Contacts of the helix formed by residues 561 - 569 (chain C) in PDB entry 3B60
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 THR 561 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
543C GLU 5.5 1.6 - - - +
545C ALA 4.9 9.4 - - - +
546C ASP 4.8 7.1 + - - -
547C GLU* 5.2 2.0 - - - +
548C ILE* 4.0 4.9 - - - +
560C GLY* 1.3 73.1 - - - +
562C HIS* 1.3 81.9 + - + +
563C SER* 2.7 20.3 + - - +
564C GLU* 3.0 30.1 + - - +
565C LEU* 3.0 20.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 562 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
543C GLU* 3.2 64.5 + - + +
545C ALA 5.2 0.2 + - - -
548C ILE* 3.6 12.1 - - + +
561C THR* 1.3 78.4 - - + +
563C SER* 1.3 59.4 + - - +
565C LEU* 4.1 0.9 - - - +
566C LEU* 3.1 38.6 + - + +
572C TYR* 2.9 31.5 + - - +
576C HIS* 3.4 33.1 + + - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 563 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
561C THR* 2.7 14.6 + - - +
562C HIS* 1.3 80.2 - - - +
564C GLU* 1.3 68.4 + - - -
566C LEU* 3.1 6.5 + - - +
567C ALA* 2.9 25.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 564 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
558C GLU* 5.3 0.9 - - - +
559C ARG 5.0 2.1 - - - +
560C GLY* 3.6 11.2 - - - -
561C THR* 3.0 39.2 + - - +
563C SER* 1.3 74.8 + - - +
565C LEU* 1.3 52.7 + - - +
567C ALA* 3.3 6.5 + - - +
568C GLN* 2.7 39.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 565 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548C ILE* 3.3 24.2 - - + +
550C VAL* 3.2 29.8 - - + -
558C GLU* 2.7 40.8 + - + +
560C GLY 2.9 27.8 - - - +
561C THR 3.0 10.3 + - - +
562C HIS 4.1 1.1 - - - +
564C GLU* 1.3 77.9 - - - +
566C LEU* 1.3 65.9 + - - +
568C GLN* 2.9 19.2 + - - +
569C HIS* 3.2 8.5 + - - -
570C GLY 4.3 3.5 + - - +
572C TYR* 3.4 32.9 - - + +
573C ALA* 4.5 1.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 566 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
562C HIS* 3.1 25.5 + - + +
563C SER* 3.1 6.4 + - - +
565C LEU* 1.3 79.4 - - - +
567C ALA* 1.3 63.0 + - - +
569C HIS* 3.1 21.3 + - + -
572C TYR* 3.4 22.7 - - + -
573C ALA* 3.6 18.9 - - + +
576C HIS* 3.2 39.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 567 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
563C SER* 2.9 17.1 + - - +
564C GLU* 3.5 6.3 - - - +
566C LEU* 1.3 76.3 - - - +
568C GLN* 1.3 63.0 + - - +
569C HIS* 3.1 21.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 568 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
558C GLU* 3.2 36.9 + - + +
564C GLU* 2.7 22.3 + - - +
565C LEU* 2.9 6.7 + - - +
567C ALA* 1.3 73.0 - - - +
569C HIS* 1.3 67.2 + - - +
570C GLY* 4.4 9.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 569 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
565C LEU 3.2 2.0 + - - -
566C LEU* 3.1 21.3 + - + -
567C ALA* 3.1 22.7 + - - -
568C GLN* 1.3 77.9 - - - +
570C GLY* 1.3 57.5 + - - +
571C VAL 3.9 2.7 + - - -
573C ALA* 3.6 20.5 - - + +
574C GLN 5.6 0.4 - - - -
----------------------------------------------------------
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