Contacts of the strand formed by residues 22 - 28 (chain A) in PDB entry 1IL8


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 ILE 22 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     17A  PHE*     3.1    43.3    -      -       +      -
     19A  PRO*     2.6    34.4    +      -       +      +
     20A  LYS      4.5     1.4    -      -       -      +
     21A  PHE*     1.3    80.4    -      -       +      +
     23A  LYS*     1.3    68.3    +      -       -      +
     24A  GLU      4.0     8.3    -      -       -      +
     25A  LEU*     4.7     4.5    -      -       +      -
     41A  VAL*     3.5    25.8    -      -       +      -
     42A  LYS      3.9     2.0    -      -       -      -
     43A  LEU*     3.7    27.4    -      -       +      -
     51A  LEU*     6.1     0.2    -      -       +      -
     61A  VAL      6.0     0.7    -      -       -      +
     65A  PHE*     3.8    33.4    -      -       +      -
     29B  GLU*     4.6     3.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 23 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     20A  LYS      5.3     6.4    +      -       -      +
     21A  PHE      3.7     1.7    +      -       -      +
     22A  ILE*     1.3    81.0    +      -       -      +
     24A  GLU*     1.3    63.2    +      -       +      +
     42A  LYS      3.3     5.5    +      -       -      +
     44A  SER*     3.6    37.5    -      -       -      +
     65A  PHE*     3.7     8.0    -      -       -      -
     68A  ARG*     6.2     0.2    -      -       -      +
     28B  ILE*     4.0     2.3    -      -       -      +
     29B  GLU*     3.2    40.8    +      -       +      +
     30B  SER*     4.1    23.0    +      -       -      +
     31B  GLY*     5.2     6.1    -      -       -      -
     32B  PRO*     5.9     3.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 24 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22A  ILE*     3.8     3.8    -      -       -      -
     23A  LYS*     1.3    83.9    -      -       +      +
     25A  LEU*     1.3    70.2    +      -       -      +
     26A  ARG*     4.4    11.7    +      -       -      -
     41A  VAL*     3.4     5.7    -      -       -      +
     42A  LYS*     2.8    69.4    +      -       +      +
     65A  PHE*     4.4     0.2    -      -       -      -
     26B  ARG*     4.2    20.9    +      -       -      +
     27B  VAL      3.5     7.0    -      -       -      +
     28B  ILE*     3.1    33.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 25 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22A  ILE*     4.7     4.7    -      -       +      -
     24A  GLU*     1.3    77.0    -      -       -      +
     26A  ARG*     1.3    72.6    +      -       -      +
     27A  VAL*     3.9    24.2    -      -       +      -
     39A  ILE*     4.8     4.0    -      -       +      -
     40A  ILE      4.1     9.6    -      -       -      +
     41A  VAL*     4.4    13.9    -      -       +      -
     51A  LEU*     5.8     0.2    -      -       +      -
     62A  VAL*     4.2    35.4    -      -       +      -
     65A  PHE*     3.5    34.7    -      -       +      -
     66A  LEU*     5.1    10.3    -      -       +      -
     25B  LEU*     5.9     0.9    -      -       +      -
     26B  ARG*     3.7     0.3    -      -       -      -
     27B  VAL*     2.9    43.5    +      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 26 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8A  GLN*     4.7    14.3    -      -       -      +
     24A  GLU*     4.4    17.9    +      -       +      -
     25A  LEU*     1.3    83.2    -      -       -      +
     27A  VAL*     1.3    59.7    +      -       -      +
     28A  ILE*     5.1     0.8    -      -       -      +
     39A  ILE      3.4     1.0    -      -       -      -
     40A  ILE*     2.5    77.3    +      -       +      +
     41A  VAL      4.6     0.9    -      -       -      +
     42A  LYS*     4.3    24.3    -      -       -      +
     48A  GLU*     5.2    10.1    +      -       -      +
     24B  GLU*     4.2    18.3    +      -       -      +
     25B  LEU      3.7     3.1    -      -       -      +
     26B  ARG*     3.4    31.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 27 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     25A  LEU*     3.9    24.0    -      -       +      -
     26A  ARG*     1.3    79.6    -      -       -      +
     28A  ILE*     1.3    65.9    +      -       -      +
     37A  THR*     5.1     2.2    -      -       +      -
     38A  GLU      3.8     4.9    -      -       -      +
     39A  ILE*     4.1    27.4    -      -       +      -
     24B  GLU*     3.5     1.7    -      -       -      -
     25B  LEU*     2.9    48.8    +      -       +      +
     65B  PHE*     4.0    23.6    -      -       +      -
     66B  LEU*     5.0    16.6    -      -       +      -
     69B  ALA*     4.7    12.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 28 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8A  GLN*     3.3    36.8    -      -       +      +
     26A  ARG*     4.2     2.2    +      -       -      +
     27A  VAL*     1.3    77.6    -      -       -      +
     29A  GLU*     1.3    73.5    +      -       -      +
     31A  GLY*     5.8     0.2    -      -       -      -
     33A  HIS*     4.1    22.2    -      -       +      +
     34A  CYS*     6.1     0.4    -      -       +      -
     37A  THR*     3.8     0.2    -      -       -      -
     38A  GLU*     3.1    38.9    +      -       +      +
     40A  ILE*     3.5    21.1    -      -       +      -
     23B  LYS      4.0     6.1    -      -       -      +
     24B  GLU*     3.1    36.1    -      -       +      +
----------------------------------------------------------
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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