Contacts of the strand formed by residues 92 - 98 (chain B) in PDB entry 3KCC


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 CYS 92 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     21B  HIS      3.7     0.5    -      -       -      +
     22B  LYS*     3.2     5.9    -      -       -      +
     23B  TYR*     2.6    48.3    +      -       +      +
     29B  LEU*     5.0     0.9    -      -       +      -
     42B  ILE*     4.8     2.9    -      -       -      -
     44B  LYS      3.1     5.6    -      -       -      +
     45B  GLY*     3.8     3.6    -      -       -      -
     46B  SER      3.3    40.4    -      -       -      -
     47B  VAL*     3.7    17.9    -      -       +      -
     88B  ALA*     4.2     4.3    -      -       +      -
     90B  THR      3.6     7.4    -      -       -      -
     91B  ALA*     1.3    73.5    -      -       -      +
     93B  GLU*     1.3    59.8    +      -       -      +
     94B  VAL*     3.7    19.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 93 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     20B  ILE*     4.5     9.6    -      -       +      -
     21B  HIS      3.3     7.4    -      -       -      +
     22B  LYS*     4.5    13.2    -      -       +      +
     43B  VAL*     2.9    36.7    +      -       +      -
     44B  LYS*     2.8    30.3    +      -       +      +
     92B  CYS*     1.3    72.7    -      -       -      +
     94B  VAL*     1.3    61.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 94 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19B  HIS      3.7     1.6    -      -       -      +
     20B  ILE*     3.5     4.0    -      -       -      +
     21B  HIS*     2.8    36.8    +      -       -      +
     23B  TYR*     3.6    28.5    +      -       +      -
     29B  LEU*     3.7    22.0    -      -       +      -
     40B  TYR*     3.6    38.8    -      -       +      -
     41B  TYR      3.4    12.8    -      -       -      +
     42B  ILE*     4.7     7.9    -      -       +      +
     70B  ILE*     4.8     2.0    -      -       +      -
     92B  CYS*     3.7    12.3    -      -       +      -
     93B  GLU*     1.3    77.8    -      -       -      +
     95B  ALA*     1.3    64.1    +      -       -      +
     96B  GLU*     4.8     1.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 95 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     15B  LEU*     3.5    32.1    -      -       +      -
     18B  CYS*     3.7    17.3    -      -       +      -
     19B  HIS      3.6     5.4    -      -       -      -
     20B  ILE*     3.9    10.3    -      -       +      -
     39B  LEU      3.8     0.6    -      -       -      +
     40B  TYR*     3.1     6.2    -      -       -      -
     41B  TYR*     2.8    43.2    +      -       +      +
     43B  VAL*     4.2     5.0    -      -       +      +
     94B  VAL*     1.3    74.8    -      -       -      +
     96B  GLU*     1.3    59.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 96 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     17B  HIS      4.5     0.2    -      -       -      +
     18B  CYS*     3.2     7.3    -      -       -      -
     19B  HIS*     2.8    42.5    +      -       +      +
     21B  HIS*     6.3     1.6    -      -       +      -
     23B  TYR*     5.8     1.1    -      -       -      +
     38B  THR*     3.0    34.8    -      -       +      -
     39B  LEU      3.4     3.1    -      -       -      -
     40B  TYR*     3.6    18.6    -      -       +      +
     94B  VAL      4.8     2.0    -      -       -      +
     95B  ALA*     1.3    75.5    -      -       -      +
     97B  ILE*     1.3    61.2    +      -       -      +
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Residues in contact with ILE 97 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     14B  PHE*     4.1    17.5    -      -       +      -
     17B  HIS*     4.0    20.0    -      -       +      +
     18B  CYS*     3.9     6.1    -      -       -      -
     38B  THR*     3.6     4.3    -      -       -      +
     39B  LEU*     2.8    65.8    +      -       +      +
     96B  GLU*     1.3    76.8    -      -       -      +
     98B  SER*     1.3    73.0    +      -       -      +
    101B  LYS*     3.7    16.6    -      -       +      -
    102B  PHE*     3.8    15.7    -      -       +      +
    105B  LEU*     3.7    30.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 98 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37B  GLU      3.7    10.5    -      -       -      -
     38B  THR*     4.4     4.5    -      -       -      +
     97B  ILE*     1.3    80.0    -      -       -      +
     99B  TYR*     1.3    63.6    +      -       -      +
    100B  LYS*     3.5     9.3    +      -       -      +
    101B  LYS*     2.9    28.6    +      -       -      +
    102B  PHE*     3.0    20.3    +      -       -      +
----------------------------------------------------------
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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