Contacts of the strand formed by residues 98 - 102 (chain S) in PDB entry 5IYB


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 98 (chain S).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     47S  LEU*     4.0    37.0    -      -       +      -
     48S  GLU*     4.0    14.6    -      -       -      -
     49S  ARG*     3.1    48.9    -      -       +      +
     50S  ASP*     4.4     1.9    -      -       -      +
     96S  GLN      4.8     1.1    -      -       -      -
     97S  PRO*     1.3    75.5    -      -       +      +
     99S  LEU*     1.3    59.7    +      -       -      +
    100S  LEU      4.1     0.4    -      -       -      +
    111S  LYS*     3.5    10.4    -      -       -      +
    112S  GLY*     2.5    46.6    +      -       -      +
    144S  TYR*     2.9    63.0    +      +       +      -
    146S  PHE*     4.5     8.5    -      +       +      -
     96T  PHE*     5.0     9.2    -      +       -      -
     98T  GLU*     4.7    17.0    -      -       +      -
    104T  LEU*     5.2     9.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 99 (chain S). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     47S  LEU*     3.7     4.8    -      -       -      +
     48S  GLU*     2.8    53.1    +      -       +      +
     49S  ARG      5.2     2.2    -      -       -      +
     50S  ASP*     3.9    31.6    -      -       -      +
     51S  LEU*     5.4     4.9    -      -       +      +
     98S  TRP*     1.3    74.9    -      -       -      +
    100S  LEU*     1.3    60.3    +      -       -      +
    101S  ARG*     4.1    27.9    +      -       +      +
    109S  LYS*     5.9     1.8    -      -       +      -
    110S  PHE      3.9    13.9    -      -       -      +
    111S  LYS*     4.8     3.1    -      -       +      -
    149S  LEU*     4.0    22.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 100 (chain S). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29S  MET*     4.6     9.0    -      -       +      -
     31S  PHE*     4.5     8.1    -      -       +      -
     42S  TRP*     5.0     4.3    -      -       +      -
     45S  ALA*     4.5     7.6    -      -       +      -
     46S  ARG      3.2    20.6    -      -       -      +
     47S  LEU*     4.2    17.3    -      -       +      -
     98S  TRP      4.1     1.0    -      -       -      -
     99S  LEU*     1.3    73.1    -      -       -      +
    101S  ARG*     1.3    62.9    +      -       -      +
    102S  VAL*     4.0    22.8    +      -       +      -
    109S  LYS*     3.5     3.5    -      -       -      +
    110S  PHE*     2.8    72.5    +      -       +      +
    111S  LYS*     4.9     0.2    -      -       -      +
    112S  GLY      5.9     0.7    -      -       -      +
    146S  PHE*     3.7    28.3    -      -       +      -
      7T  LEU*     5.1     4.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 101 (chain S). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     45S  ALA*     3.3     0.5    -      -       -      -
     46S  ARG*     2.4    69.2    +      -       +      +
     48S  GLU*     2.7    41.9    +      -       +      +
     99S  LEU*     4.4    24.3    -      -       +      +
    100S  LEU*     1.3    78.1    -      -       -      +
    102S  VAL*     1.3    58.6    +      -       -      +
    103S  ASN      4.0     0.2    +      -       -      -
    104S  GLY*     4.3    13.6    +      -       -      -
    108S  ARG      4.3     2.0    -      -       -      -
    109S  LYS*     4.4    25.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 102 (chain S). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     42S  TRP*     3.6    41.5    -      -       +      +
     44S  GLN      3.2    16.4    -      -       -      +
     45S  ALA*     3.8    11.2    -      -       +      +
    100S  LEU*     4.0    25.6    -      -       +      -
    101S  ARG*     1.3    73.2    -      -       -      +
    103S  ASN*     1.3    83.0    +      -       -      +
    104S  GLY      2.9    14.9    +      -       -      +
    107S  GLY*     3.2    11.6    -      -       -      -
    108S  ARG*     3.0    22.6    +      -       +      +
    110S  PHE*     4.5     6.3    -      -       +      -
----------------------------------------------------------
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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