Contacts of the strand formed by residues 79 - 85 (chain K) in PDB entry 1IBL


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 SER 79 (chain K).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     15K  ALA      3.5     0.6    +      -       -      -
     16K  SER*     3.2    20.3    -      -       -      -
     17K  GLY      3.0    23.4    +      -       -      -
     77K  MET*     3.2     5.2    -      -       -      +
     78K  GLN*     1.3    83.2    -      -       -      +
     80K  VAL*     1.3    63.6    +      -       -      +
     81K  ASP*     5.4     1.1    +      -       -      -
    103K  LEU*     3.9     3.2    -      -       -      +
    104K  GLN*     3.3    21.4    +      -       -      +
    106K  LYS*     3.4    23.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 80 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     17K  GLY      2.9    24.2    -      -       -      +
     18K  ARG      3.2     6.3    -      -       -      +
     19K  ALA*     3.1    39.0    -      -       +      +
     32K  ILE*     4.6     1.6    -      -       +      -
     77K  MET*     3.6    15.9    -      -       +      -
     79K  SER*     1.3    77.4    +      -       -      +
     81K  ASP*     1.3    61.5    +      -       -      +
     82K  VAL*     3.7     2.9    +      -       +      +
     98K  LEU*     5.6     3.4    -      -       +      -
    103K  LEU*     3.5    33.7    -      -       +      -
    104K  GLN      2.7    11.8    +      -       -      +
    105K  VAL*     3.5     7.5    -      -       +      +
    106K  LYS*     2.7    31.5    +      -       -      -
    107K  SER      3.7     0.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with ASP 81 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16K  SER*     5.7     2.4    -      -       -      -
     17K  GLY      3.1    14.8    +      -       -      +
     18K  ARG*     3.5    16.4    -      -       +      +
     19K  ALA      3.2    16.7    +      -       -      -
     79K  SER*     5.5     0.9    +      -       -      -
     80K  VAL*     1.3    75.6    -      -       -      +
     82K  VAL*     1.3    63.9    +      -       -      +
     83K  ILE*     3.7     7.1    +      -       +      +
    106K  LYS*     4.6     9.7    -      -       -      +
    107K  SER*     3.1    26.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 82 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19K  ALA*     3.3    14.4    -      -       +      +
     21K  ILE*     3.7    29.2    -      -       +      -
     80K  VAL*     4.6     3.1    -      -       +      +
     81K  ASP*     1.3    75.6    -      -       -      +
     83K  ILE*     1.3    69.7    +      -       -      +
     84K  VAL*     4.2     9.4    -      -       +      -
     95K  ILE*     5.0     5.2    -      -       +      -
     98K  LEU*     3.6    22.7    -      -       +      -
    105K  VAL*     3.5    29.8    -      -       +      -
    107K  SER*     2.8    15.8    +      -       -      +
    108K  ILE*     3.5    10.8    +      -       +      -
    109K  VAL*     3.0    24.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 83 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     18K  ARG*     3.8    17.7    -      -       +      +
     19K  ALA      2.8    12.8    +      -       -      +
     20K  TYR*     3.3    54.4    -      -       +      +
     21K  ILE      3.0    25.6    +      -       -      +
     81K  ASP*     3.7     8.7    -      -       +      +
     82K  VAL*     1.3    78.9    -      -       -      +
     84K  VAL*     1.3    61.7    +      -       -      +
     85K  ARG*     4.6     9.0    -      -       +      +
    109K  VAL*     3.4    14.4    -      -       +      +
    111K  ASP*     4.3    18.8    -      -       +      -
     84R  LYS*     5.2    12.3    -      -       -      +
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Residues in contact with VAL 84 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     21K  ILE*     3.9     9.2    -      -       +      +
     82K  VAL*     4.2     7.9    -      -       +      -
     83K  ILE*     1.3    74.3    -      -       -      +
     85K  ARG*     1.3    63.8    +      -       -      +
     91K  ARG*     3.3    42.0    -      -       +      -
     95K  ILE*     3.7    23.8    -      -       +      -
    108K  ILE*     3.9    19.1    -      -       +      -
    109K  VAL      2.5    16.9    +      -       -      +
    110K  ASP*     3.1    10.6    -      -       -      +
    111K  ASP      2.5    33.6    +      -       -      -
    112K  THR      3.7     0.3    +      -       -      -
     88R  LYS*     3.5     9.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 85 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    707A    C      2.9    29.8    +      -       -      +
    708A    C      2.9    27.3    +      -       -      -
     20K  TYR*     3.4    28.1    -      -       +      -
     21K  ILE      2.9    14.4    +      -       -      +
     22K  HIS*     4.6    11.4    -      -       -      +
     23K  ALA*     3.1    24.7    +      -       -      +
     83K  ILE*     4.6     9.4    -      -       +      +
     84K  VAL*     1.3    80.0    -      -       -      +
     86K  GLY*     1.3    68.2    +      -       -      +
    111K  ASP*     3.1    41.8    +      -       +      +
    112K  THR*     3.4     6.7    -      -       -      +
    113K  PRO*     3.9    15.9    -      -       +      +
     84R  LYS*     6.1     0.4    -      -       -      +
----------------------------------------------------------
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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