Contacts of the strand formed by residues 134 - 139 (chain D) in PDB entry 5UH8


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 TYR 134 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    133D  ALA*     1.3    76.2    -      -       -      +
    135D  VAL*     1.3    59.5    +      -       -      +
    234D  LEU*     3.4     6.4    -      -       -      +
    235D  ILE*     2.9    38.2    +      -       +      +
    236D  VAL      6.1     0.2    -      -       -      -
    238D  GLU*     4.4    27.5    +      -       +      +
    241D  TYR*     3.3    69.7    -      +       +      -
    242D  ARG*     5.8     0.5    +      -       -      -
    254D  GLY      5.1     1.1    -      -       -      -
    255D  ALA*     3.9     9.2    -      -       -      -
    256D  MET*     3.8    41.1    -      -       +      -
    364D  GLU*     5.9     2.1    -      -       -      +
    368D  ASN*     5.0     7.1    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 135 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    120D  LEU*     5.8     2.5    -      -       +      -
    128D  ILE*     3.6    49.8    -      -       +      -
    134D  TYR*     1.3    76.0    -      -       -      +
    136D  ILE*     1.3    78.7    +      -       -      +
    137D  THR*     3.2     5.4    +      -       +      +
    232D  LYS*     4.3    13.7    -      -       -      -
    233D  GLN      3.3    12.8    -      -       -      +
    234D  LEU*     4.6     1.3    -      -       +      -
    254D  GLY*     4.9     0.4    -      -       -      -
    255D  ALA      3.0    33.3    +      -       -      +
    256D  MET*     4.7     0.2    -      -       -      -
    260D  SER*     3.9    14.4    -      -       -      +
    261D  ILE*     5.6     0.9    -      -       +      -
    264D  LEU*     4.7    10.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 136 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    135D  VAL*     1.3    75.2    -      -       -      +
    137D  THR*     1.3    61.6    +      -       -      +
    138D  SER      4.1    20.2    -      -       -      +
    139D  VAL*     5.0     1.1    -      -       +      -
    229D  LEU*     3.8    30.5    -      -       +      -
    230D  ALA      3.4    29.6    -      -       -      +
    231D  PRO      4.1     0.2    -      -       -      -
    232D  LYS      3.2    22.7    +      -       -      -
    233D  GLN*     2.8    21.0    +      -       +      +
    235D  ILE*     3.6    26.9    -      -       +      +
    241D  TYR*     4.7     1.8    -      -       +      -
    252D  PHE*     3.5    30.1    -      -       +      -
    253D  THR      4.1     2.0    -      -       -      +
    254D  GLY*     4.5     3.6    -      -       -      -
    264D  LEU*     4.3     1.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with THR 137 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    135D  VAL      3.2     6.3    +      -       -      +
    136D  ILE*     1.3    75.0    -      -       -      +
    138D  SER*     1.3    61.8    +      -       -      +
    231D  PRO*     3.9    14.5    -      -       -      +
    253D  THR*     2.2    51.0    +      -       +      +
    255D  ALA*     3.7    25.9    +      -       +      -
    260D  SER*     4.0    24.2    -      -       -      +
    263D  LYS*     4.3    20.8    -      -       +      +
    264D  LEU*     4.0    17.1    -      -       +      +
    267D  ASN*     4.8     7.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER 138 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    136D  ILE*     3.7     4.5    -      -       -      +
    137D  THR*     1.3    82.7    +      -       -      +
    139D  VAL*     1.3    62.6    +      -       -      +
    231D  PRO*     4.5     7.6    -      -       -      -
    252D  PHE*     3.4     5.5    -      -       -      +
    253D  THR*     2.8    52.9    +      -       -      +
    263D  LYS*     4.7    11.0    +      -       -      -
    267D  ASN*     5.2     5.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 139 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    136D  ILE*     5.0     2.5    -      -       +      -
    138D  SER*     1.3    78.6    -      -       -      +
    140D  ASP*     1.3    62.7    +      -       -      +
    141D  GLU*     3.2    38.8    +      -       +      +
    144D  ARG*     4.5    11.7    -      -       +      +
    229D  LEU*     4.2    16.8    -      -       +      +
    230D  ALA*     4.1     8.1    -      -       -      -
    231D  PRO*     3.6    30.0    -      -       +      +
    251D  TYR*     3.8    12.6    -      -       +      +
    252D  PHE*     4.3     7.4    -      -       +      +
----------------------------------------------------------
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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