Contacts of the strand formed by residues 88 - 94 (chain B) in PDB entry 1EEJ


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 HIS 88 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     86B  GLU*     3.8     1.4    -      -       -      +
     87B  LYS*     1.3    87.8    +      -       +      +
     89B  VAL*     1.3    68.8    +      -       -      +
     90B  ILE*     5.2     0.4    -      -       +      -
    115B  GLY      3.1     6.6    +      -       -      +
    116B  ILE*     4.5     5.8    -      -       +      -
    117B  THR*     2.9    25.9    +      -       -      -
    203B  LYS*     4.1    15.7    -      -       +      -
    206B  LEU*     3.3    61.3    +      -       +      +
    207B  ASP*     2.8    27.8    +      -       -      -
    210B  GLN*     3.0    30.4    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 89 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     86B  GLU*     3.2    40.8    -      -       +      +
     88B  HIS*     1.3    75.1    -      -       -      +
     90B  ILE*     1.3    66.6    +      -       -      +
     91B  THR*     5.4     0.2    -      -       -      +
    117B  THR*     3.6     7.6    -      -       +      -
    119B  ARG*     3.6    43.3    -      -       +      +
    187B  LEU      4.6     0.2    -      -       -      -
    188B  SER*     3.9    29.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 90 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     88B  HIS*     5.2     0.4    -      -       +      -
     89B  VAL*     1.3    81.0    -      -       -      +
     91B  THR*     1.3    62.0    +      -       -      +
     92B  VAL*     3.8    21.5    -      -       +      -
    104B  LEU*     6.3     1.1    -      -       +      -
    111B  TYR*     5.8     1.6    -      -       +      -
    116B  ILE*     3.8    17.3    -      -       +      -
    117B  THR      3.0    13.7    +      -       -      +
    118B  VAL*     3.6    10.7    -      -       +      -
    119B  ARG*     2.9    27.5    +      -       -      +
    185B  VAL*     3.8    22.7    -      -       +      -
    186B  VAL      3.8     3.1    -      -       -      +
    187B  LEU*     4.3     6.3    -      -       +      -
    202B  MET*     4.4    20.2    -      -       +      -
    206B  LEU*     3.9    34.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 91 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     71B  LEU*     4.2     9.7    -      -       +      +
     78B  MET*     4.1    23.3    -      -       +      -
     89B  VAL*     5.4     0.2    -      -       -      +
     90B  ILE*     1.3    72.0    -      -       -      +
     92B  VAL*     1.3    63.2    +      -       -      +
     93B  PHE*     4.2     2.0    +      -       +      -
    119B  ARG*     2.8    40.3    +      -       -      +
    121B  LEU*     4.1    20.2    -      -       +      -
    184B  ALA      3.7     0.9    -      -       -      +
    185B  VAL*     3.5     2.3    -      -       -      -
    186B  VAL*     2.7    56.8    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 92 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     90B  ILE*     3.8    22.2    -      -       +      -
     91B  THR*     1.3    78.4    -      -       -      +
     93B  PHE*     1.3    75.1    +      -       -      +
     94B  THR*     3.4     2.4    +      -       -      +
    104B  LEU*     4.1    15.3    -      -       +      -
    118B  VAL*     3.8    19.1    -      -       +      -
    119B  ARG      2.8     9.7    +      -       -      +
    120B  TYR*     3.4    24.1    -      -       +      -
    121B  LEU      3.1    23.8    +      -       -      +
    183B  PRO*     3.9    19.3    -      -       +      -
    184B  ALA      3.4     7.9    -      -       -      +
    185B  VAL*     4.2    11.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 93 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     71B  LEU*     4.7     2.7    -      -       +      -
     91B  THR*     5.1     2.0    -      -       +      -
     92B  VAL*     1.3    72.9    -      -       -      +
     94B  THR*     1.3    59.2    +      -       -      +
    121B  LEU*     3.5    40.4    -      -       +      -
    122B  ALA      4.5     1.1    -      -       -      -
    123B  PHE*     3.9    28.0    -      +       +      -
    170B  HIS      3.4    25.6    -      -       -      -
    173B  LEU*     4.6     4.3    -      -       +      -
    174B  GLY*     3.7    14.6    -      -       -      -
    177B  LEU*     4.0    16.4    -      -       +      -
    179B  VAL*     3.7    20.9    -      -       +      -
    182B  THR*     3.8     3.9    -      -       +      +
    183B  PRO*     3.4     7.4    -      -       -      +
    184B  ALA*     2.8    42.6    +      -       +      +
    186B  VAL*     3.6    28.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 94 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     92B  VAL*     4.5     3.4    -      -       -      -
     93B  PHE*     1.3    75.1    -      -       -      +
     95B  ASP*     1.3    66.9    +      -       -      +
    101B  CYS*     3.3    25.6    -      -       -      +
    104B  LEU*     6.2     0.2    -      -       -      +
    120B  TYR*     3.5    42.9    -      -       +      -
    121B  LEU      3.0    12.0    +      -       -      +
    122B  ALA      3.7     0.3    -      -       -      -
    123B  PHE      2.8    27.2    +      -       -      +
    136B  MET*     3.7     6.0    -      -       -      +
    140B  TRP*     4.2     4.7    -      -       +      -
    149B  PHE*     3.9    24.5    -      -       +      -
    153B  MET*     4.6     0.7    -      -       -      +
    182B  THR*     4.4     0.9    -      -       -      -
    183B  PRO*     5.3     0.6    -      -       -      +
----------------------------------------------------------
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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