Contacts of the strand formed by residues 90 - 94 (chain A) in PDB entry 1SOT


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 TYR 90 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     84A  ILE*     3.7     3.6    -      -       -      +
     85A  MSE      2.8    33.2    +      -       -      +
     86A  ASP*     3.7    11.4    +      -       -      +
     88A  ARG*     3.5    52.2    +      -       +      -
     89A  GLY*     1.3    76.7    -      -       -      +
     91A  ILE*     1.3    54.9    +      -       -      +
    119A  VAL*     4.1    12.6    -      -       +      -
    129A  VAL*     3.8    12.6    -      -       +      -
    130A  LEU      3.2     9.4    -      -       -      +
    131A  LYS*     3.4    36.9    -      -       +      -
    245A  MSE      4.2    17.7    -      -       -      -
    249A  ILE*     3.8    36.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 91 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     59A  VAL*     4.1    11.7    -      -       +      -
     61A  VAL*     4.9     0.9    -      -       +      -
     82A  GLY*     4.2     2.7    -      -       -      -
     83A  VAL      3.2    20.0    -      -       -      +
     84A  ILE*     4.1    17.0    -      -       +      -
     89A  GLY      3.7     7.2    -      -       -      +
     90A  TYR*     1.3    79.6    -      -       -      +
     92A  ILE*     1.3    75.2    +      -       -      +
     93A  THR      4.1     0.2    +      -       -      -
    106A  VAL*     3.7    33.9    -      -       +      -
    128A  ALA      3.9     0.2    -      -       -      +
    129A  VAL*     3.3     6.0    -      -       -      +
    130A  LEU*     2.8    50.1    +      -       +      +
    132A  ILE*     3.7    30.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 92 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     82A  GLY*     3.2     4.5    -      -       -      -
     83A  VAL*     2.8    33.4    +      -       -      +
     85A  MSE      3.4    37.9    -      -       +      -
     91A  ILE*     1.3    75.2    -      -       -      +
     93A  THR*     1.3    71.3    +      -       -      +
    127A  LEU*     4.2    15.5    -      -       +      -
    128A  ALA      3.5     7.6    -      -       -      +
    129A  VAL*     4.5     8.3    -      -       +      -
    202A  GLY      3.8     2.5    -      -       -      +
    215A  ILE*     4.0    27.8    -      -       +      -
    241A  ALA*     3.9    32.5    -      -       +      +
    245A  MSE      4.0    15.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 93 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     61A  VAL*     4.1     6.9    -      -       +      +
     81A  SER      2.6    27.3    +      -       -      -
     82A  GLY*     4.2     3.6    -      -       -      -
     92A  ILE*     1.3    79.6    -      -       -      +
     94A  ASN*     1.3    78.6    +      -       -      +
     97A  VAL*     4.0    12.6    -      -       -      +
     98A  ILE*     4.0    21.1    -      -       +      -
    127A  LEU*     3.5     8.6    -      -       -      +
    128A  ALA*     3.0    36.6    +      -       +      +
    130A  LEU*     4.1    16.8    -      -       +      -
    202A  GLY*     4.2     6.8    -      -       -      -
    215A  ILE*     5.0     0.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with ASN 94 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     93A  THR*     1.3    88.2    +      -       -      +
     95A  LYS*     1.3    66.2    +      -       -      +
     96A  HIS*     3.6    12.3    -      -       +      +
     97A  VAL*     3.0    22.4    +      -       +      +
     98A  ILE*     3.6     4.3    +      -       -      +
    126A  ASP*     3.1    32.3    +      -       -      +
    127A  LEU*     4.3     6.5    -      -       -      +
    128A  ALA*     4.2     1.8    -      -       -      -
    201A  SER*     2.6    30.5    +      -       -      -
    202A  GLY*     2.8    18.0    +      -       -      -
    216A  ASN      3.4    14.8    +      -       -      +
    217A  THR*     3.6    10.6    -      -       -      -
----------------------------------------------------------
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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