Contacts of the strand formed by residues 108 - 112 (chain B) in PDB entry 1UEX


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 TRP 108 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     83A  TRP*     3.5    24.0    -      +       -      -
     89A  VAL*     5.2     0.2    -      -       +      -
     91A  TYR*     3.6    11.2    +      +       -      -
     92A  GLU*     3.6    31.0    -      -       +      -
     93A  ASN*     3.1    29.0    +      -       +      +
     94A  VAL*     3.5    22.9    -      -       +      +
     95A  ASP*     2.9    24.8    +      -       -      +
     44B  VAL*     3.6    37.8    -      -       +      +
     50B  GLY*     6.2     0.6    -      -       -      -
     68B  ILE*     3.9    12.1    -      -       +      +
     70B  LEU*     3.7    31.6    -      -       +      -
     99B  PHE*     3.9    13.0    -      +       +      -
    100B  VAL      3.3     6.7    -      -       -      +
    101B  ALA*     4.6    12.6    -      -       +      +
    106B  ASN      3.3    19.5    +      -       -      -
    107B  LYS*     1.3    74.8    -      -       -      +
    109B  ILE*     1.3    59.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 109 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     95A  ASP*     4.6    16.4    -      -       +      +
     65B  LEU*     4.9     1.8    -      -       +      -
     99B  PHE*     3.4     5.9    -      -       -      -
    100B  VAL*     2.9    44.1    +      -       +      +
    102B  GLU*     4.6    14.1    -      -       +      -
    107B  LYS*     4.3     6.7    -      -       +      +
    108B  TRP*     1.3    80.5    -      -       -      +
    110B  GLN*     1.3    83.9    +      -       -      +
    111B  TRP*     4.2    11.7    -      -       +      -
    659C  LEU*     3.7    37.2    -      -       +      +
    660C  LYS*     6.1     0.4    -      -       -      -
    663C  ARG*     3.3    19.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 110 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     78A  GLN*     6.1     0.2    -      -       -      +
     94A  VAL*     4.1     9.9    -      -       -      +
     96A  GLU      3.6    19.2    +      -       -      +
     97A  PRO*     4.4     0.3    -      -       -      +
     98A  THR*     3.6    26.1    +      -       -      +
     97B  ILE*     3.8    26.0    -      -       +      -
     98B  CYS      3.2     7.9    -      -       -      -
     99B  PHE*     3.8    17.1    -      -       +      -
    109B  ILE*     1.3    82.5    -      -       -      +
    111B  TRP*     1.3    59.3    +      -       -      +
    663C  ARG*     2.6    48.1    +      -       -      +
    667C  LYS*     5.9     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with TRP 111 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     65B  LEU*     4.0    21.3    -      -       +      -
     67B  TRP*     4.0    18.8    -      +       +      -
     97B  ILE*     4.9     1.1    -      -       -      +
     98B  CYS*     2.8    28.4    +      -       -      +
    100B  VAL*     3.6    28.3    -      -       +      -
    109B  ILE*     4.1    13.7    -      -       +      +
    110B  GLN*     1.3    82.2    -      -       -      +
    112B  THR*     1.3    93.9    +      -       -      +
    113B  CYS*     3.2     2.9    +      -       -      -
    115B  ARG*     4.5     1.3    -      -       +      +
    117B  LYS*     3.4    22.8    -      -       -      +
    659C  LEU*     3.7    15.5    -      -       +      -
    662C  ILE*     4.2    13.0    -      -       +      -
    663C  ARG*     3.4    49.1    +      -       +      +
    666C  GLU*     2.6    31.9    +      -       -      +
    667C  LYS*     5.3     2.5    -      -       -      +
    674C  ALA*     5.1     0.7    -      -       +      -
    676C  VAL*     5.4     0.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 112 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     67B  TRP*     3.2    14.4    -      -       -      -
     95B  GLU*     5.5    11.7    +      -       -      +
     96B  PRO      5.6     2.5    -      -       -      -
    111B  TRP*     1.3    76.8    -      -       -      +
    113B  CYS*     1.3    62.9    +      -       -      +
    114B  ASN*     3.1    26.7    -      -       -      +
    115B  ARG*     3.5    43.5    -      -       -      +
    663C  ARG*     5.1     0.5    -      -       -      +
    666C  GLU      6.1     0.4    -      -       -      -
    667C  LYS*     3.0    42.1    -      -       +      +
----------------------------------------------------------
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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