Contacts of the strand formed by residues 89 - 94 (chain P) in PDB entry 1HI0


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 HIS 89 (chain P).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     45P  SER      5.4     0.3    -      -       -      +
     51P  LEU*     5.1     0.5    -      -       -      +
     54P  LYS*     3.6    13.2    +      -       -      +
     86P  GLY      2.7    28.0    -      -       -      -
     87P  MET      2.7    10.3    +      -       -      +
     88P  ARG*     1.3    76.0    -      -       -      +
     90P  MET*     1.3    68.6    +      -       -      +
     91P  ASN*     3.1    17.5    +      -       -      +
    206P  GLN      5.8     0.2    -      -       -      -
    207P  SER      3.5    21.8    -      -       -      +
    208P  THR*     3.9     0.4    -      -       -      -
    209P  ASP*     3.2    38.8    +      -       +      -
    211P  ILE*     3.5    22.4    -      -       +      +
    247P  LYS*     5.0     7.9    -      -       +      -
    264P  PHE*     4.4     1.2    -      -       -      -
    265P  PHE*     3.2    13.9    +      -       +      +
    266P  CYS      3.4    22.8    +      -       -      -
    267P  GLU*     4.3    12.7    -      -       +      -
    268P  ARG      5.4     0.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with MET 90 (chain P). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     45P  SER*     4.6     1.8    -      -       -      -
     46P  VAL*     4.0    18.4    -      -       +      -
     51P  LEU*     3.2    44.6    -      -       +      -
     89P  HIS*     1.3    73.1    -      -       -      +
     91P  ASN*     1.3    64.7    +      -       -      +
     92P  GLY      3.1     0.2    +      -       -      -
     93P  PHE*     3.0    28.9    +      -       +      +
    249P  ALA*     4.1    12.8    -      -       +      -
    252P  LEU*     3.8    29.4    -      -       +      -
    258P  ILE*     5.2     0.7    -      -       -      -
    259P  ASP      5.1     1.3    -      -       -      +
    260P  VAL*     4.6    13.9    -      -       -      -
    261P  PRO*     5.0     0.2    -      -       -      -
    264P  PHE*     3.4    28.9    -      -       +      -
    265P  PHE      2.8    19.9    +      -       -      +
    266P  CYS*     5.1     0.2    -      -       -      -
    267P  GLU*     4.7     1.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with ASN 91 (chain P). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     36P  ALA*     3.7     3.3    -      -       -      -
     37P  ILE*     3.4    31.3    +      -       +      +
     39P  THR*     4.6     1.4    +      -       -      -
     45P  SER*     2.8    38.7    +      -       -      -
     50P  PHE*     5.0     0.2    -      -       -      -
     54P  LYS*     3.1    25.2    -      -       -      +
     89P  HIS*     3.1    10.1    +      -       -      +
     90P  MET*     1.3    68.9    -      -       -      +
     92P  GLY*     1.3    58.2    +      -       -      +
     93P  PHE*     4.3     0.5    -      -       -      -
    207P  SER*     3.8    10.0    -      -       -      +
    267P  GLU*     3.2    22.0    -      -       -      +
    526P  PHE      3.5    11.9    +      -       -      -
    527P  SER*     3.6    22.4    +      -       -      +
    528P  PRO*     4.5     3.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 92 (chain P). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     34P  GLU*     3.6     2.9    -      -       -      +
     35P  GLY      3.0    38.3    +      -       -      +
     37P  ILE*     3.5    12.8    -      -       -      +
     91P  ASN*     1.3    73.7    -      -       -      +
     93P  PHE*     1.3    61.2    +      -       -      +
     94P  PRO*     3.6     9.1    -      -       -      +
    267P  GLU*     2.9    15.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 93 (chain P). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     34P  GLU*     3.4    18.4    -      -       +      +
     35P  GLY*     3.5    14.6    -      -       -      -
     36P  ALA*     3.3    33.7    -      -       -      -
     46P  VAL*     3.8    16.6    -      -       +      -
     90P  MET*     3.0    21.4    +      -       +      +
     91P  ASN      4.3     0.4    -      -       -      -
     92P  GLY*     1.3    79.5    -      -       -      +
     94P  PRO*     1.3    57.4    -      -       -      +
    252P  LEU*     3.2    41.7    -      -       +      -
    256P  TYR*     3.6    18.4    -      +       -      -
    258P  ILE*     3.7    20.2    -      -       +      -
    266P  CYS*     3.3    15.2    -      -       -      +
    267P  GLU*     2.7    33.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with PRO 94 (chain P). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     32P  PHE*     3.5    26.9    -      -       +      -
     33P  LYS      4.8     0.4    -      -       -      +
     34P  GLU*     3.4    18.8    -      -       +      +
     92P  GLY      3.6     9.2    -      -       -      +
     93P  PHE*     1.3    83.5    -      -       -      +
     95P  MET*     1.3    69.1    +      -       -      +
     96P  ILE*     3.8     0.2    -      -       -      +
    251P  ARG*     3.1    22.2    +      -       -      -
    266P  CYS*     3.4     5.8    -      -       -      +
    267P  GLU*     3.4    10.5    -      -       +      +
    269P  ARG*     3.5    45.5    -      -       +      +
----------------------------------------------------------
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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