Contacts of the strand formed by residues 18 - 25 (chain U) in PDB entry 1KYO


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 LEU 18 (chain U).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      9U  ALA      4.0    10.5    -      -       -      +
     12U  VAL*     4.4    16.1    -      -       +      +
     16U  GLN      4.1     1.4    +      -       -      -
     17U  SER*     1.3    71.2    -      -       -      +
     19U  SER*     1.3    63.5    +      -       -      +
     20U  LEU*     4.3    12.1    -      -       +      -
     81U  LEU*     3.9     5.2    -      -       +      +
     82U  LYS*     3.3     7.3    -      -       -      +
     83U  LEU*     3.0    47.0    +      -       +      +
     86U  VAL*     4.1    16.9    -      -       +      +
     90U  ASP*     5.5     2.0    -      -       +      -
     94U  TYR*     3.9    25.6    -      -       +      +
    118U  VAL*     3.6    49.6    -      -       +      -
    120U  VAL*     6.6     0.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 19 (chain U). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8U  GLY*     4.0     2.9    -      -       -      -
      9U  ALA*     3.8    21.5    +      -       -      +
     17U  SER*     3.6    10.8    +      -       -      -
     18U  LEU*     1.3    81.2    +      -       -      +
     20U  LEU*     1.3    68.6    +      -       -      +
     21U  THR*     4.5     2.9    +      -       -      +
     81U  LEU      3.6     6.5    -      -       -      -
     82U  LYS*     4.2    15.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 20 (chain U). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6U  GLU*     5.7     0.9    -      -       +      +
      7U  SER      4.2     2.7    -      -       -      +
      8U  GLY*     3.8    22.4    -      -       -      +
      9U  ALA      4.6     1.1    -      -       -      +
     18U  LEU*     4.3     9.6    -      -       +      -
     19U  SER*     1.3    77.4    -      -       -      +
     21U  THR*     1.3    62.9    +      -       -      +
     37U  TRP*     3.8    20.8    -      -       +      -
     80U  PHE*     3.3     7.4    -      -       -      +
     81U  LEU*     2.9    46.8    +      -       +      +
     94U  TYR*     3.6    36.8    -      -       +      -
    116U  THR*     3.5    31.4    -      -       +      +
    118U  VAL*     4.2    14.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 21 (chain U). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5U  GLN      4.0     0.5    -      -       -      +
      6U  GLU*     3.4     5.4    -      -       -      +
      7U  SER*     2.7    58.1    +      -       -      +
      8U  GLY*     5.9     0.2    -      -       -      -
     19U  SER*     5.4     2.7    -      -       -      +
     20U  LEU*     1.3    76.5    -      -       -      +
     22U  CYS*     1.3    60.9    +      -       -      +
     23U  SER*     4.0     2.9    +      -       -      -
     37U  TRP*     4.2     2.3    -      -       -      -
     78U  GLN*     5.0     7.9    +      -       -      +
     80U  PHE*     3.3    34.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with CYS 22 (chain U). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4U  LEU*     4.0    15.3    -      -       -      -
      5U  GLN      3.8     2.5    -      -       -      -
      6U  GLU*     4.5     0.9    -      -       -      +
     21U  THR*     1.3    72.2    -      -       -      +
     23U  SER*     1.3    62.2    +      -       -      +
     37U  TRP*     3.5    16.8    -      -       +      -
     78U  GLN*     3.3     5.6    -      -       -      +
     79U  PHE*     2.9    58.9    +      -       +      +
     96U  CYS*     2.0    48.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 23 (chain U). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      3U  LYS      3.5     0.3    -      -       -      +
      4U  LEU*     3.0     6.4    -      -       -      -
      5U  GLN*     2.8    51.8    +      -       -      -
      7U  SER*     5.1     3.5    +      -       -      -
     21U  THR*     4.0     3.7    +      -       -      -
     22U  CYS*     1.3    72.1    -      -       -      +
     24U  VAL*     1.3    62.1    +      -       -      +
     25U  THR*     5.9     2.9    -      -       -      -
     76U  LYS      5.9     0.2    -      -       -      -
     77U  ASN      4.3     0.7    -      -       -      -
     78U  GLN*     2.7    31.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 24 (chain U). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      2U  VAL*     3.9    15.3    -      -       +      -
      3U  LYS      3.1     9.0    -      -       -      +
      4U  LEU*     3.8    16.8    -      -       +      -
     22U  CYS      4.0     1.3    -      -       -      +
     23U  SER*     1.3    80.3    -      -       -      +
     25U  THR*     1.3    72.1    +      -       -      +
     27U  TYR      3.7    16.6    -      -       -      +
     29U  ILE*     3.6    26.7    -      -       +      -
     35U  TRP*     3.8    20.6    -      -       +      -
     76U  LYS      5.2     0.3    -      -       -      +
     77U  ASN*     2.7    30.2    +      -       -      +
     79U  PHE*     3.8    19.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 25 (chain U). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      1U  GLU      3.4     3.9    -      -       -      +
      2U  VAL*     3.5     3.5    -      -       -      +
      3U  LYS*     3.0    43.1    +      -       -      +
      5U  GLN*     5.5     1.2    +      -       -      -
     23U  SER*     5.6     3.4    -      -       -      -
     24U  VAL*     1.3    82.0    -      -       -      +
     26U  GLY*     1.3    66.0    +      -       -      +
     27U  TYR      3.2     3.5    +      -       -      +
     77U  ASN*     4.7     0.9    -      -       -      -
----------------------------------------------------------
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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