Contacts of the strand formed by residues 145 - 153 (chain A) in PDB entry 1HIB


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 ASP 145 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12A  ASP*     3.1    10.2    -      -       -      +
     13A  SER*     2.9    44.8    +      -       -      +
    106A  ILE*     4.7     8.2    -      -       -      +
    109A  LYS*     3.4    33.0    +      -       +      +
    110A  LEU      3.2     5.7    -      -       -      +
    111A  GLU*     4.0    14.4    -      -       -      +
    143A  ILE*     3.7     2.4    -      -       +      +
    144A  THR*     1.3    80.8    +      -       -      +
    146A  PHE*     1.3    64.3    +      -       -      +
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Residues in contact with PHE 146 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10A  LEU*     4.6    10.8    -      -       +      -
     11A  ARG      3.0    13.7    -      -       -      +
     12A  ASP*     3.5    34.3    -      -       +      +
     13A  SER*     5.9     0.2    -      -       -      -
     18A  LEU*     4.1    23.6    -      -       +      -
    109A  LYS*     3.5     9.4    -      -       -      +
    110A  LEU*     2.7    48.9    +      -       -      +
    112A  PHE*     4.2    24.0    -      +       +      -
    122A  ILE*     3.5    47.8    -      -       +      -
    124A  THR*     4.1    11.0    -      -       +      -
    143A  ILE      4.5     5.2    -      -       -      -
    144A  THR      3.5    14.4    -      -       -      -
    145A  ASP*     1.3    74.6    -      -       -      +
    147A  THR*     1.3    71.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 147 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10A  LEU*     3.3     9.6    -      -       -      +
     11A  ARG*     2.7    46.4    +      -       -      +
     12A  ASP      4.9     3.6    +      -       -      +
     13A  SER*     6.0     2.7    -      -       -      -
    108A  ASN      4.7     7.9    -      -       -      +
    109A  LYS*     4.7    14.6    -      -       +      -
    110A  LEU*     5.1     2.2    -      -       -      -
    146A  PHE*     1.3    79.0    -      -       -      +
    148A  MET*     1.3    65.4    +      -       -      +
    149A  GLN*     3.3    19.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with MET 148 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6A  LEU*     3.9    36.1    -      -       +      -
      8A  CYS*     4.1    15.7    -      -       +      -
      9A  GLY      3.5     3.4    -      -       -      -
     10A  LEU*     3.9    15.0    -      -       +      -
     44A  MET*     4.0    17.9    -      -       +      +
    103A  LYS*     4.7     7.0    -      -       -      -
    110A  LEU*     3.6    29.5    -      -       +      +
    147A  THR*     1.3    75.4    -      -       -      +
    149A  GLN*     1.3    69.1    +      -       -      +
    150A  PHE*     4.4     5.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLN 149 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8A  CYS*     3.1    13.0    -      -       -      +
      9A  GLY      2.7    37.2    +      -       -      +
     10A  LEU      4.7     0.2    -      -       -      -
     11A  ARG*     3.5    49.0    +      -       +      +
     17A  SER*     5.7     0.2    -      -       -      +
     39A  GLN*     3.3    25.8    -      -       -      +
    147A  THR*     3.3    21.2    +      -       -      +
    148A  MET*     1.3    82.4    -      -       -      +
    150A  PHE*     1.3    67.1    +      -       -      +
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Residues in contact with PHE 150 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7A  ASN      5.5     2.5    -      -       -      -
      8A  CYS*     5.3     0.7    -      -       -      +
     37A  GLU*     4.6     5.5    -      -       -      +
     39A  GLN*     3.5    12.0    +      -       -      -
    148A  MET      5.3     4.7    -      -       -      -
    149A  GLN*     1.3    82.1    +      -       -      +
    151A  VAL*     1.3    62.1    +      -       -      +
    152A  SER*     4.0    17.7    -      -       -      +
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Residues in contact with VAL 151 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7A  ASN*     4.5    21.5    +      -       +      +
      8A  CYS*     4.7     2.0    -      -       -      -
      9A  GLY      5.3     0.7    -      -       -      +
     37A  GLU*     5.5     2.8    -      -       -      +
     38A  GLN*     4.9    10.8    -      -       +      +
     39A  GLN*     3.4    27.8    -      -       +      +
     41A  VAL*     3.5    43.5    -      -       +      -
     63A  LYS*     6.0     2.2    -      -       -      +
    149A  GLN      4.6     3.1    -      -       -      +
    150A  PHE*     1.3    76.9    -      -       -      +
    152A  SER*     1.3    80.2    +      -       -      +
    153A  SER*     5.3     0.7    -      -       -      -
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Residues in contact with SER 152 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    150A  PHE*     4.0    20.6    -      -       -      +
    151A  VAL*     1.3    91.7    +      -       -      +
    153A  SER*     1.3    73.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with SER 153 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    151A  VAL      5.3     0.2    -      -       -      -
    152A  SER*     1.3    83.2    -      -       -      +
----------------------------------------------------------
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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