Contacts of the strand formed by residues 92 - 97 (chain D) in PDB entry 3IKH


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 THR 92 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     15B  TRP*     3.6    24.6    -      -       -      -
     31B  LYS*     4.8    13.5    +      -       +      +
     10D  THR*     3.8     3.6    -      -       -      -
     11D  VAL*     3.4    20.6    -      -       +      +
     13D  GLU*     5.5     7.9    -      -       +      -
     65D  ASN*     3.9    22.7    -      -       -      +
     90D  SER      3.4    11.0    -      -       -      +
     91D  ASP*     1.3    81.1    -      -       -      +
     93D  SER*     1.3    63.5    +      -       -      +
    106D  ILE      4.0     0.9    -      -       -      +
    107D  THR*     3.6     1.7    -      -       -      +
    108D  THR*     2.8    34.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 93 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10D  THR*     3.8     2.6    +      -       -      -
     11D  VAL      3.0     7.8    +      -       -      +
     12D  ASP*     3.4    19.9    -      -       -      -
     13D  GLU*     2.9    29.9    +      -       -      +
     92D  THR*     1.3    74.5    -      -       -      +
     94D  ILE*     1.3    63.1    +      -       -      +
     95D  ILE*     3.7     2.1    +      -       -      -
    105D  ILE*     4.3     6.1    -      -       -      -
    106D  ILE      3.3     4.3    -      -       -      -
    107D  THR*     2.8    33.3    +      -       -      +
    501D  GOL      2.9    20.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 94 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     13B  GLU*     5.5     0.4    -      -       -      +
     15B  TRP*     3.4    52.5    -      -       +      +
     93B  SER*     3.8    20.4    -      -       -      +
     95B  ILE*     6.0     3.6    -      -       +      -
     13D  GLU*     3.7    17.0    -      -       -      +
     15D  TRP*     4.2    16.4    -      -       +      +
     93D  SER*     1.3    72.1    -      -       -      +
     95D  ILE*     1.3    62.3    +      -       -      +
     96D  LEU*     3.6    29.8    -      -       +      +
    104D  ALA      3.7     0.9    -      -       -      +
    105D  ILE*     3.4     5.5    -      -       -      +
    106D  ILE*     2.9    43.9    +      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 95 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12D  ASP*     3.7    33.2    -      -       +      -
     13D  GLU      2.8    14.7    +      -       -      +
     14D  THR*     3.4    21.4    -      -       +      +
     15D  TRP      2.8    27.5    +      -       -      -
     93D  SER*     4.4     6.3    -      -       -      +
     94D  ILE*     1.3    76.3    -      -       -      +
     96D  LEU*     1.3    60.3    +      -       -      +
     97D  ASN      3.2     4.3    +      -       -      -
    103D  ASN*     4.1    25.4    -      -       +      -
    104D  ALA      3.7     2.7    -      -       -      -
    105D  ILE*     4.3    21.3    -      -       +      -
    228D  THR*     3.9    33.2    -      -       +      +
    270D  THR*     4.8     0.9    -      -       -      +
    501D  GOL      4.8     3.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 96 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     20B  ILE*     5.8     0.7    -      -       +      -
     21B  PRO*     5.3     5.4    -      -       +      -
     95B  ILE*     4.9    11.7    -      -       +      -
    106B  ILE*     3.8    31.9    -      -       +      -
     15D  TRP*     3.6    19.3    -      -       +      -
     17D  ILE*     3.9    20.2    -      -       +      -
     20D  ILE*     5.0     9.4    -      -       +      +
     21D  PRO*     4.9     6.1    -      -       +      -
     94D  ILE*     3.6    25.8    -      -       +      +
     95D  ILE*     1.3    67.7    -      -       -      +
     97D  ASN*     1.3    60.6    +      -       -      +
     98D  SER*     2.9    10.1    +      -       -      -
    102D  ASP      4.7     0.2    -      -       -      +
    103D  ASN*     3.4     2.0    -      -       -      -
    104D  ALA*     2.8    48.4    +      -       +      +
    106D  ILE*     5.2     9.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 97 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     14D  THR*     4.1    18.9    -      -       +      +
     15D  TRP      2.6    17.9    +      -       -      +
     16D  SER*     4.1    19.5    +      -       -      -
     17D  ILE*     3.4    17.9    +      -       -      +
     32D  VAL*     5.7     2.4    -      -       -      +
     95D  ILE      3.2     3.0    +      -       -      -
     96D  LEU*     1.3    67.7    -      -       -      +
     98D  SER*     1.3    72.0    +      -       -      +
     99D  ALA*     3.2     9.6    +      -       -      +
    101D  GLY      5.4     0.5    -      -       -      +
    103D  ASN*     2.9    26.8    +      -       -      +
----------------------------------------------------------
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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