Contacts of the strand formed by residues 90 - 95 (chain B) in PDB entry 3ISL


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 ASP 90 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     88B  GLU      3.4     4.0    +      -       -      +
     89B  ASP*     1.3    70.9    -      -       -      +
     91B  VAL*     1.3    62.0    +      -       -      +
    113B  ASN*     3.3    17.4    -      -       -      +
    115B  HIS*     2.9    29.7    -      -       +      +
    137B  VAL*     4.2    13.7    -      -       +      +
    138B  LYS      4.5     3.0    -      -       -      +
    139B  PRO*     3.7    18.7    -      -       +      +
    140B  LYS*     3.0    29.9    +      -       -      +
    141B  ILE      3.4     4.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 91 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     81B  LEU*     5.2     0.7    -      -       +      -
     85B  ILE*     3.9    20.6    -      -       +      -
     89B  ASP*     3.9     3.6    -      -       +      +
     90B  ASP*     1.3    77.1    -      -       -      +
     92B  LEU*     1.3    62.6    +      -       -      +
     93B  ILE*     3.7    27.9    +      -       +      +
    107B  ALA*     4.3     8.3    -      -       +      -
    112B  ALA*     3.5    29.6    -      -       +      -
    113B  ASN      2.9    10.4    +      -       -      +
    114B  VAL*     3.5     4.6    -      -       +      -
    115B  HIS*     2.8    28.3    +      -       -      +
    141B  ILE*     3.3    32.3    -      -       +      -
    143B  ALA*     4.4     4.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 92 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     91B  VAL*     1.3    72.6    -      -       -      +
     93B  ILE*     1.3    61.3    +      -       -      +
     94B  PRO*     3.9     9.0    -      -       +      +
    115B  HIS*     3.3    30.1    -      -       +      +
    116B  MET*     5.0     0.4    -      -       -      -
    117B  LEU*     4.4    12.3    -      -       +      -
    130B  ILE*     4.1    11.4    -      -       +      +
    133B  GLU*     3.8    26.0    -      -       +      +
    134B  ILE*     3.6    46.2    -      -       +      +
    137B  VAL*     4.8     2.0    -      -       +      -
    139B  PRO*     3.9    15.9    -      -       +      +
    141B  ILE      2.8    11.6    +      -       -      +
    142B  VAL*     3.2     7.5    -      -       +      -
    143B  ALA      3.0    24.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 93 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     81B  LEU*     6.3     0.2    -      -       +      -
     91B  VAL*     3.8    27.6    -      -       +      +
     92B  LEU*     1.3    81.2    -      -       -      +
     94B  PRO*     1.3    65.9    -      -       -      +
     95B  ILE*     3.5     7.3    +      -       +      +
    100B  GLY*     3.8    11.4    -      -       -      +
    103B  LEU*     3.7    37.9    -      -       +      +
    104B  THR*     3.7    31.6    -      -       +      -
    107B  ALA*     4.0     5.2    -      -       +      -
    114B  VAL*     4.2     6.3    -      -       +      -
    115B  HIS      2.8    12.0    +      -       -      +
    116B  MET*     3.4     8.0    -      -       -      +
    117B  LEU      3.3    18.3    +      -       -      -
    143B  ALA*     3.4    17.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with PRO 94 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     92B  LEU*     3.9     7.0    -      -       +      +
     93B  ILE*     1.3    85.6    -      -       -      +
     95B  ILE*     1.3    60.1    +      -       -      +
     96B  TYR*     3.9    12.8    +      -       -      -
    100B  GLY*     5.1     2.6    -      -       -      -
    117B  LEU*     3.7    14.1    -      -       +      +
    125B  PHE*     3.8    12.1    -      -       +      -
    130B  ILE*     3.7    48.5    -      -       +      -
    142B  VAL*     4.6     5.4    -      -       +      -
    143B  ALA      3.3    15.9    -      -       -      +
    144B  MET*     4.0    24.6    -      -       +      +
    145B  VAL*     5.3     1.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 95 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     93B  ILE*     3.6     9.9    -      -       +      +
     94B  PRO*     1.3    75.9    -      -       -      +
     96B  TYR*     1.3    60.1    +      -       -      +
     97B  GLY      3.3    26.9    -      -       -      +
    100B  GLY*     3.8    20.2    -      -       -      +
    101B  TYR*     3.5    42.6    -      -       +      +
    104B  THR*     3.4    28.7    -      -       +      -
    116B  MET*     3.9    18.8    -      -       +      -
    117B  LEU      2.8    13.0    +      -       -      +
    118B  GLU*     3.2     9.2    -      -       +      +
    119B  CYS      3.1    24.1    +      -       -      +
    121B  TRP*     5.1     1.4    +      -       -      +
    125B  PHE*     3.5     3.1    -      -       -      -
----------------------------------------------------------
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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