Contacts of the strand formed by residues 1557 - 1560 (chain F) in PDB entry 5YWB


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 ILE1557 (chain F).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1364F  HIS      5.6     0.6    +      -       -      -
   1365F  VAL*     3.6    39.3    -      -       +      -
   1366F  ASN      5.1     6.7    -      -       -      +
   1367F  ALA*     5.2     3.8    -      -       +      -
   1377F  ILE*     5.3     1.3    -      -       +      -
   1388F  PHE*     4.5    16.6    -      -       +      -
   1550F  MET*     3.8    30.1    -      -       +      +
   1551F  VAL      3.2    28.0    -      -       -      +
   1552F  LEU*     3.6    26.0    -      -       +      +
   1553F  LYS*     3.6     9.8    +      -       -      +
   1556F  ALA*     1.3    83.0    -      -       -      +
   1558F  LEU*     1.3    76.8    +      -       -      +
   1559F  GLU*     6.1     0.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU1558 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1550F  MET*     3.1     4.6    -      -       -      -
   1551F  VAL*     2.9    37.9    +      -       +      +
   1553F  LYS*     3.3    28.3    -      -       -      +
   1557F  ILE*     1.3    83.6    -      -       -      +
   1559F  GLU*     1.3    65.7    +      -       -      +
   1560F  PHE*     3.5    33.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU1559 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1366F  ASN      4.9     4.3    -      -       -      +
   1367F  ALA*     3.1    31.3    -      -       +      +
   1368F  LEU*     3.3    31.1    +      -       -      +
   1369F  ILE*     5.3     0.2    -      -       -      +
   1548F  LEU*     5.5     9.5    -      -       +      +
   1549F  VAL      3.7     5.2    -      -       -      +
   1550F  MET*     3.6    26.8    -      -       +      +
   1557F  ILE*     5.9     1.3    -      -       +      -
   1558F  LEU*     1.3    74.7    -      -       -      +
   1560F  PHE*     1.3    81.2    +      -       -      +
   1561F  ASP*     4.8     6.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE1560 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1548F  LEU*     3.7     0.2    -      -       -      -
   1549F  VAL*     2.9    40.0    +      -       -      +
   1551F  VAL*     4.8     4.0    -      -       +      -
   1558F  LEU*     3.5    44.4    -      -       +      -
   1559F  GLU*     1.3    90.2    -      -       -      +
   1561F  ASP*     1.3    67.5    +      -       -      +
   1565F  THR*     5.9     2.0    -      -       +      -
   1566F  LEU*     3.5    33.9    -      -       +      -
   1569F  GLN*     4.5    22.2    -      -       +      -
   1570F  LYS*     4.2    31.4    -      -       +      -
----------------------------------------------------------
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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