Contacts of the strand formed by residues 184 - 189 (chain H) in PDB entry 1U3H


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 ILE 184 (chain H).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     96H  GLN*     5.7     0.7    -      -       +      -
     97H  PRO*     3.6    25.8    -      -       +      +
     99H  VAL*     3.7    34.3    -      -       +      +
    173H  CYS      3.5     1.0    -      -       -      +
    174H  HIS*     3.5     0.2    -      -       -      -
    175H  VAL*     2.9    37.0    +      -       +      +
    180H  LEU*     3.6    33.7    -      -       +      -
    182H  SER      3.7     1.3    +      -       -      +
    183H  PRO*     1.3    74.5    -      -       -      +
    185H  THR*     1.3    70.6    +      -       -      +
    186H  VAL*     4.1     9.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 185 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    172H  THR*     4.1    13.9    -      -       +      -
    173H  CYS      3.2     7.0    -      -       -      +
    174H  HIS*     3.5    30.1    -      -       +      +
    183H  PRO*     3.8     7.7    +      -       +      +
    184H  ILE*     1.3    85.1    -      -       -      +
    186H  VAL*     1.3    65.5    +      -       -      +
    187H  GLU*     4.4     4.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 186 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     99H  VAL*     3.6    44.9    -      -       +      +
    100H  VAL*     5.1     0.7    -      -       -      -
    101H  ILE*     3.5    30.6    -      -       +      +
    172H  THR*     3.2     4.7    -      -       -      +
    173H  CYS*     2.8    31.1    +      -       +      +
    184H  ILE*     4.1     7.0    -      -       +      -
    185H  THR*     1.3    79.9    -      -       -      +
    187H  GLU*     1.3    70.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 187 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    101H  ILE*     4.1     2.0    -      -       -      +
    170H  VAL*     4.2    13.2    -      -       +      +
    171H  TYR      3.3     7.0    -      -       -      +
    172H  THR*     4.0    15.2    +      -       +      +
    185H  THR*     5.2     4.0    -      -       -      +
    186H  VAL*     1.3    89.5    -      -       -      +
    188H  TRP*     1.3    61.7    +      -       -      +
    189H  ARG*     3.0    35.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with TRP 188 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    101H  ILE*     3.7    45.0    +      -       +      -
    102H  SER*     5.4     0.2    -      -       -      +
    103H  LEU*     3.7    29.3    -      -       +      +
    107H  GLU*     3.7    22.7    -      -       -      -
    115H  LEU*     3.9    17.1    -      -       +      +
    163H  MET*     3.9    17.0    -      -       +      -
    165H  PRO*     4.3     8.1    -      -       +      -
    169H  GLU      4.1     0.5    -      -       -      +
    170H  VAL*     4.0     1.0    -      -       -      -
    171H  TYR*     2.8    50.5    +      +       +      +
    187H  GLU*     1.3    77.6    -      -       -      +
    189H  ARG*     1.3    72.8    +      -       -      +
    190H  ALA*     3.2    35.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 189 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    168H  GLY*     5.3     3.7    +      -       -      -
    169H  GLU      4.2     4.9    -      -       -      +
    170H  VAL*     2.9    41.4    -      -       +      +
    187H  GLU*     3.0    36.5    +      -       -      +
    188H  TRP*     1.3    90.6    +      -       -      +
    190H  ALA*     1.3    70.2    +      -       -      +
----------------------------------------------------------
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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