Contacts of the strand formed by residues 69 - 74 (chain H) in PDB entry 1UB6


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 PHE 69 (chain H).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     40H  ARG*     4.1     0.9    -      -       -      -
     50H  VAL*     3.6    25.6    -      -       +      +
     61H  TYR*     3.2    22.1    -      -       +      -
     65H  VAL*     3.1    43.1    +      -       +      +
     66H  ALA      4.5     4.3    -      -       -      +
     67H  GLY      5.0     0.9    -      -       -      -
     68H  ARG*     1.3   109.1    +      -       +      +
     70H  THR*     1.3    66.0    +      -       -      +
     82H  LEU*     4.4    10.1    -      -       +      -
     83H  GLN      3.3     3.1    -      -       -      +
     84H  MET*     3.7    42.0    -      -       +      -
     85H  SER      4.2     2.2    -      -       -      -
     87H  LEU*     4.1     5.2    -      -       +      -
     91H  ASP*     3.8    24.7    -      -       -      -
     95H  TYR*     4.0    12.8    -      +       -      -
----------------------------------------------------------
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Residues in contact with THR 70 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     61H  TYR*     3.4     7.4    +      -       -      +
     68H  ARG      4.9     2.1    +      -       -      -
     69H  PHE*     1.3    77.1    +      -       -      +
     71H  ILE*     1.3    71.4    +      -       -      +
     72H  SER*     3.9     9.0    +      -       -      -
     81H  TYR*     4.3     0.3    -      -       -      +
     82H  LEU*     3.6     3.5    +      -       -      -
     83H  GLN*     2.7    54.5    +      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 71 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     36H  MET      3.8    23.1    -      -       -      +
     37H  SER*     4.4     1.1    -      -       -      -
     38H  TRP*     3.4    25.1    -      -       +      +
     51H  ALA*     4.0    11.7    -      -       +      +
     52H  SER*     3.7    30.3    -      -       -      +
     53H  ILE*     3.8    13.8    -      -       +      +
     59H  THR*     3.8    20.0    -      -       +      +
     61H  TYR*     2.9    30.4    +      -       +      +
     70H  THR*     1.3    77.1    -      -       -      +
     72H  SER*     1.3    65.4    +      -       -      +
     80H  LEU*     4.0     9.9    -      -       +      -
     81H  TYR      3.4    13.7    -      -       -      +
     82H  LEU*     4.4     2.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 72 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     53H  ILE*     4.3     9.2    -      -       -      -
     70H  THR*     3.9     9.2    +      -       -      -
     71H  ILE*     1.3    76.4    -      -       -      +
     73H  ARG*     1.3    60.2    +      -       -      +
     80H  LEU*     3.1     9.6    -      -       -      +
     81H  TYR*     2.8    54.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 73 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29H  PHE*     3.0    31.9    +      -       +      -
     30H  SER*     3.6    20.1    +      -       -      +
     34H  TYR      3.1    16.4    +      -       -      -
     36H  MET*     3.9     6.2    -      -       -      +
     53H  ILE*     3.9    29.0    +      -       +      +
     54H  SER      2.4    27.6    +      -       -      -
     55H  SER      3.3    15.4    +      -       -      -
     57H  GLY*     3.8     7.9    -      -       -      +
     72H  SER*     1.3    79.6    -      -       -      +
     74H  ASP*     1.3    62.2    +      -       -      +
     75H  ASN*     2.9    39.5    +      -       -      +
     79H  ILE      3.4    10.5    -      -       -      +
     80H  LEU*     4.2     7.6    -      -       +      -
     81H  TYR*     4.8     2.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with ASP 74 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     73H  ARG*     1.3    71.4    -      -       -      +
     75H  ASN*     1.3    53.6    +      -       -      +
     76H  VAL*     2.9    21.5    +      -       -      +
     77H  ARG*     2.8    51.1    +      -       -      +
     78H  ASN*     2.8    32.6    +      -       -      -
     79H  ILE*     2.8    24.0    +      -       +      +
     81H  TYR*     4.1    21.1    +      -       +      -
----------------------------------------------------------
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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