Contacts of the strand formed by residues 87 - 93 (chain E) 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 87 (chain E).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19A    C      4.2     0.7    +      -       -      -
     82E  VAL      4.1     0.2    -      -       -      +
     83E  GLU*     3.4     2.8    -      -       -      +
     84E  PHE*     2.5    43.0    +      -       -      +
     86E  ALA*     1.3    80.4    -      -       -      +
     88E  LYS*     1.3    57.5    +      -       -      +
    125E  SER*     2.5    34.7    +      -       -      -
    127E  ASN      3.9     4.9    +      -       -      -
    130E  ASN*     3.5    27.5    -      -       -      +
    131E  ILE*     3.5    15.0    -      -       -      -
    134E  ALA*     4.9     1.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 88 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    560A    U      5.5     1.8    +      -       -      -
    566A    G      5.8     5.5    -      -       -      -
     81E  GLU*     2.6    37.6    +      -       -      +
     82E  VAL      3.3     8.3    -      -       -      +
     83E  GLU*     3.6    37.9    -      -       +      +
     86E  ALA      4.9     2.5    -      -       -      +
     87E  SER*     1.3    75.9    -      -       -      +
     89E  ILE*     1.3    64.7    +      -       -      +
     90E  VAL*     4.9     1.6    -      -       +      -
    122E  GLU*     3.6     2.8    -      -       -      -
    123E  LEU*     2.7    75.1    +      -       +      +
    124E  GLY*     4.7     0.9    -      -       -      +
    131E  ILE*     3.9     4.1    -      -       -      +
    134E  ALA*     5.2     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 89 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     80E  ILE      4.2     0.6    -      -       -      +
     81E  GLU*     3.5     2.3    -      -       -      -
     82E  VAL      2.9    30.3    +      -       -      +
     88E  LYS*     1.3    75.9    -      -       -      +
     90E  VAL*     1.3    93.7    +      -       -      +
     91E  LEU*     3.7    18.8    -      -       +      -
    106E  PRO*     4.3    12.3    -      -       +      -
    120E  THR*     4.0    11.2    -      -       +      +
    121E  LYS      3.7    11.9    -      -       -      +
    122E  GLU*     4.5     7.4    -      -       +      +
    131E  ILE*     4.5     6.5    -      -       +      -
    134E  ALA*     4.0    18.1    -      -       +      +
    135E  THR*     3.9    22.0    -      -       -      +
    138E  ALA*     3.9    26.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 90 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7A    G      4.6    21.8    -      -       +      +
     79E  GLU*     6.3     0.9    -      -       +      -
     80E  ILE      3.8     3.6    -      -       -      +
     81E  GLU*     3.3    36.1    -      -       +      +
     88E  LYS*     4.2     3.8    -      -       +      +
     89E  ILE*     1.3    82.8    -      -       -      +
     91E  LEU*     1.3    70.8    +      -       -      +
     92E  LYS*     5.0     4.7    -      -       +      +
    119E  LEU      5.5     0.2    -      -       -      +
    120E  THR*     3.3     6.6    -      -       -      -
    121E  LYS*     3.0    42.0    +      -       +      +
    123E  LEU*     4.0    22.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 91 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     76E  ILE*     5.4     3.4    -      -       +      -
     78E  HIS      4.8     1.3    -      -       -      +
     79E  GLU*     3.2     7.8    -      -       -      +
     80E  ILE*     2.8    55.7    +      -       +      +
     89E  ILE*     3.7    20.0    -      -       +      -
     90E  VAL*     1.3    79.8    -      -       -      +
     92E  LYS*     1.3    60.8    +      -       -      +
     93E  PRO*     4.7     0.2    -      -       -      -
    106E  PRO*     5.3     0.4    -      -       +      -
    110E  LEU*     4.2    11.7    -      -       +      -
    118E  ILE*     3.9    22.2    -      -       +      -
    119E  LEU      3.5     1.6    -      -       -      -
    120E  THR*     3.0    27.8    -      -       -      +
    135E  THR*     4.8     6.3    -      -       +      -
    138E  ALA*     4.0    13.0    -      -       +      -
    139E  LEU*     4.0    28.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 92 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6A    G      3.7    26.3    -      -       -      -
      7A    G      3.4    44.1    +      -       +      +
    298A    A      5.4     2.0    +      -       -      -
     76E  ILE*     4.4     0.9    -      -       -      -
     79E  GLU*     3.9    14.6    -      -       +      -
     90E  VAL*     5.3     6.5    -      -       +      -
     91E  LEU*     1.3    75.9    -      -       -      +
     93E  PRO*     1.3    77.7    -      -       +      +
    118E  ILE*     3.3     6.5    -      -       -      +
    119E  LEU*     2.6    57.1    +      -       +      +
    105H  ARG*     5.2     6.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with PRO 93 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6A    G      4.6     2.4    -      -       -      +
     75E  THR*     3.4    11.9    -      -       +      +
     76E  ILE*     3.2    28.0    -      -       +      +
     78E  HIS*     3.3    35.2    -      -       -      +
     79E  GLU*     3.4     9.6    -      -       +      -
     92E  LYS*     1.3    91.9    -      -       +      +
     94E  ALA*     1.3    59.6    +      -       -      +
    118E  ILE*     4.9     0.2    -      -       +      -
    119E  LEU*     4.3     5.7    -      -       -      +
    105H  ARG*     3.3    47.6    +      -       +      +
----------------------------------------------------------
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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