Contacts of the strand formed by residues 150 - 155 (chain B) in PDB entry 1HRN


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 150 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    137B  PHE*     3.5    12.0    -      -       -      -
    148B  GLU*     3.1    18.2    +      -       +      +
    149B  ASP*     1.3    79.4    -      -       -      +
    151B  PHE*     1.3    58.7    +      -       -      +
    168B  GLY*     2.5    32.9    +      -       -      -
    169B  GLY*     3.7    24.2    -      -       -      +
    312B  GLU*     3.4    33.9    -      -       +      +
    313B  PHE      3.3     7.0    -      -       -      +
    314B  ASP*     3.7    30.3    -      -       +      +
    315B  ARG      4.5     0.2    -      -       -      +
    316B  ARG*     5.6     0.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 151 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33B  THR*     3.7    13.0    -      -       +      -
    123B  MET*     3.6    48.2    -      -       +      -
    137B  PHE*     3.8    28.0    -      +       +      -
    150B  VAL*     1.3    76.1    -      -       -      +
    152B  SER*     1.3    58.7    +      -       -      +
    153B  PHE*     3.6    20.4    -      +       -      -
    165B  ILE*     4.7     2.0    -      -       +      -
    166B  VAL      3.0    12.8    -      -       -      +
    167B  LEU*     3.7    18.4    -      -       +      -
    190B  TRP*     3.9    16.4    -      +       -      -
    312B  GLU      3.6     0.2    -      -       -      -
    313B  PHE*     2.7    70.8    +      +       +      +
    315B  ARG*     4.7     2.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 152 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    151B  PHE*     1.3    70.4    -      -       -      +
    153B  PHE*     1.3    65.7    +      -       -      +
    164B  GLN      3.6     0.7    -      -       -      +
    165B  ILE*     3.0    10.0    -      -       -      +
    166B  VAL*     2.7    35.1    +      -       -      -
    169B  GLY      2.9    21.6    +      -       -      -
    170B  SER*     3.3     8.1    -      -       -      -
    310B  TYR*     3.3    28.3    -      -       -      -
    311B  THR      3.3     4.7    -      -       -      -
    312B  GLU*     3.3    23.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 153 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6B  LEU*     4.8     1.3    -      -       +      -
     31B  PHE*     3.5    32.5    -      -       +      -
     33B  THR*     4.4     0.2    -      -       +      -
    123B  MET*     4.5     4.7    -      -       +      -
    151B  PHE*     3.6    29.6    -      +       -      -
    152B  SER*     1.3    78.0    -      -       -      +
    154B  TYR*     1.3    59.6    +      -       -      +
    155B  TYR*     3.7    23.3    -      +       -      -
    164B  GLN      3.5     1.6    -      -       -      -
    165B  ILE*     3.6    34.5    -      -       +      -
    216B  THR*     3.5    27.8    -      -       +      -
    306B  ILE*     4.0    18.3    -      -       +      +
    310B  TYR*     3.8     9.4    -      -       -      -
    311B  THR*     2.8    33.9    +      -       -      +
    313B  PHE*     3.6    17.7    -      +       +      -
----------------------------------------------------------
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Residues in contact with TYR 154 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    153B  PHE*     1.3    72.9    -      -       -      +
    155B  TYR*     1.3    78.0    +      -       -      +
    156B  ASN*     3.0    39.8    +      -       +      -
    161B  LEU*     3.9    18.2    -      -       +      +
    163B  GLY*     3.0    13.8    -      -       -      -
    164B  GLN*     2.8    45.8    +      -       +      +
    174B  HIS*     3.7    47.3    +      +       +      +
    306B  ILE*     5.0     0.4    -      -       -      -
    310B  TYR*     3.6    20.9    -      +       +      +
    325B  ALA*     4.2    15.3    -      -       +      -
    326B  ARG*     3.7    25.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 155 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6B  LEU*     3.5    25.2    -      -       +      +
     14B  TYR*     3.4    51.2    +      +       +      +
     30B  VAL*     5.4     0.5    -      -       -      +
     31B  PHE      4.1     2.8    +      -       -      -
    153B  PHE*     3.7    20.4    -      +       -      -
    154B  TYR*     1.3    97.2    -      -       -      +
    156B  ASN*     1.3    60.8    +      -       -      +
    157B  ARG*     5.2     0.3    -      -       -      +
    162B  GLY      4.0     0.7    -      -       -      -
    216B  THR*     2.6    37.2    +      -       -      -
    303B  ALA*     3.8    32.1    -      -       +      -
    306B  ILE*     3.9    30.7    +      -       +      +
    307B  ARG*     3.5    26.9    -      -       +      +
----------------------------------------------------------
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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