Contacts of the helix formed by residues 174 - 183 (chain D) in PDB entry 6N0M
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 174 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172D LEU 2.9 18.4 + - - -
173D ILE* 1.3 75.4 + - - +
175D LYS* 1.3 70.3 + - + +
176D GLU* 3.5 34.1 - - - +
177D HIS* 2.8 35.6 + - - +
178D ILE* 3.2 12.3 + - - +
474D ALA* 3.6 7.9 - - - -
477D ARG* 6.1 4.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 175 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174D THR* 1.3 77.1 - - + +
176D GLU* 1.3 72.4 + - - +
178D ILE* 3.4 5.7 + - - +
179D GLN* 2.8 33.0 + - - +
474D ALA* 3.7 15.4 - - - +
477D ARG* 3.4 36.0 - - + +
478D TYR* 3.4 34.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 176 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174D THR* 2.9 22.4 - - - +
175D LYS* 1.3 101.5 + - - +
177D HIS* 1.3 66.5 + - + +
179D GLN* 3.1 11.0 + - + +
180D ALA* 2.9 21.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 177 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161D GLU* 3.6 33.0 + - + +
162D ILE* 4.9 12.5 - - + +
165D LEU* 3.4 22.0 - - + +
172D LEU* 3.3 20.5 + - + -
173D ILE* 3.7 8.7 - - + -
174D THR* 2.8 42.0 + - - +
176D GLU* 1.3 73.9 - - + +
178D ILE* 1.3 60.4 + - - +
180D ALA* 3.3 22.7 + - + +
181D LEU* 3.4 14.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 178 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162D ILE* 3.8 26.9 - - + -
173D ILE* 4.9 1.6 - - + -
174D THR 3.2 11.9 + - - +
175D LYS* 3.6 8.1 - - - +
177D HIS* 1.3 71.3 - - - +
179D GLN* 1.3 69.5 + - - +
181D LEU* 3.3 5.5 + - - +
182D LEU* 3.3 40.1 + - + +
191D LEU* 5.0 0.9 - - + -
194D LEU* 4.2 12.6 - - + -
198D LEU* 5.0 1.6 - - + -
471D ALA 4.5 4.7 - - - +
474D ALA* 4.2 4.5 - - + -
475D ILE* 3.4 48.0 - - + +
478D TYR* 4.1 17.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 179 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175D LYS 2.8 17.4 + - - +
176D GLU* 3.1 15.5 - - + +
178D ILE* 1.3 69.9 - - - +
180D ALA* 1.3 66.1 + - - +
182D LEU* 3.0 14.6 + - - +
183D LYS* 3.0 55.2 + - + +
478D TYR* 3.7 26.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 180 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158D LYS* 3.9 7.3 - - + +
176D GLU 2.9 12.4 + - - +
177D HIS* 3.3 15.0 - - + +
178D ILE 3.3 0.2 - - - -
179D GLN* 1.3 76.6 - - - +
181D LEU* 1.3 65.6 + - + +
183D LYS 3.2 6.2 - - - +
184D THR* 3.0 31.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 181 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158D LYS* 3.5 50.9 + - + +
159D LEU* 3.9 15.5 - - + +
161D GLU* 6.4 0.4 - - + -
162D ILE* 4.1 23.8 - - + +
177D HIS 3.4 13.4 + - - +
178D ILE* 3.3 7.5 + - + +
179D GLN 3.0 1.4 + - - -
180D ALA* 1.3 81.7 - - + +
182D LEU* 1.3 60.0 + - - +
183D LYS 3.5 1.2 - - - +
189D TRP* 3.1 33.8 + - + -
194D LEU* 3.3 43.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 182 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178D ILE* 3.5 26.7 - - + +
179D GLN 3.0 3.1 + - - +
181D LEU* 1.3 76.3 - - - +
183D LYS* 1.3 75.7 + - - +
188D THR* 2.6 20.9 + - - +
189D TRP* 3.0 39.1 - - + +
190D SER* 3.6 18.2 - - - +
191D LEU* 3.8 19.1 - - + +
194D LEU* 4.1 12.1 - - + -
478D TYR* 3.7 29.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 183 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158D LYS* 3.3 7.4 + - - -
179D GLN* 3.0 44.6 + - + +
180D ALA 3.2 6.1 - - - +
181D LEU 3.5 0.9 - - - +
182D LEU* 1.3 91.0 + - - +
184D THR* 1.3 84.4 + - - +
188D THR* 3.7 5.8 + - - -
478D TYR* 2.9 26.0 + - - -
----------------------------------------------------------
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