Contacts of the helix formed by residues 209 - 220 (chain D) in PDB entry 3HU1
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 CYS 209 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206D ILE* 3.7 39.0 + - + -
207D GLY 3.3 4.0 - - - +
208D GLY* 1.3 84.8 - - - +
210D ARG* 1.3 57.4 + - - +
212D GLN* 3.0 28.1 + - + +
213D LEU* 2.9 41.5 + - + +
249D THR 4.8 0.7 - - - -
254D ILE* 4.5 4.5 - - + -
369D ILE* 4.0 25.6 - - - -
370D GLY 6.0 0.4 - - - -
800D AGS 4.4 3.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 210 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14D THR* 3.6 27.6 + - - +
17D LEU* 3.5 36.5 - - + +
18D LYS* 5.7 1.0 - - - +
208D GLY 3.8 1.0 - - - -
209D CYS* 1.3 76.6 - - - +
211D LYS* 1.3 63.9 + - - +
213D LEU* 3.3 9.5 + - + +
214D ALA* 3.1 19.3 + - - +
379D GLU* 4.9 17.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 211 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454C TRP* 6.0 2.8 - - - -
458C GLN* 5.6 6.5 - - - +
13D SER* 4.1 23.4 + - - +
14D THR* 5.6 4.9 - - - -
209D CYS 3.4 0.6 - - - -
210D ARG* 1.3 77.4 - - - +
212D GLN* 1.3 66.4 + - - +
214D ALA* 3.4 7.7 - - - +
215D GLN* 3.2 43.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 212 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208D GLY 4.5 2.5 + - - +
209D CYS* 3.1 33.8 - - + +
211D LYS* 1.3 82.5 + - - +
213D LEU* 1.3 59.5 + - - +
214D ALA 3.2 1.3 - - - -
215D GLN* 3.2 17.8 + - - +
216D ILE* 3.0 33.9 + - + +
254D ILE* 5.5 0.4 - - + -
367D VAL* 3.7 18.5 - - + +
368D ASP 2.9 28.5 + - - +
369D ILE* 3.8 18.0 - - + +
370D GLY 4.2 8.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 213 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17D LEU* 4.2 13.0 - - + -
203D TYR* 3.7 41.1 - - + +
206D ILE* 4.1 38.4 - - + +
209D CYS* 2.9 32.9 + - + +
210D ARG* 3.8 9.9 - - + +
212D GLN* 1.3 68.0 - - - +
214D ALA* 1.3 59.8 + - - +
216D ILE* 3.3 8.2 + - + +
217D LYS* 2.9 35.6 + - + +
254D ILE* 4.5 19.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 214 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13D SER 4.8 2.7 - - - +
14D THR* 4.6 12.1 - - - -
16D ILE* 4.0 15.7 - - + +
17D LEU* 3.8 26.5 - - + +
210D ARG 3.1 12.2 + - - +
211D LYS* 3.4 12.6 - - - +
213D LEU* 1.3 77.4 - - - +
215D GLN* 1.3 55.9 + - + +
217D LYS* 3.3 3.1 + - - +
218D GLU* 3.0 36.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 215 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211D LYS* 3.2 26.0 + - + +
212D GLN* 3.2 29.0 + - - +
214D ALA* 1.3 75.7 - - + +
216D ILE* 1.3 57.8 + - - +
218D GLU* 3.1 18.8 + - - +
219D MET* 2.9 49.0 + - + +
366D GLU 4.1 15.1 - - - +
367D VAL* 4.0 20.9 - - + +
368D ASP 5.3 1.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 216 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203D TYR* 5.2 6.3 - - + +
212D GLN 3.0 24.0 + - - +
213D LEU* 3.3 10.1 + - + +
215D GLN* 1.3 75.7 - - - +
217D LYS* 1.3 56.7 + - + +
219D MET* 5.0 1.1 - - - -
220D VAL* 2.7 46.2 + - + +
221D GLU* 6.3 0.2 - - + -
241D ILE* 5.2 1.6 - - + -
243D LEU* 3.9 28.0 - - + -
254D ILE* 3.8 30.7 - - + -
258D VAL* 4.1 23.6 - - + -
344D MET* 4.1 14.1 - - + -
367D VAL* 4.4 13.2 - - + -
369D ILE* 4.9 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 217 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432C LEU* 3.8 23.6 - - + +
433C GLU* 5.8 1.0 + - - -
16D ILE* 3.9 21.0 + - + +
17D LEU* 4.2 25.4 + - + +
203D TYR* 3.6 42.0 - - + +
213D LEU* 2.9 20.2 + - + +
214D ALA* 3.7 4.5 - - - +
216D ILE* 1.3 76.7 - - + +
218D GLU* 1.3 55.5 + - - +
221D GLU* 3.3 17.8 + - + +
222D LEU* 2.8 34.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 218 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417C GLU* 5.3 0.5 - - - +
420C LEU* 3.9 22.0 - - + +
424C ARG* 3.1 50.3 + - + -
13D SER* 3.9 3.8 - - - +
16D ILE* 3.8 28.1 - - + +
214D ALA* 3.0 19.4 + - - +
215D GLN* 3.2 21.0 - - - +
217D LYS* 1.3 77.8 - - - +
219D MET* 1.3 65.8 + - + +
222D LEU* 3.5 11.8 - - + +
223D PRO* 3.4 19.6 - - - +
230D PHE* 4.1 7.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 219 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417C GLU* 4.2 15.5 - - - +
420C LEU* 5.0 9.2 - - + -
215D GLN* 2.9 37.8 + - + +
216D ILE* 4.3 1.1 - - - +
218D GLU* 1.3 84.6 - - + +
220D VAL* 1.3 61.2 + - + +
223D PRO* 3.4 16.9 - - - +
238D PRO* 4.1 18.4 - - + +
241D ILE* 3.8 31.9 - - + +
342D ILE* 4.1 4.2 - - - +
365D ARG* 3.8 44.2 - - + -
366D GLU 5.1 4.7 - - - +
367D VAL* 4.5 14.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 220 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216D ILE* 2.7 32.7 + - + +
219D MET* 1.3 80.4 - - + +
221D GLU* 1.3 63.7 + - - +
223D PRO* 3.3 8.5 - - - +
224D LEU* 3.4 25.0 - - + +
241D ILE* 4.3 10.5 - - + -
258D VAL* 5.4 1.8 - - + -
300D ILE* 3.7 36.1 - - + -
342D ILE* 4.2 19.6 - - + +
344D MET* 3.9 33.9 - - + -
----------------------------------------------------------
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