Contacts of the helix formed by residues 368 - 375 (chain F) in PDB entry 6IWQ
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 368 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353F ARG* 3.7 10.3 - - - +
366F PRO 4.0 4.3 - - - +
367F LEU* 1.3 76.7 - - - +
369F PRO* 1.3 71.5 - - - +
370F GLN* 3.4 13.3 - - - +
371F GLU* 3.0 14.9 + - - +
372F LYS* 2.8 26.8 + - - +
519F TYR* 3.0 24.8 + - + -
520F ASP* 3.1 36.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 369 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347F ASP* 5.6 3.4 - - - +
367F LEU 4.1 3.4 - - - +
368F THR* 1.3 86.0 - - - +
370F GLN* 1.3 71.4 + - - +
372F LYS* 3.0 17.6 + - + +
373F ARG* 2.8 48.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 370 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368F THR* 3.4 13.7 - - - +
369F PRO* 1.3 85.0 - - - +
371F GLU* 1.3 61.6 + - - +
373F ARG* 3.3 38.2 + - - +
374F LEU* 3.6 13.4 + - - +
519F TYR* 3.4 42.7 - - + +
520F ASP* 5.8 1.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 371 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353F ARG* 4.1 20.0 + - - +
367F LEU* 3.7 20.4 - - + -
368F THR* 3.0 14.3 + - - +
370F GLN* 1.3 79.5 - - - +
372F LYS* 1.3 60.4 + - - +
374F LEU* 3.4 22.6 + - - +
375F ARG* 3.4 21.2 - - - -
382F TYR* 5.1 2.1 - - + +
383F ARG* 2.9 59.7 + - - +
519F TYR* 2.7 28.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 372 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347F ASP* 3.0 42.0 + - - +
348F GLU* 5.3 3.2 + - - -
351F TYR* 5.7 3.8 - - - -
367F LEU* 3.7 34.1 + - + -
368F THR 2.8 22.6 - - - +
369F PRO* 3.3 13.4 - - + +
371F GLU* 1.3 75.4 - - - +
373F ARG* 1.3 65.6 + - - +
375F ARG* 2.9 37.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 373 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369F PRO* 2.8 40.9 + - - +
370F GLN* 3.4 30.8 + - - +
371F GLU 3.3 0.2 - - - -
372F LYS* 1.3 73.0 - - - +
374F LEU* 1.3 69.2 + - + +
375F ARG 4.0 2.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 374 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370F GLN 3.7 13.7 - - - +
371F GLU* 3.4 21.1 + - - +
372F LYS 3.1 0.4 - - - -
373F ARG* 1.3 82.5 - - + +
375F ARG* 1.3 63.2 + - + +
376F LYS* 3.7 4.3 + - - +
383F ARG* 4.7 21.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 375 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351F TYR* 5.1 1.4 - - - -
367F LEU* 4.1 14.6 - - - +
371F GLU* 3.4 20.6 + - - +
372F LYS* 2.9 31.0 + - - +
373F ARG 4.0 3.1 - - - +
374F LEU* 1.3 81.6 - - + +
376F LYS* 1.3 63.4 + - - +
377F THR 3.7 7.9 + - - +
378F LYS* 2.6 32.2 + - - +
379F THR 3.8 1.6 - - - -
380F GLU* 2.6 40.0 + - - +
381F PRO 3.0 23.8 + - - +
382F TYR* 3.4 31.9 - - - +
434F PRO* 4.5 2.4 - - - +
----------------------------------------------------------
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