Contacts of the strand formed by residues 250 - 255 (chain A) 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 VAL 250 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    185A  PHE*     4.0    17.9    -      -       +      -
    195A  ILE*     3.8     6.1    -      -       +      +
    197A  VAL*     3.9    24.7    -      -       +      -
    239A  ALA*     4.4     6.3    -      -       +      +
    240A  ILE*     4.6    10.1    -      -       +      -
    243A  ALA*     3.6    23.1    -      -       +      -
    249A  PRO*     1.3    77.0    -      -       -      +
    251A  TYR*     1.3    62.2    +      -       -      +
    252A  ILE*     4.6     8.5    -      -       +      -
    272A  PRO*     6.1     0.9    -      -       +      -
    273A  LEU      3.0    10.6    +      -       -      +
    274A  VAL*     3.3    27.3    -      -       +      +
    275A  PHE*     3.0    26.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 251 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     72A  VAL*     3.2    22.0    +      -       -      +
    194A  VAL*     4.5     8.1    -      -       +      -
    195A  ILE      2.8    21.1    +      -       -      +
    196A  LEU*     3.4    19.3    -      -       +      -
    197A  VAL*     3.0    28.9    +      -       -      +
    250A  VAL*     1.3    73.9    -      -       -      +
    252A  ILE*     1.3    65.3    +      -       -      +
    253A  THR*     3.8    13.9    -      -       +      -
    275A  PHE*     3.8    23.8    -      +       +      +
    277A  GLU*     2.7    48.6    +      -       +      +
    328A  VAL*     3.5    13.6    -      -       +      +
    391A  ILE*     4.4    15.9    -      -       +      -
    392A  PHE*     3.7    28.9    -      +       -      -
----------------------------------------------------------
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Residues in contact with ILE 252 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    197A  VAL*     4.3    15.0    -      -       +      +
    199A  ALA*     4.8     7.9    -      -       +      -
    232A  GLU*     5.9     1.3    -      -       -      +
    236A  VAL*     4.0    44.6    -      -       +      +
    239A  ALA*     4.5    14.8    -      -       +      -
    240A  ILE*     5.0     1.3    -      -       +      -
    250A  VAL*     4.6     8.5    -      -       +      -
    251A  TYR*     1.3    77.2    -      -       -      +
    253A  THR*     1.3    71.8    +      -       -      +
    255A  VAL*     3.6    14.8    -      -       +      +
    264A  ILE*     4.0    13.5    -      -       +      -
    274A  VAL*     4.1    11.4    -      -       +      -
    275A  PHE      2.9    18.8    +      -       -      +
    277A  GLU*     3.0    26.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 253 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     73A  ASN*     4.1     9.4    -      -       -      +
    165A  GLN*     3.6    23.1    +      -       -      +
    196A  LEU*     3.8    27.6    -      -       +      -
    197A  VAL      2.7    27.6    +      -       -      +
    198A  HIS*     3.9     6.4    -      -       -      +
    199A  ALA      5.3     2.6    +      -       -      -
    232A  GLU*     5.5     0.2    -      -       -      +
    251A  TYR*     3.8    13.0    -      -       +      -
    252A  ILE*     1.3    80.7    -      -       -      +
    254A  LYS*     1.3    78.1    +      -       -      +
    255A  VAL      3.3     1.0    +      -       -      -
    277A  GLU*     3.6    13.7    -      -       -      +
    305A  PRO*     5.3     1.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 254 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     73A  ASN*     3.7    22.2    -      -       -      +
     75A  TYR*     4.7    18.7    -      -       -      -
     78A  LYS*     5.1    10.7    -      -       -      +
    165A  GLN*     6.0     1.1    -      -       -      +
    170A  TYR*     5.8     0.2    +      -       -      -
    198A  HIS*     4.2    18.8    +      -       -      -
    232A  GLU*     3.7     1.6    -      -       -      +
    253A  THR*     1.3    78.1    -      -       -      +
    255A  VAL*     1.3    64.7    +      -       -      +
    256A  MET*     3.1    19.7    +      -       +      +
    277A  GLU*     3.0    18.7    +      -       -      +
    279A  ILE*     4.0    23.1    -      -       +      -
    303A  THR*     4.7     9.5    +      -       -      +
    304A  SER      2.9    27.5    +      -       -      +
    305A  PRO*     3.4    23.3    -      -       +      +
    332A  GLY*     4.7    11.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 255 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    232A  GLU*     3.8     4.7    -      -       -      -
    252A  ILE*     3.6    24.7    -      -       +      +
    253A  THR      4.2     0.4    -      -       -      -
    254A  LYS*     1.3    69.8    -      -       -      +
    256A  MET*     1.3    71.7    +      -       -      +
    257A  SER      4.2     6.5    -      -       -      +
    260A  ALA*     4.4     6.3    -      -       +      -
    261A  ALA*     4.1    33.0    -      -       +      +
    264A  ILE*     3.9    11.7    -      -       +      -
    276A  GLY*     4.2     1.6    -      -       -      -
    277A  GLU      3.1    32.5    +      -       -      +
    278A  PRO*     3.6    11.9    -      -       +      +
    282A  SER*     3.0    10.2    +      -       -      -
    317A  LEU*     3.9     9.6    -      -       +      +
    326A  LEU*     4.6     7.4    -      -       +      -
----------------------------------------------------------
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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