Contacts of the strand formed by residues 94 - 98 (chain Q) 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 ILE 94 (chain Q).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    300A  ALA*     5.1    16.2    -      -       +      -
     44Q  LYS*     4.5     5.2    -      -       -      +
     45Q  GLU*     3.8    39.3    +      -       +      +
     46Q  GLU*     6.1     0.9    -      -       -      +
     74Q  CYS*     5.2     4.5    -      -       -      -
     75Q  ARG      4.4     1.6    -      -       -      -
     76Q  MET*     4.4    23.6    -      -       +      -
     77Q  ARG*     6.1     0.2    -      -       -      -
     92Q  TYR*     3.5    21.1    -      -       +      +
     93Q  PHE*     1.3    79.4    -      -       -      +
     95Q  ASN*     1.3    66.3    +      -       -      +
     96Q  TYR*     3.7    31.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with ASN 95 (chain Q). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     42Q  CYS*     2.4    47.6    +      -       -      +
     43Q  VAL      3.9     6.0    +      -       -      -
     44Q  LYS*     4.7     1.4    -      -       -      +
     74Q  CYS*     3.3    27.7    -      -       -      +
     75Q  ARG*     3.3    33.2    +      -       +      +
     77Q  ARG*     4.2    26.2    -      -       +      +
     94Q  ILE*     1.3    76.0    -      -       -      +
     96Q  TYR*     1.3    80.9    +      -       -      +
     97Q  ARG*     4.4     4.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 96 (chain Q). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37Q  LEU*     4.1     9.8    -      -       +      +
     41Q  SER      3.1    14.6    -      -       -      +
     42Q  CYS*     3.9     3.5    -      -       -      -
     43Q  VAL*     4.2     7.8    +      -       -      +
     45Q  GLU*     3.3    54.4    +      -       +      -
     48Q  MET*     4.6    18.4    -      -       -      -
     60Q  ARG*     4.9     4.5    -      -       -      +
     63Q  LEU*     3.9    28.7    -      -       +      +
     64Q  ASN*     5.8     0.7    +      -       -      -
     67Q  LYS*     5.1     8.3    -      -       +      -
     72Q  ILE*     3.9    34.1    -      -       +      -
     73Q  LYS      3.6     2.7    -      -       -      -
     74Q  CYS*     4.1    12.8    -      -       -      -
     94Q  ILE*     3.7    23.3    -      -       +      +
     95Q  ASN*     1.3    85.0    +      -       -      +
     97Q  ARG*     1.3    60.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 97 (chain Q). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37Q  LEU*     4.6     8.7    -      -       -      +
     40Q  ASN*     3.6    24.1    +      -       -      +
     41Q  SER      3.4    16.8    -      -       -      +
     42Q  CYS*     4.3    11.1    -      -       -      -
     72Q  ILE*     3.6     2.2    -      -       -      -
     73Q  LYS*     2.7    68.0    +      -       +      +
     74Q  CYS*     4.8     5.7    +      -       -      +
     75Q  ARG*     3.2    38.8    -      -       -      +
     95Q  ASN*     4.4     6.0    +      -       -      +
     96Q  TYR*     1.3    77.4    -      -       -      +
     98Q  THR*     1.3    69.1    +      -       -      +
    100Q  VAL*     5.0     9.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with THR 98 (chain Q). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     34Q  LEU*     4.4     7.9    +      -       +      +
     37Q  LEU*     3.2    43.9    +      -       -      +
     38Q  ILE*     3.7    10.9    +      -       +      +
     40Q  ASN*     6.2     0.4    -      -       -      +
     71Q  PHE      3.9    14.1    +      -       -      +
     72Q  ILE*     4.7     0.2    -      -       -      +
     97Q  ARG*     1.3    82.2    -      -       -      +
     99Q  LEU*     1.3    77.4    +      -       -      +
    100Q  VAL*     3.5    11.6    +      -       -      +
----------------------------------------------------------
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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