Contacts of the strand formed by residues 734 - 738 (chain B) in PDB entry 1KT8


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 GLN 734 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    728B  LEU*     3.1     8.6    -      -       -      -
    729B  TYR*     2.8    65.2    +      -       +      +
    730B  GLY*     4.8     1.4    -      -       -      -
    732B  ASP*     3.3    28.5    -      -       -      +
    733B  HIS*     1.3    76.3    -      -       -      +
    735B  LEU*     1.3    63.9    +      -       -      +
    736B  THR*     3.6     6.3    +      -       +      +
    762B  ASN*     4.7    12.1    -      -       -      +
    790B  THR*     4.0    28.1    +      -       +      +
    791B  ILE      3.1    15.0    -      -       -      +
    792B  THR*     4.0     4.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 735 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    726B  LEU*     3.9    22.7    -      -       +      -
    727B  TRP      4.0     3.8    -      -       -      -
    728B  LEU*     4.1     2.9    -      -       +      -
    734B  GLN*     1.3    75.5    -      -       -      +
    736B  THR*     1.3    59.2    +      -       -      +
    743B  ILE*     3.7    32.5    -      -       +      -
    745B  VAL*     5.1     5.8    -      -       +      -
    759B  PRO*     3.0    23.4    -      -       -      +
    791B  ILE*     2.9    42.9    +      -       +      +
    792B  THR      3.5    23.3    -      -       -      +
    793B  MET*     3.5    17.3    -      -       -      +
    796B  LEU*     4.3    19.5    -      -       +      -
    823B  ILE*     5.4     0.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 736 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    692B  ARG*     5.5     2.2    +      -       -      +
    726B  LEU*     5.2     0.4    -      -       -      +
    727B  TRP*     2.8    36.2    +      -       -      +
    728B  LEU      4.5     0.4    -      -       -      -
    729B  TYR*     3.5    33.0    -      -       +      -
    734B  GLN*     3.9     9.2    -      -       +      +
    735B  LEU*     1.3    74.8    -      -       -      +
    737B  GLU*     1.3    70.9    +      -       -      +
    742B  ASN*     5.1     0.7    -      -       -      +
    743B  ILE*     3.4    16.1    +      -       -      +
    759B  PRO*     3.6    10.4    -      -       -      +
    764B  VAL*     4.9    11.7    -      -       +      -
    765B  ILE*     3.7    29.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 737 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    692B  ARG*     2.2    54.6    +      -       -      +
    726B  LEU*     3.8     5.4    -      -       -      +
    727B  TRP*     2.9    31.5    +      -       +      -
    736B  THR*     1.3    88.0    +      -       -      +
    738B  VAL*     1.3    58.2    +      -       -      +
    739B  GLY      5.2     0.9    -      -       -      +
    741B  MET      3.0    17.3    -      -       -      +
    742B  ASN*     3.6    11.0    -      -       -      +
    743B  ILE*     4.1     7.4    -      -       -      +
    765B  ILE*     3.6     6.4    -      -       +      -
    766B  LEU      3.3    20.5    +      -       -      -
    900B  ILP      2.8    33.1    +      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 738 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    684B  LEU*     3.0    45.8    -      -       +      -
    724B  GLN*     4.1     8.1    -      -       -      +
    725B  VAL      3.2     9.6    -      -       -      +
    726B  LEU*     4.0    12.8    -      -       +      +
    737B  GLU*     1.3    72.9    -      -       -      +
    739B  GLY*     1.3    61.2    +      -       -      +
    740B  THR      3.0     0.9    +      -       -      -
    741B  MET*     2.9    54.8    +      -       +      +
    742B  ASN      4.1     3.1    -      -       -      +
    743B  ILE*     4.2    10.3    -      -       +      -
    809B  PHE      5.3     0.4    -      -       -      -
    810B  GLY*     4.1    14.4    -      -       -      +
    820B  VAL*     5.5     2.7    -      -       +      -
----------------------------------------------------------
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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