Contacts of the strand formed by residues 438 - 448 (chain B) in PDB entry 1KCX


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 GLU 438 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    367B  ASP*     3.8     5.9    -      -       -      +
    417B  MET*     5.2    14.7    -      -       +      +
    418B  LYS      3.5     5.6    -      -       -      +
    419B  THR*     3.4    21.0    +      -       +      +
    436B  GLY      3.3     7.7    +      -       -      +
    437B  MET*     1.3    74.7    -      -       -      +
    439B  CYS*     1.3    61.8    +      -       -      +
    440B  HIS*     3.8    21.3    +      -       +      +
----------------------------------------------------------
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Residues in contact with CYS 439 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    363B  THR*     3.3    37.0    -      -       +      -
    364B  VAL*     4.8     0.2    -      -       -      -
    367B  ASP*     3.4    21.1    -      -       +      -
    417B  MET*     3.2     4.3    -      -       -      +
    418B  LYS*     2.8    38.5    +      -       -      +
    420B  ILE*     4.0    13.2    -      -       -      -
    437B  MET*     3.7    35.2    -      -       -      -
    438B  GLU*     1.3    73.7    -      -       -      +
    440B  HIS*     1.3    63.0    +      -       -      +
    441B  GLY      3.7     2.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with HIS 440 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    366B  TRP*     3.2    17.9    +      -       -      -
    367B  ASP*     2.9    30.8    +      -       -      +
    371B  ALA*     4.2    18.0    -      -       +      +
    414B  PRO      3.0    19.0    -      -       -      +
    415B  ASP*     5.5     1.1    -      -       -      -
    416B  LYS      4.1     8.7    -      -       -      +
    417B  MET*     4.3    16.8    -      -       +      +
    438B  GLU*     3.8    20.4    +      -       +      +
    439B  CYS*     1.3    77.1    -      -       -      +
    441B  GLY*     1.3    56.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 441 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    363B  THR*     3.3    24.4    -      -       -      +
    366B  TRP*     3.8    11.8    -      -       -      -
    412B  TRP*     3.1    18.9    -      -       -      -
    413B  ASP      3.4    14.4    -      -       -      -
    414B  PRO      3.9     2.9    -      -       -      -
    416B  LYS      3.3     9.6    +      -       -      -
    418B  LYS*     5.7     0.2    -      -       -      -
    439B  CYS      3.7     1.6    -      -       -      -
    440B  HIS*     1.3    75.5    -      -       -      +
    442B  SER*     1.3    59.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with SER 442 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    363B  THR*     4.2     6.3    -      -       -      -
    412B  TRP*     3.6     9.6    -      -       -      -
    413B  ASP*     3.0    30.6    +      -       -      +
    416B  LYS*     2.9    36.6    +      -       -      +
    418B  LYS*     4.4    19.2    -      -       -      +
    441B  GLY*     1.3    75.1    -      -       -      -
    443B  PRO*     1.3    76.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with PRO 443 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     98B  ALA      4.3     9.0    -      -       -      +
     99B  GLY*     3.6    32.1    -      -       -      +
    100B  GLY*     3.8     3.4    -      -       -      +
    363B  THR*     4.4     6.1    -      -       -      +
    410B  VAL*     4.0     7.0    -      -       +      -
    411B  ILE      3.7     5.4    -      -       -      +
    412B  TRP*     3.6    18.8    -      -       +      -
    416B  LYS*     4.5     7.6    +      -       -      -
    442B  SER*     1.3    97.5    +      -       -      +
    444B  LEU*     1.3    61.4    +      -       -      +
    446B  VAL*     4.0    23.1    -      -       +      -
    454B  PHE*     3.9    13.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 444 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     63B  ARG*     3.6    46.2    -      -       +      +
    411B  ILE*     2.7    25.4    +      -       +      +
    413B  ASP*     4.2    20.0    -      -       +      +
    416B  LYS*     4.4    20.2    -      -       -      +
    442B  SER      3.8     0.4    +      -       -      -
    443B  PRO*     1.3    74.3    -      -       -      +
    445B  VAL*     1.3    68.5    +      -       +      +
    454B  PHE*     3.8    14.9    -      -       -      -
    455B  GLU*     3.9     9.2    -      -       -      -
    456B  ASP*     4.2     7.6    +      -       -      +
    457B  GLY      4.9     1.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 445 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     58B  ILE*     4.4    20.9    -      -       +      -
    409B  VAL      4.7     0.2    -      -       -      -
    410B  VAL*     3.2     5.9    -      -       -      +
    411B  ILE*     2.8    53.2    +      -       +      -
    444B  LEU*     1.3    92.8    -      -       +      +
    446B  VAL*     1.3    70.6    +      -       -      +
    447B  ILE*     4.1    24.0    -      -       +      -
    452B  ILE*     4.4     7.0    -      -       +      -
    454B  PHE*     3.2    13.9    -      -       -      +
    455B  GLU*     4.4    10.8    -      -       +      +
    456B  ASP      5.3     0.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 446 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     97B  LEU*     3.4    28.0    -      -       +      +
    100B  GLY*     4.1     4.9    -      -       -      +
    102B  THR*     4.0    23.1    -      -       +      -
    409B  VAL      3.6     2.5    -      -       -      -
    410B  VAL*     4.0    11.0    -      -       +      -
    443B  PRO*     4.0    22.4    -      -       +      -
    445B  VAL*     1.3    79.7    -      -       -      +
    447B  ILE*     1.3    68.3    +      -       -      +
    452B  ILE*     3.6     1.4    -      -       -      +
    453B  VAL*     2.9    39.2    +      -       +      -
    454B  PHE*     2.9    30.3    +      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 447 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     17B  LEU*     3.8    21.3    -      -       +      -
     19B  ILE*     3.9    26.2    -      -       +      -
     37B  LEU*     4.1    10.1    -      -       +      -
     58B  ILE*     4.3    10.8    -      -       +      -
    102B  THR*     3.7     7.0    -      -       -      +
    407B  ALA      3.9     3.6    -      -       -      +
    408B  ASP*     3.2     5.2    -      -       -      -
    409B  VAL*     2.6    47.9    +      -       +      +
    411B  ILE*     5.7     1.8    -      -       +      -
    445B  VAL*     4.1    12.6    -      -       +      -
    446B  VAL*     1.3    79.4    -      -       -      +
    448B  SER*     1.3    59.0    +      -       -      +
    450B  GLY*     3.4    39.7    -      -       -      +
    451B  LYS      3.2     6.3    -      -       -      +
    452B  ILE*     4.2     9.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 448 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     97B  LEU*     4.1    22.0    -      -       -      -
    102B  THR*     4.6     6.9    +      -       -      -
    132B  CYS      4.3     4.4    +      -       -      -
    133B  CYS*     4.1    21.3    -      -       -      +
    134B  ASP*     4.7     1.4    +      -       -      -
    408B  ASP*     3.8     7.3    +      -       -      -
    446B  VAL      4.3     0.2    -      -       -      -
    447B  ILE*     1.3    73.0    -      -       -      +
    449B  GLN*     1.3    81.6    +      -       -      +
    450B  GLY      3.1     0.4    -      -       -      -
    451B  LYS*     2.9    24.3    +      -       -      +
    453B  VAL*     4.2    15.0    -      -       -      +
----------------------------------------------------------
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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