Contacts of the strand formed by residues 193 - 201 (chain N) in PDB entry 7K60


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 GLY 193 (chain N).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    106N  TYR*     5.0    13.5    -      -       -      -
    118N  GLY      5.7     1.6    -      -       -      -
    119N  SER*     5.6     4.7    -      -       -      -
    187N  LYS      3.5     1.4    -      -       -      +
    188N  GLN*     3.5     3.7    -      -       -      -
    189N  THR*     3.1    37.1    +      -       -      +
    190N  PRO      4.8     0.2    -      -       -      -
    191N  ARG      3.4     3.6    +      -       -      +
    192N  GLN*     1.3    82.4    -      -       -      +
    194N  LEU*     1.3    62.7    +      -       -      -
    195N  GLU*     4.9     1.2    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 194 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     55N  TYR*     6.0     1.1    -      -       +      -
     57N  GLN*     4.0     5.4    -      -       -      +
     63N  PRO*     4.7    11.0    -      -       +      -
    106N  TYR*     3.5    47.5    -      -       +      -
    117N  PHE*     3.7    49.1    +      -       +      +
    118N  GLY      5.2     1.8    +      -       -      +
    186N  VAL*     3.6    22.0    -      -       +      -
    187N  LYS      3.5     1.8    -      -       -      -
    188N  GLN*     3.2    33.7    -      -       +      +
    192N  GLN      4.1     4.5    -      -       -      +
    193N  GLY*     1.3    73.4    -      -       -      -
    195N  GLU*     1.3    62.5    +      -       -      +
    244N  TYR*     4.4     7.4    -      -       +      -
    259N  TRP*     4.8     2.0    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLU 195 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     20N  ASP*     5.4     4.7    -      -       -      +
    115N  TYR      3.9    11.1    -      -       -      +
    116N  THR*     5.1     4.5    -      -       -      +
    117N  PHE*     4.5     3.4    +      -       -      -
    186N  VAL*     3.2     7.2    -      -       -      +
    187N  LYS*     2.6    55.2    +      -       +      +
    189N  THR*     6.4     0.9    -      -       +      -
    192N  GLN*     5.5     6.5    -      -       +      +
    193N  GLY      4.9     1.8    -      -       -      +
    194N  LEU*     1.3    78.9    -      -       -      +
    196N  TRP*     1.3    76.6    +      -       -      +
    197N  ILE      3.7     0.2    +      -       -      -
    210N  ASN*     3.7    16.3    +      -       -      -
    212N  LYS*     3.2    26.6    +      -       -      +
    213N  PHE*     3.7    27.8    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with TRP 196 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    113N  SER      3.2    25.8    -      -       -      -
    114N  PRO*     3.8     7.2    -      -       +      -
    115N  TYR*     3.4    52.2    -      +       +      +
    117N  PHE*     4.2    13.4    -      +       +      -
    184N  GLN*     2.8    26.6    +      -       +      -
    185N  TRP      3.9    13.0    -      -       -      -
    186N  VAL*     4.5    10.5    -      -       +      +
    195N  GLU*     1.3    81.0    +      -       -      +
    197N  ILE*     1.3    57.9    +      -       -      +
    198N  GLY*     3.5    27.3    +      -       -      -
    199N  TYR*     3.6    22.7    -      +       -      -
    208N  LYS*     4.3    20.9    -      -       +      -
    209N  TYR      4.5     1.1    -      -       -      -
    210N  ASN*     2.8    54.0    +      -       +      +
    213N  PHE*     4.3     0.2    -      -       -      -
    256N  LEU*     5.2     2.5    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 197 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    185N  TRP*     2.9    16.7    +      -       +      +
    186N  VAL      4.4     2.7    -      -       -      -
    187N  LYS*     3.7    17.3    -      -       +      +
    196N  TRP*     1.3    75.2    -      -       -      +
    198N  GLY*     1.3    62.0    +      -       -      +
    209N  TYR*     3.6     5.8    -      -       +      +
    210N  ASN*     2.7    29.7    +      -       -      +
    213N  PHE*     3.9    33.6    -      -       +      +
    217N  ALA*     3.7    28.3    -      -       +      -
    219N  LEU*     5.9     1.8    -      -       +      -
    230N  MET*     3.9    19.5    -      -       +      -
    232N  LEU*     5.3     1.8    -      -       +      -
    243N  TYR*     3.5    38.6    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLY 198 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    184N  GLN*     3.6     0.9    -      -       -      -
    185N  TRP*     2.9    29.8    +      -       -      +
    196N  TRP*     3.5    18.7    +      -       -      -
    197N  ILE*     1.3    84.5    -      -       -      +
    199N  TYR*     1.3    60.8    +      -       -      +
    208N  LYS      3.1    14.4    -      -       -      -
    209N  TYR*     4.4     1.3    -      -       -      -
    219N  LEU*     4.1     8.1    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with TYR 199 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    115N  TYR*     4.6    12.8    -      +       -      -
    182N  THR*     4.1    17.0    -      -       +      -
    183N  ILE      3.1    13.0    -      -       -      +
    184N  GLN*     3.2    29.8    -      -       -      +
    196N  TRP*     3.6    18.6    -      +       -      -
    198N  GLY*     1.3    73.2    -      -       -      -
    200N  ILE*     1.3    69.3    +      -       -      +
    201N  TYR*     4.6     5.8    -      -       +      -
    206N  GLY      4.6     6.1    -      -       -      -
    207N  THR*     3.4     6.9    -      -       -      -
    208N  LYS*     3.2    68.9    +      -       +      +
    219N  LEU*     3.4    11.6    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 200 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    182N  THR*     3.3     3.6    -      -       -      -
    183N  ILE*     3.1    33.1    +      -       +      +
    185N  TRP*     5.5     0.2    -      -       -      +
    199N  TYR*     1.3    78.5    -      -       -      +
    201N  TYR*     1.3    67.5    +      -       -      +
    202N  PRO*     3.3     7.5    -      -       +      +
    205N  ALA*     4.5    12.3    -      -       +      +
    206N  GLY      3.3     4.5    -      -       -      +
    207N  THR*     3.5    16.6    -      -       +      -
    219N  LEU*     3.8    32.5    -      -       +      +
    220N  THR*     3.8    20.4    -      -       -      -
    221N  SER*     3.9    13.9    -      -       -      +
    228N  VAL*     3.4    27.6    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with TYR 201 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     89G  ASN      3.3    20.4    -      -       -      -
     90G  ASP*     3.1     8.6    +      -       -      -
     91G  GLU*     2.5    37.7    +      -       +      +
    179N  THR      4.4     3.6    -      -       -      -
    180N  SER      4.0    12.6    -      -       -      -
    181N  TYR      4.6     0.7    -      -       -      -
    182N  THR*     3.3    26.7    -      -       +      -
    199N  TYR*     4.3     6.9    -      -       +      -
    200N  ILE*     1.3    72.5    -      -       -      +
    202N  PRO*     1.3    55.6    -      -       +      +
    203N  TYR*     3.0    26.7    +      +       +      -
    204N  ASN*     3.0    23.2    +      -       -      +
    205N  ALA*     2.7    33.2    +      -       -      -
    206N  GLY*     2.7    18.7    +      -       -      +
    250N  SER*     3.7    21.2    +      -       -      -
----------------------------------------------------------
 Back to top of page


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