3.7    31.0    -      -       +      -
    130B  ILE*     3.9    21.3    -      -       +      +
    133B  ALA*     4.0    15.5    -      -       +      +
    138B  PHE*     3.7    12.6    -      -       +      -
    139B  ALA      2.8    12.9    +      -       -      +
    140B  MET*     3.4    43.5    -      -       +      -
    141B  LEU*     3.1    22.5    +      -       -      -
    167B  PHE*     1.3    75.6    -      -       -      +
    169B  HIS*     1.3    59.2    +      -       -      +
    170B  PHE*     3.5     9.9    +      -       +      -
----------------------------------------------------------
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Residues in contact with HIS 169 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     14B  THR*     4.0     1.7    -      -       -      +
    108B  VAL*     4.9     1.2    -      -       +      +
    109B  PHE      2.9     7.3    +      -       -      +
    110B  HIS*     3.0    36.5    -      +       +      +
    111B  VAL*     2.9    24.4    +      -       -      +
    141B  LEU*     3.3    16.2    +      -       +      +
    143B  SER*     3.2    34.8    -      -       -      -
    149B  ALA*     3.3    20.4    +      -       -      -
    152B  MET*     3.6    12.7    -      -       +      +
    153B  ALA*     3.9    12.6    -      -       +      -
    156B  ALA*     4.0    20.5    -      -       +      +
    167B  PHE      4.1     0.6    -      -       -      -
    168B  MET*     1.3    73.3    -      -       -      +
    170B  PHE*     1.3    63.7    +      -       -      +
    171B  PHE*     3.3    21.9    -      +       -      -
----------------------------------------------------------
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Residues in contact with PHE 170 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    111B  VAL*     3.2    16.8    -      -       +      +
    113B  ALA*     4.4     8.3    -      -       +      -
    127B  HIS*     4.2    16.6    -      +       -      -
    130B  ILE*     3.6    55.9    -      -       +      -
    140B  MET*     3.9    24.7    -      -       +      -
    141B  LEU      3.0     6.7    +      -       -      +
    142B  ALA*     3.5    34.6    -      -       +      -
    143B  SER*     3.1    27.2    +      -       -      -
    168B  MET*     3.7    16.2    -      -       +      -
    169B  HIS*     1.3    75.2    -      -       -      +
    171B  PHE*     1.3    67.7    +      -       -      +
    276B  MET*     3.9    15.5    -      -       +      -
    277B  GLY*     5.8     0.9    -      -       -      -
    305B  TYR*     4.8     2.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 171 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10B  GLY*     4.0     8.3    -      -       -      -
     11B  ASN*     3.8    10.3    -      -       -      -
     14B  THR*     3.4    30.1    -      -       +      -
     36B  MET*     3.9     9.9    -      -       +      -
    110B  HIS*     5.0     0.7    -      -       +      -
    111B  VAL      3.2     9.3    +      -       -      -
    112B  THR*     3.3    25.4    -      -       +      -
    113B  ALA*     3.1    20.3    +      -       -      -
    143B  SER*     3.8    22.0    -      -       -      +
    149B  ALA*     4.4     2.7    -      -       +      -
    169B  HIS*     3.3    28.9    -      +       -      -
    170B  PHE*     1.3    75.7    -      -       -      +
    172B  ASP*     1.3    69.4    +      -       -      +
    176B  THR*     3.9    17.5    -      -       +      -
    177B  SER*     3.5    40.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with ASP 172 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    113B  ALA*     4.2     4.3    -      -       -      +
    125B  GLY*     5.3     2.5    -      -       -      -
    126B  ASP      5.7     0.4    -      -       -      -
    127B  HIS*     2.7    33.8    +      -       -      -
    143B  SER      4.7     0.8    +      -       -      -
    170B  PHE*     5.2     0.3    -      -       -      -
    171B  PHE*     1.3    74.1    -      -       -      +
    173B  GLY*     1.3    66.0    +      -       -      +
    175B  ARG*     4.0    18.4    -      -       +      -
    176B  THR*     3.0    24.2    +      -       -      +
    177B  SER*     3.2    11.0    +      -       -      -
    276B  MET      4.6     0.2    -      -       -      +
    277B  GLY*     3.8     5.0    -      -       -      -
    278B  SER*     2.9    36.6    +      -       -      +
    329B  ARG*     3.7    22.4    +      -       -      +
----------------------------------------------------------
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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