Contacts of the strand formed by residues 83 - 88 (chain B) in PDB entry 4I93


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 ARG 83 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     76B  GLY      3.3    12.3    -      -       -      +
     77B  LYS*     4.5    11.9    -      -       +      -
     81B  GLN      3.4     8.6    +      -       -      +
     82B  ARG*     1.3    84.4    +      -       -      +
     84B  ILE*     1.3    63.1    +      -       -      +
    133B  GLU*     4.6     1.4    -      -       -      -
    134B  PHE*     3.3    55.4    +      -       +      +
    136B  PRO*     3.9    15.7    -      -       -      +
    191B  ASP*     3.5    24.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 84 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     49B  ILE*     4.3     6.3    -      -       +      -
     52B  ALA*     4.2    12.6    -      -       +      -
     75B  LYS*     3.4     4.5    -      -       -      -
     76B  GLY*     2.9    45.2    +      -       -      +
     77B  LYS      4.2     0.4    -      -       -      +
     78B  LEU*     4.0    42.2    -      -       +      -
     82B  ARG*     4.1    11.9    -      -       -      +
     83B  ARG*     1.3    81.1    -      -       -      +
     85B  ALA*     1.3    59.7    +      -       -      +
     86B  VAL*     3.7    22.2    -      -       +      -
    119B  LEU*     4.2     3.1    -      -       +      -
    131B  ILE*     3.9    26.5    -      -       +      -
    132B  ALA      3.4    10.8    -      -       -      +
    134B  PHE*     3.8    11.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 85 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     62B  VAL*     5.5     3.1    -      -       +      -
     73B  VAL*     4.1    15.9    -      -       +      -
     74B  TYR      3.3     5.4    -      -       -      +
     75B  LYS*     4.7     0.4    -      -       -      +
     84B  ILE*     1.3    75.1    -      -       -      +
     86B  VAL*     1.3    60.7    +      -       -      +
     87B  LYS      4.1     0.4    -      -       -      -
    130B  LEU      3.6     1.0    -      -       -      +
    131B  ILE*     3.4     4.2    -      -       -      +
    132B  ALA*     2.8    36.2    +      -       +      +
    133B  GLU      4.2    11.0    -      -       -      +
    134B  PHE*     4.1     9.3    -      -       +      +
    135B  MSE      5.6     0.2    -      -       -      +
    200B  PHE*     3.8    13.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 86 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     49B  ILE*     3.9    27.6    -      -       +      -
     53B  THR*     4.1     9.4    -      -       +      -
     56B  PHE*     4.5     8.3    -      -       +      -
     72B  VAL      3.7     0.2    -      -       -      +
     73B  VAL*     3.2     3.9    -      -       -      +
     74B  TYR*     2.7    50.0    +      -       +      +
     76B  GLY      5.2     0.2    -      -       -      +
     84B  ILE*     3.7    29.6    -      -       +      -
     85B  ALA*     1.3    78.1    -      -       -      +
     87B  LYS*     1.3    63.8    +      -       -      +
     88B  ARG      3.6     1.4    +      -       -      -
    129B  LEU*     4.2    22.0    -      -       +      -
    130B  LEU      3.3     8.3    -      -       -      +
    131B  ILE*     4.4     6.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 87 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     71B  ASN*     3.7    19.1    -      -       +      -
     72B  VAL      3.5     8.5    -      -       -      +
     73B  VAL*     4.1    11.0    -      -       +      -
     86B  VAL*     1.3    71.8    -      -       -      +
     88B  ARG*     1.3    64.3    +      -       -      +
     89B  PHE*     3.8    29.7    +      -       +      -
    128B  ARG      3.8     0.9    -      -       -      +
    129B  LEU*     3.2     7.4    -      -       -      +
    130B  LEU*     2.9    37.0    +      -       +      +
    200B  PHE*     3.9    59.7    +      -       +      +
    201B  GLY*     5.8     0.6    -      -       -      -
    203B  MSE      5.0     2.4    +      -       -      -
    205B  ASN*     2.7    30.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 88 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     56B  PHE*     3.6    35.4    -      -       +      +
     67B  GLU*     4.6     8.7    +      -       -      -
     70B  PRO      4.4     0.9    -      -       -      +
     71B  ASN*     3.5     4.2    -      -       -      -
     72B  VAL*     2.8    35.5    +      -       +      +
     74B  TYR*     3.4    41.5    +      -       +      -
     86B  VAL      3.6     0.6    +      -       -      -
     87B  LYS*     1.3    73.1    -      -       -      +
     89B  PHE*     1.3    68.4    +      -       -      +
    127B  GLU*     3.0    35.6    +      -       -      +
    129B  LEU*     3.6    20.9    -      -       +      -
----------------------------------------------------------
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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