Contacts of the strand formed by residues 197 - 201 (chain B) in PDB entry 1K4R


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 THR 197 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    130B  HIS      4.2     1.2    -      -       -      +
    131B  VAL*     4.1    15.2    -      -       -      +
    132B  TYR*     4.4    15.6    +      -       +      -
    192B  VAL*     5.8     0.5    -      -       -      +
    193B  ASP      4.5     3.6    +      -       -      -
    194B  LEU*     3.2    34.3    +      -       +      +
    195B  ALA      3.4     2.6    -      -       -      +
    196B  GLN*     1.3    79.1    -      -       -      +
    198B  VAL*     1.3    69.2    +      -       -      +
    199B  ILE*     4.0    16.8    -      -       +      -
    214B  GLN*     3.6    37.8    +      -       +      +
    215B  VAL      3.7     3.6    -      -       -      -
    217B  ARG*     5.1     0.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 198 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     56B  THR*     4.7     2.5    -      -       +      +
    129B  GLY*     3.6    28.7    -      -       -      -
    130B  HIS      3.3     9.0    -      -       -      +
    131B  VAL*     4.4    10.8    -      -       +      -
    197B  THR*     1.3    80.3    -      -       -      +
    199B  ILE*     1.3    68.6    +      -       -      +
    200B  LEU      4.5     0.4    -      -       -      +
    214B  GLN*     3.7     1.9    -      -       -      -
    215B  VAL*     2.9    45.1    +      -       +      +
    217B  ARG*     3.7    33.2    -      -       +      +
    220B  PHE*     4.0    26.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 199 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     53B  PRO*     6.2     0.4    -      -       +      -
    129B  GLY*     3.4     1.2    -      -       -      -
    130B  HIS*     2.9    51.5    +      -       +      +
    132B  TYR*     3.5    43.7    -      -       +      +
    197B  THR*     4.0    13.2    -      -       +      -
    198B  VAL*     1.3    73.9    -      -       -      +
    200B  LEU*     1.3    60.5    +      -       -      +
    212B  ALA*     3.8    25.6    -      -       +      -
    213B  TRP      3.3     4.7    -      -       -      +
    214B  GLN*     4.2     4.0    -      -       -      -
    274B  ALA*     4.1    17.5    -      -       +      -
    275B  HIS      5.8     0.7    -      -       -      +
    276B  ILE*     5.1     0.4    -      -       +      -
    281B  TYR*     3.9    23.1    -      -       +      -
    282B  HIS      5.6     0.7    -      -       -      +
    283B  LEU*     4.1    11.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 200 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    127B  ALA*     4.0    19.7    -      -       +      -
    128B  THR      3.5     8.1    -      -       -      +
    129B  GLY*     4.6     0.9    -      -       -      -
    198B  VAL*     3.6     1.6    +      -       -      -
    199B  ILE*     1.3    71.2    -      -       -      +
    201B  GLU*     1.3    59.9    +      -       -      +
    202B  LEU*     4.3     7.6    -      -       +      -
    212B  ALA*     3.3     8.5    -      -       -      +
    213B  TRP*     2.8    40.2    +      -       +      +
    215B  VAL*     4.3    14.4    -      -       +      -
    219B  TRP*     4.4    11.7    -      -       +      -
    220B  PHE*     3.7    31.9    -      -       +      -
    223B  LEU*     5.4     2.2    -      -       +      -
    264B  LEU*     4.3    13.9    -      -       +      -
    268B  LEU*     3.9    38.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 201 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     55B  LYS*     5.8     0.5    +      -       -      -
    126B  LYS      3.9     0.2    -      -       -      +
    127B  ALA*     3.4     3.5    -      -       -      -
    128B  THR*     2.8    41.9    +      -       -      +
    130B  HIS*     3.1    17.7    +      -       +      +
    200B  LEU*     1.3    74.9    -      -       -      +
    202B  LEU*     1.3    76.8    +      -       -      +
    204B  LYS*     3.7    29.7    +      -       +      +
    211B  THR      4.2     8.3    -      -       -      +
    276B  ILE*     3.5    23.6    -      -       +      -
    281B  TYR*     2.8    25.1    +      -       +      -
----------------------------------------------------------
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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