Contacts of the strand formed by residues 86 - 89 (chain B) in PDB entry 4I0A


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 TRP 86 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29B  THR*     4.6     4.7    -      -       -      +
     31B  ILE      3.2     7.2    -      -       -      +
     32B  HIS*     3.7    26.2    -      +       -      +
     33B  GLN*     3.2    60.6    +      -       +      +
     49B  ALA      4.4     0.4    -      -       -      -
     50B  VAL*     3.5     0.7    -      -       -      -
     51B  LEU*     2.8    58.8    +      -       +      +
     52B  ILE*     4.4     0.2    -      -       -      -
     53B  LYS*     3.7    62.2    -      -       +      +
     85B  ALA*     1.3    73.1    -      -       -      +
     87B  VAL*     1.3    67.2    +      -       -      +
     88B  ARG*     5.9     0.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 87 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29B  THR*     3.7     2.3    +      -       -      -
     30B  LEU*     2.9    32.2    +      -       +      -
     31B  ILE*     2.9    31.1    +      -       +      +
     48B  VAL*     3.7    35.0    -      -       +      -
     49B  ALA      3.2     4.9    -      -       -      +
     50B  VAL*     4.3     6.3    -      -       +      -
     71B  ILE*     4.0    22.0    -      -       +      -
     86B  TRP*     1.3    81.4    -      -       -      +
     88B  ARG*     1.3    62.5    +      -       -      +
    301B  CMP      3.7    29.8    -      -       -      +
----------------------------------------------------------
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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
----------------------------------------------------------
     27B  LYS*     3.6    29.9    -      -       -      +
     28B  SER      3.5     6.5    -      -       -      +
     29B  THR*     4.7     7.2    -      -       -      +
     48B  VAL*     3.3     4.2    -      -       -      -
     49B  ALA*     2.8    41.9    +      -       +      +
     51B  LEU*     3.3    35.6    -      -       +      +
     53B  LYS*     5.3     4.8    -      -       -      +
     59B  GLU*     3.0    39.6    +      -       -      -
     61B  ILE*     5.9     0.2    -      -       -      +
     86B  TRP*     5.9     0.7    -      -       +      -
     87B  VAL*     1.3    76.0    -      -       -      +
     89B  ALA*     1.3    71.4    +      -       -      +
     90B  LYS*     4.3     0.2    -      -       -      -
    171B  GLN*     5.9     0.6    +      -       -      -
    175B  GLN*     3.2    14.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 89 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     24B  TYR      4.5     0.9    -      -       -      +
     25B  PRO      3.6    20.6    -      -       -      +
     26B  SER*     4.1     0.2    -      -       -      -
     27B  LYS*     2.8    27.6    +      -       -      +
     28B  SER*     2.9    16.5    +      -       -      +
     30B  LEU*     3.8    16.5    -      -       +      +
     47B  SER      3.8     5.4    -      -       -      -
     48B  VAL*     4.2     5.4    -      -       -      +
     88B  ARG*     1.3    73.0    -      -       -      +
     90B  LYS*     1.3    58.4    +      -       -      +
     91B  THR      3.4    17.5    -      -       -      +
     93B  CYS*     4.0    11.0    -      -       +      -
----------------------------------------------------------
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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