Contacts of the strand formed by residues 140 - 142 (chain D) in PDB entry 5UQ9


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 SER 140 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    127D  GLY      3.4     4.3    -      -       -      +
    128D  VAL*     3.6     1.7    -      -       -      -
    129D  SER*     3.1    34.5    +      -       -      -
    139D  PRO*     1.3    71.8    -      -       -      +
    141D  LEU*     1.3    61.5    +      -       -      +
    142D  MET*     4.3     3.4    -      -       -      +
    170D  CYS*     3.8     7.2    -      -       -      -
    361D  MET      3.1    27.6    -      -       -      -
    364D  GLY      3.1    19.5    +      -       -      -
    365D  GLY*     4.5     0.4    -      -       -      -
    366D  CYS*     2.8    25.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 141 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     18D  LEU*     5.4     4.7    -      -       +      -
    126D  SER*     4.2     3.4    -      -       -      +
    127D  GLY      3.3     1.8    -      -       -      +
    128D  VAL*     4.0    30.5    -      -       +      -
    139D  PRO*     3.8    17.0    +      -       +      +
    140D  SER*     1.3    80.0    -      -       -      +
    142D  MET*     1.3    64.5    +      -       -      +
    143D  PRO*     3.4     8.3    -      -       -      +
    157D  PHE*     3.5    56.5    -      -       +      +
    160D  ILE*     4.2    16.2    -      -       +      -
    161D  ALA*     4.3     2.9    -      -       +      -
    170D  CYS      3.4     7.8    +      -       -      +
    171D  CYS*     3.6    28.5    -      -       -      -
    361D  MET*     3.8     6.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with MET 142 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    126D  SER*     3.2     6.5    +      -       -      -
    127D  GLY*     2.8    30.6    +      -       -      +
    129D  SER*     4.1     8.1    -      -       -      -
    140D  SER*     4.3     4.5    -      -       -      +
    141D  LEU*     1.3    77.4    -      -       -      +
    143D  PRO*     1.3    65.4    -      -       -      +
    174D  VAL*     3.8     6.3    -      -       +      -
    180D  GLY*     3.4    15.7    -      -       -      +
    183D  VAL*     3.7    24.5    -      -       +      -
    184D  LYS*     3.6    34.8    -      -       +      -
    187D  HIS*     4.3     4.3    -      -       +      -
    361D  MET*     3.6    21.3    -      -       +      +
    362D  TRP*     3.6    27.1    -      -       +      +
    366D  CYS*     4.0    18.2    -      -       -      -
----------------------------------------------------------
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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