Contacts of the helix formed by residues 231 - 248 (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 SER 231 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230D VAL* 1.3 73.2 - - - +
232D PHE* 1.3 70.5 + - - +
233D ASP* 4.7 6.9 + - - +
234D LYS* 2.7 41.2 + - - +
235D ALA 3.3 4.4 + - - -
270D TYR* 3.4 5.4 - - - -
343D LYS 4.6 2.2 - - - -
344D THR* 3.6 24.9 - - - -
345D LYS* 4.1 6.2 - - - +
346D GLU* 5.0 5.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 232 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231D SER* 1.3 67.6 - - - +
233D ASP* 1.3 78.6 + - - +
235D ALA* 2.5 34.0 + - - +
236D CYS* 3.1 17.1 + - - -
266D LEU* 5.6 1.6 - - + -
270D TYR* 2.8 57.7 + + + +
273D GLN* 3.5 51.6 - - + +
275D GLY* 4.0 22.4 - - - -
278D LYS* 3.8 21.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 233 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231D SER* 3.1 9.2 + - - +
232D PHE* 1.3 92.7 + - - +
234D LYS* 1.3 68.3 + - + +
236D CYS* 3.5 6.9 + - - +
237D GLU* 3.2 18.4 + - - +
278D LYS* 2.6 36.6 + - - +
306H LYS* 5.2 7.4 + - - -
346H GLU* 4.1 25.5 - - + +
347H VAL 5.4 3.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 234 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230D VAL* 4.5 11.7 - - + -
231D SER* 2.7 34.6 + - - +
233D ASP* 1.3 74.7 - - + +
235D ALA* 1.3 57.5 + - - +
236D CYS 2.9 2.5 - - - -
237D GLU* 2.6 44.4 + - + +
238D PHE* 2.7 25.3 + - + -
301D LEU* 4.8 10.5 - - + -
305D LEU* 4.4 27.6 - - + -
344H THR* 5.7 5.4 + - - +
346H GLU* 4.9 16.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 235 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223D ILE* 5.5 1.1 - - - -
230D VAL* 4.0 19.5 - - + +
231D SER 3.3 2.4 + - - -
232D PHE* 2.5 20.2 + - - +
234D LYS* 1.3 73.3 - - - +
236D CYS* 1.3 50.1 + - - +
238D PHE* 3.4 8.6 - - - +
239D ALA* 2.8 33.3 + - - +
265D PHE 4.4 0.9 - - - +
266D LEU* 3.5 22.4 - - + +
267D PRO* 3.8 18.2 - - + -
270D TYR* 4.1 9.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 236 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232D PHE* 3.1 37.6 + - - -
233D ASP 3.7 8.3 - - - +
234D LYS 2.9 0.6 - - - -
235D ALA* 1.3 75.4 - - - +
237D GLU* 1.3 60.1 + - - +
239D ALA* 3.7 1.9 - - - +
240D GLY* 2.9 18.5 + - - -
266D LEU* 4.5 8.7 - - - -
275D GLY* 4.4 3.4 - - - -
278D LYS* 3.8 37.2 - - + -
279D ILE* 3.9 22.4 - - + -
282D ALA* 3.6 12.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 237 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233D ASP 3.2 10.7 + - - +
234D LYS* 2.6 43.4 + - - +
236D CYS* 1.3 70.5 - - - +
238D PHE* 1.3 64.2 + - - +
240D GLY* 3.1 10.0 + - - -
241D TYR* 3.1 35.8 + - + +
282D ALA* 4.3 12.7 - - + +
301D LEU* 3.7 27.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 238 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223D ILE* 3.1 35.2 - - + -
230D VAL* 3.9 17.0 - - + -
234D LYS* 2.7 22.3 + - + -
235D ALA* 3.4 11.7 - - - +
237D GLU* 1.3 73.7 - - - +
239D ALA* 1.3 68.4 + - - +
241D TYR* 2.8 5.9 + - - -
242D GLN* 2.7 18.8 + - - +
298D TYR* 3.2 66.6 - + + +
301D LEU* 3.2 28.7 - - + -
302D ALA* 3.7 15.9 - - - -
305D LEU* 3.9 11.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 239 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235D ALA 2.8 19.5 + - - +
236D CYS 3.8 0.7 - - - +
237D GLU 3.3 0.2 - - - -
238D PHE* 1.3 74.2 - - - +
240D GLY* 1.3 63.3 + - - +
242D GLN* 3.0 12.9 + - - +
243D CYS* 2.9 27.5 + - - -
265D PHE* 3.6 21.3 + - + +
266D LEU* 4.1 0.2 - - + -
279D ILE* 3.3 40.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 240 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236D CYS 2.9 15.9 + - - -
237D GLU 3.4 5.8 - - - -
238D PHE 2.9 1.4 - - - -
239D ALA* 1.3 77.9 - - - +
241D TYR* 1.3 64.0 + - - +
243D CYS* 3.1 4.2 + - - +
244D GLN* 3.1 19.2 + - - +
279D ILE* 3.7 19.3 - - - -
282D ALA* 3.9 5.2 - - - -
283D HIS* 3.9 15.8 - - - -
286D CYS* 4.6 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 241 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237D GLU* 3.1 32.5 + - + +
238D PHE* 2.8 10.3 + + - +
240D GLY* 1.3 73.3 - - - +
242D GLN* 1.3 58.9 + - - +
244D GLN* 3.1 6.5 + - - +
245D ILE* 2.8 36.3 + - + +
282D ALA* 5.6 1.6 - - + -
286D CYS* 3.5 25.6 - - - -
289D MET* 4.7 6.7 - - + -
294D ALA* 4.2 11.2 - - + +
297D ARG* 4.0 38.3 + - + +
298D TYR* 3.6 41.7 - + + -
301D LEU* 4.3 17.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 242 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216D TYR* 3.5 23.6 - - + +
220D ARG* 4.4 11.5 - - + +
224D LEU* 3.7 24.4 - - - +
238D PHE* 2.7 12.3 + - - +
239D ALA* 3.0 11.3 + - - +
241D TYR* 1.3 77.9 - - - +
243D CYS* 1.3 55.7 + - - +
245D ILE* 3.8 1.0 - - - +
246D GLN* 3.0 51.1 + - - +
264D ASP 2.9 26.3 + - - -
265D PHE* 3.1 27.7 - - + +
298D TYR* 4.5 9.1 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 243 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239D ALA 2.9 14.5 + - - -
240D GLY 3.5 7.0 - - - +
242D GLN* 1.3 75.6 - - - +
244D GLN* 1.3 61.2 + - - +
245D ILE 3.0 1.1 - - - -
247D PHE* 2.7 61.9 + - + +
260D LEU* 3.5 23.1 - - - -
265D PHE* 3.7 7.0 - - - -
279D ILE* 3.6 13.5 - - - -
280D PHE* 5.0 0.9 - - - -
283D HIS* 3.3 30.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 244 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240D GLY 3.1 10.6 + - - +
241D TYR* 3.1 10.5 + - - +
243D CYS* 1.3 76.6 - - - +
245D ILE* 1.3 59.7 + - - +
248D GLY* 3.0 35.5 + - - -
249D PRO* 3.4 13.1 - - - +
250D HIS 4.0 0.8 - - - +
283D HIS* 3.1 27.3 + - - -
286D CYS* 3.4 30.9 - - + +
287D GLY 3.2 17.4 + - - +
289D MET* 2.9 31.0 + - + +
290D SER 4.7 0.4 - - - +
291D GLU* 4.8 5.2 + - - +
294D ALA* 4.2 14.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 245 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216D TYR* 3.3 45.1 - - + +
241D TYR* 2.8 22.8 + - + +
242D GLN 3.8 4.3 - - - +
244D GLN* 1.3 80.3 - - - +
246D GLN* 1.3 66.3 + - + +
247D PHE 3.6 0.3 + - - -
248D GLY* 4.4 1.6 + - - -
291D GLU* 2.5 45.8 - - + +
294D ALA* 3.8 17.9 - - + +
295D LYS* 3.4 47.1 - - + +
298D TYR* 5.1 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 246 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216D TYR* 4.9 2.7 - - + +
220D ARG* 5.2 10.0 - - - +
242D GLN* 3.0 46.9 + - + +
245D ILE* 1.3 86.5 - - + +
247D PHE* 1.3 78.4 + - + +
265D PHE* 3.2 16.5 - - - -
291D GLU* 4.7 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 247 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243D CYS* 2.7 57.0 + - + +
245D ILE 4.9 0.2 - - - -
246D GLN* 1.3 92.3 - - + +
248D GLY* 1.3 63.5 + - - +
249D PRO 4.5 2.0 - - - +
255D HIS* 3.9 26.1 - + - +
259D PHE* 4.7 16.4 - + - -
260D LEU* 3.6 20.9 - - + -
265D PHE* 3.6 22.2 - + - -
280D PHE* 5.3 0.7 - + - -
283D HIS* 3.6 9.0 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 248 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243D CYS 3.6 0.2 + - - -
244D GLN* 3.0 22.6 + - - +
245D ILE 4.4 1.2 + - - -
246D GLN 3.9 0.2 - - - -
247D PHE* 1.3 78.0 - - - +
249D PRO* 1.3 82.0 - - - +
283D HIS* 3.2 16.6 + - - -
289D MET 5.9 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