Contacts of the strand formed by residues 33 - 38 (chain A) in PDB entry 1H9O


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 THR 33 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26A  LEU*     3.7    18.7    -      -       +      +
     29A  LYS*     3.7    23.6    -      -       +      +
     30A  ARG*     2.6    38.6    +      -       -      +
     32A  GLY*     1.3    75.9    -      -       -      +
     34A  PHE*     1.3    63.6    +      -       -      +
     49A  VAL*     3.4     0.5    -      -       -      -
     50A  VAL*     3.0    29.1    +      -       -      +
    104A  TYR*     3.1    21.6    -      -       +      +
    105A  PRO      4.6     0.7    -      -       -      +
    106A  VAL*     3.9    16.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 34 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6A  HIS*     3.8     9.2    -      +       -      -
     12A  TRP*     3.6    28.5    -      +       +      +
     26A  LEU*     4.3     2.9    -      -       -      -
     32A  GLY      3.7     1.8    -      -       -      -
     33A  THR*     1.3    75.8    -      -       -      +
     35A  LEU*     1.3    73.5    +      -       -      +
     36A  VAL*     4.4     5.4    -      -       +      -
     47A  CYS*     4.7     0.9    -      -       -      -
     48A  SER      3.2    13.0    -      -       -      +
     49A  VAL*     4.0    14.1    -      -       +      -
     83A  VAL*     3.7    38.1    -      -       +      -
    102A  LEU*     3.5    48.9    -      -       +      -
    104A  TYR      3.0    13.4    +      -       -      -
    105A  PRO*     3.5    20.5    -      -       +      +
    106A  VAL*     3.0    27.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 35 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12A  TRP      3.3    13.2    -      -       -      +
     14A  VAL*     3.9    19.7    -      -       +      -
     22A  ALA*     4.0    17.7    -      -       +      -
     25A  LEU*     4.1    21.1    -      -       +      -
     26A  LEU*     4.1    25.8    -      -       +      -
     34A  PHE*     1.3    79.5    -      -       -      +
     36A  VAL*     1.3    67.8    +      -       -      +
     37A  ARG*     3.9    19.7    -      -       +      -
     47A  CYS*     3.4     7.1    -      -       -      -
     48A  SER*     3.0    44.6    +      -       -      +
    106A  VAL*     4.0    15.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 36 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12A  TRP*     2.9    36.3    +      -       +      -
     13A  ASN*     3.6     6.6    -      -       -      +
     14A  VAL*     2.9    27.2    +      -       -      +
     34A  PHE*     4.4     6.7    -      -       +      -
     35A  LEU*     1.3    79.4    -      -       -      +
     37A  ARG*     1.3    67.7    +      -       -      +
     45A  TYR*     4.7     2.9    -      -       +      -
     46A  ALA      3.4    11.2    -      -       -      +
     47A  CYS*     4.8     5.6    -      -       +      -
     60A  ILE*     4.2    22.4    -      -       +      -
     79A  LEU*     4.3    25.6    -      -       +      -
     82A  LEU*     6.0     0.2    -      -       +      -
     83A  VAL*     4.0    14.4    -      -       +      -
    102A  LEU*     5.8     0.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 37 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     13A  ASN*     5.0     1.3    -      -       -      -
     14A  VAL*     3.8    11.2    -      -       +      -
     15A  GLY*     3.4    11.2    -      -       -      +
     17A  SER*     3.5    18.1    +      -       -      +
     18A  ASN*     4.0     3.8    -      -       -      +
     19A  ARG*     3.7    19.2    -      -       -      +
     22A  ALA*     3.7    20.1    -      -       -      +
     35A  LEU*     3.9     4.9    -      -       +      -
     36A  VAL*     1.3    77.5    -      -       -      +
     38A  GLU*     1.3    73.6    +      -       -      +
     45A  TYR*     3.3    12.5    -      -       -      +
     46A  ALA*     2.8    50.4    +      -       +      +
     48A  SER*     3.0    15.7    +      -       -      -
     57A  HIS*     3.2    28.1    +      -       -      +
      1B  PTR      2.8    43.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 38 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     15A  GLY*     2.9    21.0    +      -       -      +
     16A  SER*     2.8    37.6    +      -       -      -
     17A  SER      3.5     7.4    -      -       -      +
     18A  ASN*     5.2     0.5    -      -       -      -
     37A  ARG*     1.3    92.8    +      -       -      +
     39A  SER*     1.3    63.8    +      -       -      +
     44A  CYS      4.0     6.5    -      -       -      +
     45A  TYR*     4.0    22.9    +      -       +      -
----------------------------------------------------------
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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