Contacts of the strand formed by residues 181 - 189 (chain N) in PDB entry 7K63


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 181 (chain N).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     92G  GLU*     4.8     4.1    +      -       -      -
    104H  GLY*     5.0     4.9    -      -       -      -
    105H  GLU*     3.5    27.1    +      -       +      +
    176N  TYR*     3.4    28.3    -      +       +      -
    177N  THR*     3.5     7.6    -      -       -      -
    178N  PHE      3.5     7.6    +      -       -      +
    179N  THR      3.3     0.8    -      -       -      -
    180N  SER*     1.3    92.9    -      -       -      +
    182N  THR*     1.3    64.4    +      -       -      +
    183N  ILE*     3.8     3.5    +      -       -      +
    201N  TYR*     4.2     3.6    -      -       -      -
    202N  PRO*     3.2    18.4    -      -       -      +
    247N  ARG*     3.6    58.4    +      -       +      -
    248N  LYS      3.9     2.0    -      -       -      +
    249N  SER*     3.5    38.4    -      -       -      +
    257N  ASP*     5.0     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with THR 182 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    181N  TYR*     1.3    75.1    -      -       -      +
    183N  ILE*     1.3    60.0    +      -       -      +
    184N  GLN*     2.8    27.3    +      -       -      +
    199N  TYR*     4.1    13.2    -      -       +      -
    200N  ILE      3.4    11.9    -      -       -      -
    201N  TYR*     3.4    30.5    -      -       +      -
    247N  ARG*     3.6     4.0    -      -       -      -
    248N  LYS*     2.6    50.8    +      -       -      +
    249N  SER      4.9     0.2    -      -       -      +
    250N  SER*     4.5    13.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 183 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    153N  LEU*     4.2    14.1    -      -       +      -
    171N  CYS*     4.3     9.0    -      -       -      -
    173N  ALA*     5.0     0.2    -      -       +      -
    176N  TYR*     3.2    27.6    -      -       -      +
    178N  PHE*     4.4     8.5    -      -       +      -
    181N  TYR      4.3     5.6    -      -       -      +
    182N  THR*     1.3    77.6    -      -       -      +
    184N  GLN*     1.3    62.4    +      -       -      +
    185N  TRP*     3.9    23.8    +      -       +      +
    199N  TYR*     3.2    21.6    -      -       -      -
    200N  ILE*     3.1    20.8    +      -       +      -
    202N  PRO*     4.4     3.4    -      -       +      -
    228N  VAL*     3.8    22.4    -      -       +      -
    245N  CYS*     4.1    19.3    -      -       +      -
    246N  ALA      3.6     3.8    -      -       -      +
    247N  ARG*     4.4     7.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 184 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    115N  TYR*     3.6     8.9    +      -       -      -
    182N  THR*     2.8    23.4    +      -       -      +
    183N  ILE*     1.3    73.0    -      -       -      +
    185N  TRP*     1.3    60.8    +      -       -      +
    186N  VAL*     4.7     0.2    -      -       -      -
    196N  TRP*     2.5    37.7    +      -       +      +
    198N  GLY      3.8     2.0    -      -       -      -
    199N  TYR*     3.2    27.0    -      -       -      +
    244N  TYR      3.6     0.2    -      -       -      +
    245N  CYS*     3.2     1.9    -      -       -      -
    246N  ALA*     2.5    53.2    +      -       -      +
    248N  LYS*     3.6    33.1    -      -       +      +
    256N  LEU*     3.8    23.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with TRP 185 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    155N  GLN*     3.5    28.9    -      -       -      -
    169N  MET*     3.7    36.6    -      -       +      -
    170N  PRO      4.6     4.7    -      -       -      -
    171N  CYS*     3.9    19.3    -      -       +      -
    183N  ILE*     3.9    16.0    -      -       +      +
    184N  GLN*     1.3    76.0    -      -       -      +
    186N  VAL*     1.3    62.3    +      -       -      +
    196N  TRP*     3.9     2.6    -      -       -      -
    197N  ILE*     2.9    31.5    +      -       +      +
    198N  GLY      2.9    17.0    +      -       -      +
    219N  LEU*     3.4    25.4    -      -       +      +
    228N  VAL*     3.6    18.3    -      -       +      +
    230N  MET*     3.5    41.1    -      -       +      -
    243N  TYR*     4.2    14.4    -      -       +      -
    244N  TYR      3.4    12.1    -      -       -      -
    245N  CYS*     4.1    11.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 186 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    117N  PHE*     3.9    22.4    -      -       +      -
    184N  GLN      4.6     2.2    -      -       -      +
    185N  TRP*     1.3    81.1    -      -       -      +
    187N  LYS*     1.3    60.0    +      -       -      +
    194N  LEU*     3.6    28.7    -      -       +      -
    195N  GLU      3.3    17.0    -      -       -      +
    196N  TRP*     4.7     4.3    -      -       +      -
    197N  ILE*     3.9     3.1    -      -       -      -
    242N  VAL      3.8     0.5    -      -       -      +
    243N  TYR*     3.3     3.5    -      -       -      +
    244N  TYR*     2.7    46.1    +      -       +      +
    246N  ALA*     4.7     0.4    -      -       +      -
    256N  LEU*     3.8    28.5    -      -       +      -
    259N  TRP*     3.9    17.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 187 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    186N  VAL*     1.3    72.6    -      -       -      +
    188N  GLN*     1.3    61.2    +      -       -      +
    189N  THR*     3.6    24.1    -      -       +      +
    192N  GLN*     4.7     6.9    +      -       -      +
    193N  GLY      3.6     1.7    -      -       -      +
    194N  LEU*     3.4     1.6    -      -       -      -
    195N  GLU*     2.7    60.1    +      -       +      +
    197N  ILE*     3.4    20.7    -      -       +      +
    213N  PHE*     3.8    23.0    -      -       +      -
    238N  GLU*     3.8    20.5    +      -       -      +
    239N  ASP*     4.1    10.8    +      -       -      +
    241N  ALA*     3.6    18.8    -      -       +      -
    242N  VAL      3.6     3.6    -      -       -      -
    243N  TYR*     3.7    24.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLN 188 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     57N  GLN*     2.8    45.7    +      -       -      +
    106N  TYR*     3.8     5.7    +      -       -      -
    187N  LYS*     1.3    73.3    -      -       -      +
    189N  THR*     1.3    70.7    +      -       -      +
    190N  PRO*     4.5     1.6    -      -       +      +
    193N  GLY*     3.6     5.7    -      -       -      +
    194N  LEU*     3.6    27.1    -      -       +      +
    241N  ALA*     3.2     4.5    -      -       -      +
    242N  VAL*     2.7    45.9    +      -       +      +
    244N  TYR*     3.1    27.6    +      -       +      -
----------------------------------------------------------
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Residues in contact with THR 189 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    187N  LYS*     3.6    21.7    -      -       +      +
    188N  GLN*     1.3    81.2    -      -       -      +
    190N  PRO*     1.3    68.0    -      -       -      +
    191N  ARG*     3.1    30.0    +      -       -      +
    192N  GLN*     2.7    42.3    +      -       +      +
    193N  GLY*     3.2    21.6    +      -       -      +
    195N  GLU*     5.1     1.8    -      -       -      +
    240N  SER      4.2     0.9    -      -       -      +
    241N  ALA*     3.5    20.4    -      -       +      -
----------------------------------------------------------
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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