Contacts of the strand formed by residues 52 - 58 (chain T) 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 THR 52 (chain T).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     45T  ILE*     4.2    18.4    -      -       +      -
     46T  ALA      3.8     2.9    -      -       -      +
     47T  LYS*     3.3    38.4    -      -       +      +
     51T  ARG*     1.3    80.9    +      -       -      +
     53T  GLU*     1.3    66.5    +      -       -      +
     54T  VAL*     4.2     9.6    +      -       +      +
     85T  LEU*     5.4    10.1    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with GLU 53 (chain T). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     44T  ARG      4.2     0.5    -      -       -      +
     45T  ILE*     3.6     1.7    -      -       -      +
     46T  ALA*     2.8    52.5    +      -       +      +
     48T  THR*     5.9     3.3    -      -       +      +
     51T  ARG*     2.8    41.9    +      -       +      +
     52T  THR*     1.3    78.9    -      -       -      +
     54T  VAL*     1.3    62.2    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 54 (chain T). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19T  TRP*     4.7    17.3    -      -       +      -
     43T  LEU*     4.7     4.0    -      -       +      -
     44T  ARG      3.7     2.9    -      -       -      +
     45T  ILE*     4.0    31.6    -      -       +      +
     52T  THR*     4.2     9.8    +      -       +      +
     53T  GLU*     1.3    80.4    -      -       -      +
     55T  SER*     1.3    70.5    +      -       -      +
     82T  PRO*     4.0     3.1    -      -       -      +
     83T  PHE*     3.1    55.2    +      -       +      +
     85T  LEU*     4.8    22.4    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with SER 55 (chain T). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     43T  LEU*     3.1    12.2    -      -       -      +
     44T  ARG*     2.8    67.8    +      -       -      +
     53T  GLU      5.7     0.2    -      -       -      -
     54T  VAL*     1.3    79.1    -      -       -      +
     56T  PHE*     1.3    58.1    +      -       -      +
     57T  THR*     4.9     0.2    +      -       -      -
     80T  GLU*     3.7    22.1    +      -       -      +
     81T  HIS      3.4    11.7    -      -       -      -
     82T  PRO*     4.3     2.9    -      -       -      -
     83T  PHE*     4.2     3.1    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 56 (chain T). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16S  VAL*     3.8    19.7    -      -       +      -
    127S  PHE*     5.5     3.4    -      +       -      -
     27T  LEU*     4.1    26.0    -      -       +      -
     31T  TRP*     4.3    18.2    -      +       -      -
     40T  VAL*     4.0     7.9    -      -       +      -
     41T  GLY*     3.9    13.7    -      -       -      -
     42T  LYS      3.2    34.3    -      -       -      -
     43T  LEU*     3.6    11.7    -      -       +      -
     44T  ARG*     4.7     0.4    -      -       -      +
     55T  SER*     1.3    74.2    -      -       -      +
     57T  THR*     1.3    81.7    +      -       -      +
     58T  LEU*     3.8    10.1    -      -       +      -
     80T  GLU*     3.5     1.4    -      -       -      +
     81T  HIS*     2.6    55.1    +      +       +      +
     83T  PHE*     3.6    24.0    -      +       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with THR 57 (chain T). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     13S  GLU*     5.5     4.7    -      -       -      -
     41T  GLY*     3.6     1.0    -      -       -      -
     42T  LYS*     2.8    39.8    +      -       -      +
     44T  ARG*     3.4    26.4    +      -       -      +
     55T  SER*     4.9     0.3    +      -       -      -
     56T  PHE*     1.3    80.8    +      -       -      +
     58T  LEU*     1.3    72.7    +      -       -      +
     80T  GLU*     4.5    16.3    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 58 (chain T). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26T  TYR*     6.3     1.3    -      -       +      -
     27T  LEU*     3.7    29.8    -      -       +      -
     30T  GLN*     5.3     7.4    -      -       +      -
     40T  VAL      4.3     0.9    -      -       -      +
     41T  GLY*     4.4     0.2    -      -       -      -
     56T  PHE*     3.8    12.9    +      -       +      -
     57T  THR*     1.3    87.2    -      -       -      +
     59T  ASN*     1.3    70.1    +      -       -      +
     60T  GLU*     3.6     4.2    +      -       -      +
     62T  LEU*     4.1    19.3    -      -       +      +
     63T  ALA*     3.7    31.9    -      -       +      +
     80T  GLU      5.7     1.2    -      -       -      +
     81T  HIS*     4.9    16.9    +      -       +      +
----------------------------------------------------------
 Back to top of page


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