Contacts of the strand formed by residues 10 - 16 (chain A) 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 10 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8A  ASN*     4.0    11.4    -      -       -      +
      9A  ILE*     1.3    80.3    -      -       -      +
     11A  VAL*     1.3    62.3    +      -       -      +
     12A  ASP*     2.8    23.2    +      -       -      +
     36A  ILE*     3.4     9.4    -      -       -      +
     37A  GLY*     2.9    32.7    +      -       -      +
     38A  GLY*     3.5    15.7    +      -       -      -
     69A  ILE*     3.9     9.8    -      -       -      +
     90A  SER*     3.1    27.1    -      -       -      -
     91A  ASP*     3.7    11.0    -      -       -      +
     92A  THR*     6.3     0.2    -      -       -      -
    107A  THR*     5.8     4.7    -      -       +      -
    108A  THR      5.5     1.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 11 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10A  THR*     1.3    73.4    -      -       -      +
     12A  ASP*     1.3    62.7    +      -       -      +
     13A  GLU*     3.7    22.4    +      -       +      +
     34A  GLN*     4.0    27.8    -      -       +      +
     35A  ASP      3.5     5.2    -      -       -      +
     65A  ASN*     3.5    35.0    -      -       +      +
     68A  TRP*     3.9    14.4    -      -       +      -
     69A  ILE*     3.5    29.4    -      -       +      -
     89A  HIS*     4.9     0.2    -      -       +      -
     90A  SER      3.4     4.2    +      -       -      -
     91A  ASP*     2.7    26.9    -      -       +      +
     92A  THR      3.0     6.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 12 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10A  THR*     2.8    24.6    +      -       -      +
     11A  VAL*     1.3    72.2    -      -       -      +
     13A  GLU*     1.3    60.2    +      -       -      +
     14A  THR*     3.9     0.9    +      -       -      -
     34A  GLN*     3.3     3.1    -      -       -      -
     35A  ASP*     2.7    47.5    +      -       +      +
     37A  GLY*     3.5    18.4    -      -       -      -
     38A  GLY      4.4     2.4    +      -       -      -
     42A  ASN*     5.8     0.2    +      -       -      -
     92A  THR*     2.8    34.5    -      -       +      +
     94A  ILE*     4.0    13.9    -      -       +      +
    228A  THR*     5.2     5.4    -      -       -      +
    270A  THR*     4.4    11.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 13 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11A  VAL*     3.9     8.5    -      -       +      +
     12A  ASP*     1.3    70.5    -      -       -      +
     14A  THR*     1.3    59.5    +      -       -      +
     15A  TRP*     3.0    33.1    +      -       +      +
     31A  LYS*     3.3    14.0    +      -       -      -
     33A  SER      3.5     4.9    -      -       -      +
     34A  GLN*     3.5    31.2    +      -       +      +
     65A  ASN*     3.2    26.9    +      -       -      +
     91A  ASP*     4.7     5.5    -      -       -      +
     92A  THR      2.7    13.8    +      -       -      +
     93A  SER*     3.6     8.9    +      -       -      -
     94A  ILE*     2.6    34.4    +      -       -      +
     13C  GLU*     5.0     5.0    -      -       -      +
     15C  TRP*     5.5     2.5    -      -       -      -
     31C  LYS*     4.8     2.8    +      -       -      -
     94C  ILE*     5.1     4.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with THR 14 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12A  ASP      3.9     0.6    +      -       -      -
     13A  GLU*     1.3    72.6    -      -       -      +
     15A  TRP*     1.3    60.5    +      -       -      +
     31A  LYS*     3.9     2.3    -      -       -      -
     32A  VAL*     2.8    42.3    +      -       +      +
     33A  SER*     2.8    32.5    +      -       -      +
     35A  ASP*     4.3     9.0    +      -       -      -
     94A  ILE*     3.6    27.2    -      -       +      +
     96A  LEU*     4.6    21.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with TRP 15 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     13A  GLU*     3.0    38.8    +      -       +      +
     14A  THR*     1.3    79.9    -      -       -      +
     16A  SER*     1.3    57.1    +      -       -      +
     17A  ILE*     3.9     2.7    +      -       +      +
     29A  GLY*     4.9     0.9    -      -       -      -
     30A  VAL      3.2     8.5    -      -       -      -
     31A  LYS*     3.8    33.2    -      -       +      +
     32A  VAL*     4.4     0.7    -      -       -      -
     93A  SER*     4.8    12.7    +      -       -      -
     94A  ILE      2.8    12.7    +      -       -      +
     95A  ILE*     3.6    18.5    -      -       +      -
     96A  LEU*     2.7    36.5    +      -       -      +
     92C  THR*     3.9    15.0    -      -       -      -
     94C  ILE*     3.6    34.5    -      -       +      +
    106C  ILE*     3.9    33.7    -      -       +      -
    108C  THR*     3.5    32.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 16 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     15A  TRP*     1.3    70.9    -      -       -      +
     17A  ILE*     1.3    64.8    +      -       -      +
     29A  GLY*     3.4     1.7    -      -       -      -
     30A  VAL*     2.7    53.7    +      -       -      +
     32A  VAL*     4.1    13.1    -      -       -      +
     96A  LEU*     3.4    17.2    +      -       -      +
----------------------------------------------------------
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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