Contacts of the strand formed by residues 389 - 393 (chain A) 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 389 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    361A  PHE*     3.4    24.6    -      -       +      -
    388A  MET*     1.3    82.1    -      -       -      +
    390A  PHE*     1.3    66.8    +      -       -      +
    417A  LYS*     3.4    21.5    -      -       +      +
    418A  TYR*     5.6     2.0    -      -       +      -
    447A  GLU*     3.1    33.4    +      -       +      +
    448A  ARG      3.2    10.3    +      -       -      -
    450A  MET      4.8     0.9    -      -       -      +
    505A  LEU*     3.4    14.8    -      -       -      +
    507A  GLN*     3.4    15.7    +      -       -      +
   1063B  ALA*     4.4     7.6    -      -       +      -
   1064B  ARG*     4.4    13.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 390 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    389A  THR*     1.3    79.7    +      -       -      +
    391A  ALA*     1.3    63.9    +      -       -      +
    392A  GLU*     3.4    23.0    +      -       +      -
    447A  GLU*     4.3     1.1    -      -       -      -
    448A  ARG*     3.1    64.6    +      -       -      +
    450A  MET*     5.1     2.2    -      -       +      +
    454A  ASP*     4.7     4.3    -      -       -      +
    505A  LEU*     4.5    12.1    -      -       +      -
    506A  PRO      3.6    19.3    -      -       -      -
    507A  GLN*     2.9    36.8    -      -       -      -
    508A  SER      4.5     4.3    -      -       -      -
    509A  LEU*     4.6    15.5    -      -       +      -
    512A  ARG*     3.2    37.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 391 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    390A  PHE*     1.3    82.1    -      -       -      +
    392A  GLU*     1.3    64.0    +      -       -      +
    393A  ILE*     4.0     1.0    +      -       -      +
    445A  LYS*     5.1    15.5    -      -       +      -
    446A  VAL      3.8     4.9    -      -       -      -
    447A  GLU*     3.9    26.0    +      -       +      +
    507A  GLN*     4.2    20.6    +      -       +      +
    509A  LEU*     6.2     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 392 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    390A  PHE*     3.4    17.8    +      -       +      -
    391A  ALA*     1.3    72.7    -      -       -      +
    393A  ILE*     1.3    58.6    +      -       -      +
    398A  ASN*     4.0    14.2    +      -       -      -
    401A  ARG*     3.4    29.8    +      -       -      -
    402A  LEU*     4.2    17.6    -      -       +      +
    445A  LYS*     3.4     2.6    -      -       -      -
    446A  VAL*     2.7    44.9    +      -       -      +
    448A  ARG*     2.7    39.4    +      -       +      +
     89F  PRO*     6.1     0.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 393 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    391A  ALA      4.0     2.1    +      -       -      +
    392A  GLU*     1.3    77.4    -      -       -      +
    394A  VAL*     1.3    70.6    +      -       -      +
    395A  THR*     3.5     8.8    +      -       -      +
    398A  ASN*     3.9     8.0    +      -       -      -
    402A  LEU*     4.9     0.4    -      -       -      -
    443A  GLY*     4.7    12.3    -      -       -      +
    444A  TYR      3.9    10.3    -      -       -      +
    445A  LYS*     4.1    21.5    -      -       +      +
    509A  LEU*     5.3     4.9    -      -       +      -
     71F  LEU*     5.8     4.3    -      -       +      -
     74F  ALA*     3.7    42.4    -      -       +      +
     75F  MET*     4.4    28.0    -      -       +      -
----------------------------------------------------------
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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