Contacts of the helix formed by residues 556 - 574 (chain O) in PDB entry 5KHU
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.
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 GLN 556 (chain O).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
555O ASN* 3.7 28.7 - - - +
557O MET* 3.7 29.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 557 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
556O GLN* 3.7 29.6 - - - +
558O SER* 3.8 28.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 558 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
557O MET* 3.8 29.2 - - - +
559O GLU* 3.8 27.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 559 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
558O SER* 3.8 24.9 - - - +
560O ALA* 3.8 30.3 - - - +
562O LYS* 4.6 15.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 560 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
559O GLU* 3.8 26.5 - - - +
561O HIS* 3.8 29.8 - - - +
563O LEU* 4.6 14.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 561 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
560O ALA* 3.8 29.6 - - - +
562O LYS* 3.8 25.4 - - - +
564O LEU* 4.6 14.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 562 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
559O GLU* 4.6 14.8 - - - +
561O HIS* 3.8 25.6 - - - +
563O LEU* 3.7 29.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 563 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
560O ALA* 4.6 13.5 - - - +
562O LYS* 3.7 29.4 - - - +
564O LEU* 3.8 26.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 564 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
561O HIS* 4.6 15.3 - - - +
563O LEU* 3.8 26.7 - - - +
565O GLN* 3.8 29.6 - - - +
567O LEU* 4.6 13.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 565 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
564O LEU* 3.8 29.8 - - - +
566O LYS* 3.8 26.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 566 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
565O GLN* 3.8 26.0 - - - +
567O LEU* 3.7 28.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 567 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
564O LEU* 4.6 15.0 - - - +
566O LYS* 3.7 28.9 - - - +
568O LEU* 3.8 26.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 568 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
567O LEU* 3.8 26.5 - - - +
569O VAL* 3.8 28.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 569 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
568O LEU* 3.8 29.6 - - - +
570O HIS* 3.8 27.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 570 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
569O VAL* 3.8 24.9 - - - +
571O CYS* 3.8 30.1 - - - +
573O LYS* 4.3 16.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 571 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
570O HIS* 3.8 30.3 - - - +
572O GLN* 3.8 24.9 - - - +
574O LEU* 4.7 13.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 572 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
571O CYS* 3.8 28.9 - - - +
573O LYS* 3.8 25.1 - - - +
575O LYS* 4.6 15.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 573 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
570O HIS* 4.3 16.8 - - - +
572O GLN* 3.8 29.8 - - - +
574O LEU* 3.8 25.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 574 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
571O CYS* 4.7 14.6 - - - +
573O LYS* 3.8 29.2 - - - +
575O LYS* 3.8 24.9 - - - +
----------------------------------------------------------
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