Contacts of the strand formed by residues 221 - 227 (chain B) in PDB entry 2KH2


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 221 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    167B  ARG*     4.2    22.0    -      -       +      +
    168B  GLN      3.9     1.8    -      -       -      -
    169B  ALA*     3.5    28.3    -      -       +      +
    170B  PRO*     4.3     4.9    -      -       -      -
    175B  GLU*     6.4     0.4    -      -       -      -
    218B  GLU      5.8     0.2    -      -       -      +
    219B  ASP      3.1     9.6    +      -       -      +
    220B  THR*     1.3    77.8    -      -       -      +
    222B  VAL*     1.3    67.6    +      -       -      +
    223B  TYR*     3.7     7.6    -      -       -      -
    243B  LEU*     4.1     3.7    -      -       -      +
    244B  VAL      3.1    28.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 222 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    167B  ARG*     3.1     5.4    -      -       -      +
    168B  GLN      2.8    43.3    +      -       -      +
    170B  PRO*     4.4    12.3    -      -       +      -
    221B  ALA*     1.3    79.1    -      -       -      +
    223B  TYR*     1.3    63.0    +      -       -      +
    224B  TYR*     3.8    28.9    -      -       +      +
    240B  GLN      5.0     1.1    -      -       -      +
    241B  GLY*     3.8    18.6    -      -       -      +
    242B  THR      3.5    13.0    -      -       -      +
    243B  LEU*     3.9    20.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 223 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    135B  GLU*     3.8     3.1    -      -       -      +
    149B  LEU*     3.7    25.1    -      -       +      -
    165B  TRP*     4.6     9.3    -      +       +      -
    166B  VAL      3.8     3.4    -      -       -      +
    167B  ARG*     2.8    49.5    +      -       +      -
    177B  VAL*     4.0    20.4    -      -       +      -
    197B  PHE*     3.8     4.9    -      +       -      -
    210B  LEU*     4.1    11.9    -      -       +      -
    212B  MET*     3.6    28.4    -      -       +      +
    219B  ASP*     3.1    20.2    +      -       -      +
    221B  ALA      3.7    15.7    -      -       -      -
    222B  VAL*     1.3    75.8    -      -       -      +
    224B  TYR*     1.3    62.5    +      -       -      +
    241B  GLY*     3.0     1.6    -      -       -      -
    242B  THR*     2.8    40.9    +      -       -      +
    244B  VAL*     3.8    15.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 224 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     38B  GLN*     3.5     9.9    +      -       -      -
     42B  LYS      5.5     3.1    -      -       -      -
     43B  ALA*     5.5     0.2    -      -       -      -
     44B  PRO*     4.4    19.1    -      -       +      -
    135B  GLU*     3.4     4.7    -      -       -      +
    165B  TRP*     3.9     8.6    -      -       -      -
    166B  VAL*     2.9    31.6    +      -       -      +
    167B  ARG*     4.7     0.4    -      -       -      -
    168B  GLN*     2.8    46.2    +      -       +      -
    174B  LEU*     4.8     8.1    -      -       +      -
    222B  VAL*     3.8    33.7    -      -       +      +
    223B  TYR*     1.3    73.0    -      -       -      +
    225B  CYS*     1.3    64.2    +      -       -      +
    226B  ALA*     3.4     3.6    +      -       -      +
    238B  TRP*     3.8    20.6    -      +       +      -
    239B  GLY      3.9    11.2    -      -       -      +
    240B  GLN      3.6    17.7    -      -       -      -
    241B  GLY*     3.6    13.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with CYS 225 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    133B  LEU*     3.8    19.9    -      -       +      +
    135B  GLU*     2.7    23.7    +      -       +      +
    151B  CYS*     2.0    51.1    -      -       -      -
    163B  MET*     5.8     0.4    -      -       -      -
    164B  SER      4.6     0.9    -      -       -      -
    165B  TRP*     4.5     8.1    -      -       -      -
    208B  LEU*     3.7    19.1    -      -       -      -
    224B  TYR*     1.3    71.8    -      -       -      +
    226B  ALA*     1.3    62.6    +      -       -      +
    237B  TYR      3.5     1.6    -      -       -      +
    238B  TRP*     3.2     8.1    -      -       -      -
    239B  GLY      2.9    24.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 226 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    133B  LEU*     4.9     1.3    -      -       -      -
    163B  MET*     3.0     8.3    -      -       -      +
    164B  SER      2.9    42.7    +      -       -      +
    165B  TRP      4.5     0.2    -      -       -      +
    166B  VAL*     4.0    15.5    -      -       +      -
    224B  TYR      3.4     2.8    +      -       -      +
    225B  CYS*     1.3    76.3    -      -       -      +
    227B  ARG*     1.3    60.8    +      -       -      +
    228B  GLN*     4.3     0.2    -      -       -      -
    235B  PHE*     3.5    31.2    -      -       +      -
    237B  TYR      3.8     3.6    -      -       -      -
    238B  TRP*     4.7     6.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 227 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    131B  VAL*     3.9    15.4    -      -       -      +
    133B  LEU*     4.3    11.9    -      -       +      -
    156B  PHE*     3.6    58.9    -      -       +      +
    161B  TYR*     3.9    26.8    +      -       +      -
    162B  ASP      3.8    12.1    -      -       -      +
    163B  MET*     4.1     5.2    -      -       +      +
    226B  ALA*     1.3    74.9    -      -       -      +
    228B  GLN*     1.3    70.8    +      -       -      +
    235B  PHE*     3.1     4.8    -      -       -      +
    236B  ASP*     2.6    67.7    +      -       -      +
    237B  TYR*     3.3    25.3    +      -       +      +
----------------------------------------------------------
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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