Contacts of the helix formed by residues 209 - 225 (chain D) in PDB entry 1MK9
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 PRO 209 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
749C GLU* 2.8 24.1 - - + +
750C ALA* 1.3 78.1 - - - +
210D VAL* 1.3 77.6 + - + +
211D GLN 3.2 0.2 + - - -
212D LEU* 3.3 6.6 + - + +
213D ASN* 3.0 25.8 + - - +
292D ILE* 5.1 17.5 - - + +
295D LYS* 5.9 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 210 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209D PRO* 1.3 89.6 - - + +
211D GLN* 1.3 69.4 + - + +
213D ASN* 4.0 6.5 + - - +
214D LEU* 3.4 25.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 211 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
745C PRO* 3.8 28.9 - - + +
750C ALA* 3.3 17.6 + - + +
209D PRO 3.2 0.4 - - - -
210D VAL* 1.3 84.1 - - + +
212D LEU* 1.3 67.6 + - - +
213D ASN 3.1 0.2 - - - -
214D LEU* 3.2 17.5 + - - +
215D LEU* 3.4 25.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 212 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
745C PRO* 4.0 23.7 - - - +
746C LEU* 4.5 12.1 - - + +
748C LYS 5.9 0.2 - - - +
750C ALA 3.0 17.7 + - - +
209D PRO* 3.7 4.7 - - + +
211D GLN* 1.3 77.9 - - - +
213D ASN* 1.3 58.5 + - - +
215D LEU* 3.5 5.9 + - + +
216D TYR* 3.1 22.9 + - - +
292D ILE* 3.2 51.1 - - + +
295D LYS* 4.0 15.3 - - + +
296D VAL* 3.8 32.1 - - + +
299D VAL* 5.0 4.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 213 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209D PRO 3.0 17.4 + - - +
210D VAL* 4.0 6.8 + - - +
211D GLN 3.1 0.4 - - - -
212D LEU* 1.3 77.0 - - - +
214D LEU* 1.3 69.9 + - - +
216D TYR* 3.7 12.1 - - - -
217D VAL* 2.9 41.5 + - - +
295D LYS* 3.3 30.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 214 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210D VAL* 3.4 16.1 + - + +
211D GLN* 3.2 20.6 + - - +
213D ASN* 1.3 81.7 - - - +
215D LEU* 1.3 66.4 + - + +
217D VAL* 3.8 5.6 - - + +
218D GLN* 2.8 44.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 215 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
745C PRO* 5.0 10.8 - - + -
746C LEU* 4.4 14.1 - - + -
211D GLN* 3.4 30.5 - - - +
212D LEU* 3.8 6.3 - - + +
213D ASN 3.3 0.4 - - - -
214D LEU* 1.3 82.4 - - + +
216D TYR* 1.3 60.3 + - - +
218D GLN* 3.2 7.7 + - + +
219D ALA* 2.8 32.6 + - - +
299D VAL* 4.0 14.4 - - + -
303D ARG* 3.6 26.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 216 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212D LEU 3.1 17.6 + - - +
213D ASN* 3.7 18.6 - - - +
215D LEU* 1.3 77.6 - - - +
217D VAL* 1.3 56.0 + - + +
219D ALA* 3.7 0.7 - - - +
220D ARG* 2.8 71.5 + - + +
242D GLN* 3.5 25.6 + - - +
245D ILE* 3.3 42.8 - - + +
246D GLN* 4.9 2.1 + - - +
295D LYS* 4.1 22.7 - - + -
298D TYR* 3.9 35.2 - + + -
299D VAL* 3.6 15.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 217 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213D ASN* 2.9 43.6 + - - +
214D LEU* 3.8 7.0 - - + +
216D TYR* 1.3 77.3 - - + +
218D GLN* 1.3 66.8 + - + +
220D ARG* 3.0 34.7 - - - +
221D ASP* 3.0 37.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 218 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214D LEU* 2.8 34.4 + - + +
215D LEU* 3.5 8.5 - - + +
217D VAL* 1.3 78.9 - - + +
219D ALA* 1.3 62.7 + - - +
221D ASP* 4.1 2.5 - - - +
222D ASP* 3.1 58.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 219 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215D LEU 2.8 19.7 + - - +
216D TYR 3.8 2.5 - - - +
218D GLN* 1.3 74.1 - - - +
220D ARG* 1.3 66.6 + - - +
222D ASP* 3.4 5.4 + - - +
223D ILE* 3.0 25.6 + - - +
228D HIS* 6.3 0.2 - - - -
298D TYR* 4.1 9.9 - - + -
299D VAL* 4.7 8.3 - - + -
302D ALA* 3.8 28.3 - - + -
308D TYR* 5.4 8.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 220 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216D TYR* 2.8 55.3 + - + +
217D VAL* 3.0 45.6 + - - +
219D ALA* 1.3 71.4 - - - +
221D ASP* 1.3 69.1 + - - +
223D ILE* 2.5 29.6 + - - +
224D LEU* 2.9 36.1 + - + +
242D GLN* 4.4 11.1 - - - +
246D GLN* 5.2 12.7 - - - +
298D TYR* 3.4 21.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 221 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217D VAL* 3.0 33.3 + - - +
218D GLN* 4.2 3.1 - - - +
220D ARG* 1.3 98.9 + - - +
222D ASP* 1.3 61.7 + - - +
223D ILE 2.8 6.1 + - - -
224D LEU* 4.2 10.1 - - - +
225D ASN* 3.0 34.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 222 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218D GLN* 3.1 42.9 + - - +
219D ALA* 3.9 6.2 - - - +
220D ARG 3.2 0.2 - - - -
221D ASP* 1.3 78.3 - - - +
223D ILE* 1.3 54.7 + - - +
225D ASN* 3.6 11.6 - - - +
227D SER* 3.0 18.6 + - - -
228D HIS* 2.5 42.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 223 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219D ALA 3.0 16.8 - - - +
220D ARG 2.5 17.6 + - - +
222D ASP* 1.3 74.9 - - - +
224D LEU* 1.3 65.4 + - + +
225D ASN 3.3 1.6 - - - -
226D GLY* 3.1 11.7 + - - -
228D HIS* 3.9 25.5 - - + +
230D VAL* 3.9 31.9 - - + -
235D ALA* 5.5 1.3 - - - -
238D PHE* 3.1 45.5 - - + -
267D PRO* 3.6 19.4 - - + +
298D TYR* 4.0 12.8 - - + +
302D ALA* 4.6 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 224 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220D ARG* 2.9 43.6 + - + +
221D ASP* 3.1 11.4 + - - +
223D ILE* 1.3 81.5 - - + +
225D ASN* 1.3 57.4 + - - +
226D GLY 3.2 0.7 + - - -
242D GLN* 3.7 18.2 - - - +
263D LYS 5.4 1.5 - - - +
264D ASP* 4.4 7.6 - - - +
265D PHE* 3.3 12.1 - - - +
266D LEU* 3.1 54.5 - - - +
267D PRO* 3.8 6.7 - - + +
268D LYS* 4.2 4.0 + - - +
298D TYR* 5.3 2.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 225 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221D ASP* 3.0 31.1 + - + +
222D ASP* 3.5 5.5 + - - +
224D LEU* 1.3 75.2 - - - +
226D GLY* 1.3 58.7 + - - +
227D SER* 2.9 38.2 + - - +
268D LYS* 6.0 0.7 - - - -
----------------------------------------------------------
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