Contacts of the strand formed by residues 241 - 249 (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 ALA 241 (chain N).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    187N  LYS*     3.6    24.5    -      -       +      -
    188N  GLN      3.2    15.3    -      -       -      +
    189N  THR*     3.5    20.4    -      -       +      +
    190N  PRO*     5.3     1.8    -      -       -      -
    239N  ASP      3.1     5.9    +      -       -      +
    240N  SER*     1.3    76.8    -      -       -      +
    242N  VAL*     1.3    63.4    +      -       -      +
    243N  TYR*     3.2    11.2    -      -       +      -
    264N  SER*     4.6     2.0    -      -       -      -
    265N  VAL      3.0    27.1    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 242 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     60N  TRP*     6.0     7.2    -      -       +      -
    186N  VAL      3.8     0.5    -      -       -      +
    187N  LYS*     3.6     0.9    -      -       -      -
    188N  GLN*     2.7    47.2    +      -       +      +
    241N  ALA*     1.3    74.5    -      -       -      +
    243N  TYR*     1.3    61.8    +      -       -      +
    244N  TYR*     3.4    39.1    -      -       +      +
    261N  GLN      5.1     0.4    -      -       -      +
    262N  GLY*     4.0    16.8    -      -       -      -
    263N  THR      3.6     5.4    -      -       -      +
    264N  SER*     4.0    20.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 243 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    155N  GLN*     2.4    28.8    +      -       -      -
    169N  MET*     3.9    22.4    -      -       +      -
    185N  TRP*     4.2     9.0    -      -       +      -
    186N  VAL      3.3     4.3    -      -       -      +
    187N  LYS*     3.7    25.1    -      -       +      +
    197N  ILE*     3.5    31.6    -      -       +      -
    213N  PHE*     5.5     1.0    -      +       -      -
    230N  MET*     4.2     7.0    -      -       +      -
    232N  LEU*     3.4    27.9    -      -       +      +
    239N  ASP*     3.1    29.3    +      -       -      +
    241N  ALA*     3.2    24.7    -      -       +      -
    242N  VAL*     1.3    73.2    -      -       -      +
    244N  TYR*     1.3    55.8    +      -       -      +
    262N  GLY*     3.3     0.9    -      -       -      -
    263N  THR      2.9    28.4    +      -       -      +
    265N  VAL*     3.9    18.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 244 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     57N  GLN*     4.3     2.2    -      -       -      -
     60N  TRP*     5.3     4.5    -      -       -      -
     61N  LYS      3.8    11.3    +      -       -      -
     62N  SER*     3.9    18.8    -      -       -      -
     63N  PRO*     4.1     7.2    -      -       +      -
    155N  GLN*     3.8     2.2    -      -       -      -
    184N  GLN      3.6     0.2    -      -       -      +
    185N  TRP*     3.4     5.6    -      -       -      -
    186N  VAL*     2.7    45.1    +      -       -      +
    188N  GLN*     3.1    41.9    +      -       +      -
    194N  LEU*     4.7     3.4    -      -       +      -
    242N  VAL*     3.4    28.2    -      -       +      +
    243N  TYR*     1.3    74.1    -      -       -      +
    245N  CYS*     1.3    61.6    -      -       -      +
    259N  TRP*     3.5    31.2    -      +       +      -
    260N  GLY      3.3    19.1    -      -       -      +
    261N  GLN      3.5    19.4    +      -       -      -
    262N  GLY*     3.5     8.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with CYS 245 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    153N  LEU*     4.0     8.3    -      -       +      -
    155N  GLN*     3.4    29.0    +      -       -      +
    171N  CYS*     3.3    35.4    -      -       -      -
    183N  ILE*     4.1    10.3    -      -       +      -
    184N  GLN      3.3     4.0    -      -       -      -
    185N  TRP*     4.1    17.2    -      -       +      -
    244N  TYR*     1.3    74.7    -      -       -      +
    246N  ALA*     1.3    60.8    +      -       -      +
    259N  TRP*     3.3     5.2    -      -       -      +
    260N  GLY*     2.8    39.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 246 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    153N  LEU*     4.4     0.9    -      -       -      -
    183N  ILE*     4.4     2.7    -      -       -      +
    184N  GLN*     2.5    50.1    +      -       -      +
    186N  VAL*     4.7     1.1    -      -       +      -
    245N  CYS*     1.3    78.1    -      -       -      +
    247N  ARG*     1.3    63.0    +      -       -      +
    256N  LEU*     3.6    36.1    -      -       +      -
    258N  TYR      3.3     5.8    -      -       -      +
    259N  TRP*     4.0    19.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 247 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    105H  GLU*     4.5     6.7    +      -       -      -
    151N  VAL*     3.6    21.3    -      -       -      +
    153N  LEU*     3.7    14.6    -      -       +      +
    176N  TYR*     3.6    44.6    -      -       -      +
    181N  TYR*     3.6    52.1    +      -       +      -
    182N  THR      3.6     5.8    -      -       -      +
    183N  ILE*     4.4     4.9    -      -       +      -
    246N  ALA*     1.3    73.4    -      -       -      +
    248N  LYS*     1.3    59.9    +      -       -      +
    256N  LEU*     3.3     3.6    -      -       -      -
    257N  ASP*     2.6    64.3    +      -       -      +
    258N  TYR*     2.8    36.0    +      -       +      +
----------------------------------------------------------
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Residues in contact with LYS 248 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    110N  HIS*     4.0    15.2    -      -       -      -
    115N  TYR*     4.2    20.4    +      -       +      -
    181N  TYR*     4.2     3.1    -      -       -      -
    182N  THR*     2.6    41.7    +      -       -      +
    184N  GLN*     3.6    34.5    -      -       +      +
    246N  ALA      3.6     0.2    +      -       -      -
    247N  ARG*     1.3    76.2    -      -       -      +
    249N  SER*     1.3    70.6    +      -       -      +
    250N  SER      4.9     1.6    +      -       -      -
    251N  ARG      3.2    25.7    +      -       -      -
    252N  LEU*     4.2     7.1    +      -       -      +
    254N  SER      3.2    14.9    +      -       -      +
    255N  THR      3.5    21.5    -      -       -      +
    256N  LEU*     3.7    15.9    -      -       +      -
    257N  ASP*     4.7     0.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 249 (chain N). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     92G  GLU*     3.8     8.3    +      -       -      -
    105H  GLU*     3.3    24.4    -      -       -      +
    180N  SER      4.4     1.4    +      -       -      -
    181N  TYR*     3.5    27.0    -      -       -      +
    182N  THR*     4.5     0.9    +      -       -      +
    248N  LYS*     1.3    98.5    +      -       -      +
    250N  SER*     1.3    65.8    +      -       -      +
    251N  ARG*     3.0    14.3    +      -       -      +
    254N  SER*     3.5    25.8    -      -       -      -
    255N  THR      4.5     1.0    +      -       -      -
    257N  ASP*     5.3     2.9    +      -       -      -
----------------------------------------------------------
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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