Contacts of the strand formed by residues 41 - 50 (chain A) in PDB entry 1KKU


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 TYR 41 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6A  LYS*     3.7    11.0    +      -       -      +
      7A  THR*     3.2    28.7    -      -       +      +
      9A  VAL*     3.5    26.0    -      -       +      -
     35A  MET*     3.3    41.3    -      -       +      +
     36A  ASN*     3.3    22.4    -      -       -      +
     38A  THR*     3.2    18.4    +      -       +      -
     39A  GLY      3.6     0.6    -      -       -      -
     40A  ARG*     1.3   105.8    +      -       +      +
     42A  THR*     1.3    67.9    +      -       -      +
    152A  LYS*     4.3    16.4    +      -       -      -
    211A  HIS*     3.5    21.0    +      +       -      -
----------------------------------------------------------
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Residues in contact with THR 42 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6A  LYS*     3.2    27.3    +      -       -      +
      7A  THR      2.8    12.2    +      -       -      -
      8A  GLU*     3.4    11.9    -      -       +      +
      9A  VAL      3.0    22.4    +      -       -      -
     36A  ASN*     3.0     9.1    +      -       -      +
     41A  TYR*     1.3    76.1    +      -       -      +
     43A  VAL*     1.3    71.2    +      -       -      +
     44A  VAL*     3.6    11.3    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 43 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      9A  VAL*     3.7    15.5    -      -       +      +
     11A  LEU*     4.4    11.0    -      -       +      -
     32A  LYS*     3.7    42.0    +      -       +      +
     35A  MET*     3.7    33.2    -      -       +      -
     36A  ASN*     2.9    11.4    +      -       -      +
     42A  THR*     1.3    77.9    -      -       -      +
     44A  VAL*     1.3    65.8    +      -       -      +
     45A  LYS      4.2     3.8    -      -       -      +
     79A  TRP*     3.6    34.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 44 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8A  GLU*     3.5    36.8    -      -       +      +
      9A  VAL      2.8    16.3    +      -       -      +
     10A  VAL*     4.6     9.0    -      -       +      -
     42A  THR*     4.2    12.3    -      -       +      +
     43A  VAL*     1.3    81.0    -      -       -      +
     45A  LYS*     1.3    69.9    +      -       +      +
     79A  TRP*     5.0     7.9    -      -       -      +
    149A  PRO*     5.1     8.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 45 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      9A  VAL      3.9     2.1    +      -       -      +
     10A  VAL*     3.4    15.6    -      -       +      +
     11A  LEU*     3.0    23.2    +      -       -      +
     43A  VAL*     3.8     2.1    -      -       -      +
     44A  VAL*     1.3    89.3    -      -       +      +
     46A  GLY*     1.3    69.9    +      -       -      +
     47A  ILE*     3.7    24.9    -      -       +      -
     79A  TRP*     3.6    17.9    -      -       -      +
     81A  GLU*     3.3    34.7    +      -       -      +
    105A  LYS*     5.8     5.7    -      -       -      +
    106A  LEU*     4.9    15.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 46 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11A  LEU*     3.2     9.0    -      -       -      -
     28A  PHE*     4.0     9.6    -      -       -      -
     45A  LYS*     1.3    74.8    -      -       -      +
     47A  ILE*     1.3    68.4    +      -       -      +
     79A  TRP*     2.9    28.8    +      -       -      +
     80A  VAL*     3.4     3.1    -      -       -      -
     81A  GLU*     2.9    27.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 47 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10A  VAL*     3.4    28.0    -      -       +      -
     11A  LEU      2.6    10.9    +      -       -      +
     12A  LEU*     3.4    20.1    -      -       +      +
     13A  ALA      2.8    31.7    +      -       -      +
     28A  PHE*     3.8     6.8    -      -       -      -
     45A  LYS*     3.7    24.9    -      -       -      -
     46A  GLY*     1.3    79.6    -      -       -      +
     48A  ILE*     1.3    68.5    +      -       -      +
     49A  SER*     4.7     0.7    -      -       -      +
     81A  GLU*     3.2    10.3    -      -       -      +
     83A  ASP*     3.9    22.4    -      -       +      -
    102A  HIS*     4.2    24.2    -      -       +      +
    106A  LEU*     5.8     4.0    -      -       +      -
    151A  VAL*     5.7     0.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 48 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     13A  ALA      3.5     5.4    -      -       -      -
     17A  PHE*     3.4    29.8    -      -       +      -
     20A  ILE*     3.7    25.8    -      -       +      -
     24A  HIS*     5.9     0.4    -      -       +      -
     25A  LEU*     4.6     4.3    -      -       +      -
     28A  PHE*     3.7    26.5    -      -       +      -
     47A  ILE*     1.3    75.2    -      -       -      +
     49A  SER*     1.3    62.9    +      -       -      +
     50A  PRO*     4.0    10.3    -      -       +      +
     70A  ALA*     4.1    18.2    -      -       +      -
     74A  THR*     3.9    23.8    -      -       +      -
     80A  VAL*     4.1     9.0    -      -       +      -
     81A  GLU      2.9     9.4    +      -       -      +
     82A  VAL*     3.5     7.2    -      -       +      -
     83A  ASP      3.3    23.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 49 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12A  LEU*     4.2    18.4    -      -       -      -
     13A  ALA      2.9    12.8    +      -       -      -
     14A  CYS*     3.6    18.7    -      -       -      -
     15A  GLY      3.8     0.5    +      -       -      -
     17A  PHE*     4.0     2.7    -      -       -      -
     47A  ILE*     4.7     2.9    -      -       -      -
     48A  ILE*     1.3    75.6    -      -       -      +
     50A  PRO*     1.3    68.8    +      -       -      +
     51A  VAL      3.8     0.5    +      -       -      -
     83A  ASP      3.7    11.4    +      -       -      -
     86A  GLU*     3.0    36.3    +      -       -      +
     98A  VAL*     4.2     4.7    -      -       -      +
    102A  HIS*     4.6     6.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with PRO 50 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     15A  GLY      3.3     7.0    -      -       -      +
     16A  SER      4.5     2.7    -      -       -      +
     17A  PHE*     3.7    20.2    -      -       +      -
     48A  ILE*     3.9    13.5    -      -       +      +
     49A  SER*     1.3    90.1    +      -       -      +
     51A  VAL*     1.3    66.2    +      -       -      +
     63A  ALA*     6.2     0.2    -      -       +      -
     66A  ARG*     3.9    22.4    -      -       +      +
     67A  VAL*     4.2    31.0    -      -       +      -
     70A  ALA*     4.9     1.3    -      -       +      -
     82A  VAL*     4.2     8.3    -      -       +      -
     83A  ASP      4.0     9.4    -      -       -      +
     86A  GLU*     3.6    13.0    -      -       -      +
     87A  SER*     3.8    10.1    +      -       -      -
----------------------------------------------------------
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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