Contacts of the strand formed by residues 146 - 151 (chain B) in PDB entry 1HPL


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 VAL 146 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     69B  LYS*     6.4     0.4    -      -       -      -
     70B  THR*     3.6     7.0    -      -       +      -
     72B  PHE*     3.7    35.2    -      -       +      -
    132B  VAL*     4.4    13.9    -      -       +      -
    135B  LEU*     5.2     3.4    -      -       +      -
    141B  TYR*     4.2    19.3    -      -       +      -
    143B  PRO*     3.0    20.2    +      -       +      +
    144B  SER      4.1     0.9    -      -       -      +
    145B  ASN*     1.3    82.7    -      -       -      +
    147B  HIS*     1.3    60.7    +      -       -      +
    148B  ILE*     3.8    15.7    -      -       +      -
    169B  VAL*     3.7    14.8    -      -       +      +
    170B  GLY*     3.3    22.0    +      -       -      -
    171B  ARG*     3.4     8.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with HIS 147 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     69B  LYS*     5.9     5.4    -      -       +      +
     70B  THR      3.0     6.1    +      -       -      +
     71B  ARG*     3.3    42.4    +      -       +      +
     72B  PHE*     2.9    26.3    +      -       -      +
    146B  VAL*     1.3    74.1    -      -       -      +
    148B  ILE*     1.3    79.9    +      -       -      +
    149B  ILE*     3.6    11.8    -      -       +      +
    171B  ARG*     3.2    48.8    +      -       +      -
    173B  THR*     2.7    23.7    +      -       -      -
    270B  TYR*     3.2    26.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 148 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     72B  PHE*     3.6    18.8    -      -       +      -
     74B  ILE*     3.7    22.9    -      -       +      -
    128B  VAL*     4.0    20.2    -      -       +      -
    132B  VAL*     5.4     0.9    -      -       +      -
    146B  VAL*     3.8    13.9    -      -       +      -
    147B  HIS*     1.3    78.4    -      -       -      +
    149B  ILE*     1.3    56.4    +      -       -      +
    158B  ALA*     3.6    27.6    -      -       +      +
    161B  ALA*     4.1    15.5    -      -       +      -
    162B  GLY      4.9     0.7    -      -       -      +
    169B  VAL*     3.9    28.0    -      -       +      -
    171B  ARG      2.9     6.3    +      -       -      -
    172B  ILE*     3.0    15.3    -      -       +      +
    173B  THR      2.8    29.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 149 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     71B  ARG*     4.7     4.9    -      -       +      -
     72B  PHE      2.8    13.5    +      -       -      +
     73B  ILE*     3.3    12.3    -      -       +      +
     74B  ILE*     2.9    26.0    +      -       -      +
     85B  TRP*     5.8     0.4    -      -       +      -
     89B  MET*     3.5    31.4    -      -       +      -
     93B  MET*     4.0    16.6    -      -       +      -
    147B  HIS*     3.6    28.9    -      -       +      +
    148B  ILE*     1.3    74.8    -      -       -      +
    150B  GLY*     1.3    58.4    +      -       -      +
    173B  THR*     3.7    12.6    -      -       +      -
    175B  LEU*     3.6    30.3    -      -       +      -
    270B  TYR*     3.8    20.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 150 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     74B  ILE*     3.5     9.9    -      -       -      -
     85B  TRP*     5.8     0.2    -      -       -      -
    148B  ILE      4.1     0.6    -      -       -      -
    149B  ILE*     1.3    74.2    -      -       -      +
    151B  HIS*     1.3    59.3    +      -       -      -
    154B  GLY      3.8    17.5    -      -       -      -
    155B  SER*     2.9    13.3    +      -       -      -
    158B  ALA*     4.6     4.0    -      -       -      +
    173B  THR      3.0    11.3    +      -       -      +
    175B  LEU*     2.8    29.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with HIS 151 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     74B  ILE      3.2     5.6    +      -       -      +
     76B  GLY      3.2    11.4    +      -       -      +
     77B  PHE      4.2    10.7    +      -       -      -
     85B  TRP*     3.8    27.9    -      -       +      -
    150B  GLY*     1.3    73.7    -      -       -      -
    152B  SER*     1.3    75.7    +      -       -      +
    154B  GLY*     2.8    22.1    +      -       -      -
    155B  SER*     3.8     0.2    -      -       -      -
    175B  LEU*     3.2    33.0    -      -       +      -
    176B  ASP      4.9     0.7    -      -       -      -
    263B  HIS*     2.9    38.5    +      +       -      -
    264B  LEU*     4.1     7.2    -      -       +      -
    266B  SER*     3.3    14.3    +      -       -      -
    267B  TYR*     3.5    32.6    -      +       -      -
----------------------------------------------------------
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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