Contacts of the helix formed by residues 241 - 260 (chain R) in PDB entry 6DDE
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 PHE 241 (chain R).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237R PHE* 3.2 34.6 + + - +
240R ALA* 1.3 79.7 - - - +
242R ILE* 1.3 75.2 + - + +
244R PRO* 3.6 5.6 - - - -
245R VAL* 3.3 47.1 + - + +
289R PHE* 4.8 4.3 - + - -
290R ILE* 4.9 13.7 - - + -
293R TRP* 3.2 38.1 - + + -
294R THR* 3.9 17.5 - - - -
297R HIS* 3.7 24.2 - + + +
298R ILE* 5.4 6.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 242 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237R PHE* 3.1 47.0 + - + +
238R ILE* 3.7 19.7 - - + +
241R PHE* 1.3 87.8 - - + +
243R MET* 1.3 63.6 + - + +
245R VAL* 4.1 1.8 - - - +
246R LEU* 2.9 37.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 243 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156R PHE* 6.4 0.9 - - + -
238R ILE 3.3 18.7 + - - +
239R PHE* 4.5 18.8 - - + +
242R ILE* 1.3 83.6 - - + +
244R PRO* 1.3 63.1 - - + +
246R LEU* 3.7 7.6 - - - +
247R ILE* 2.9 39.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 244 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155R ILE* 3.7 15.0 - - + +
156R PHE* 5.9 1.6 - - + -
159R CYS* 3.6 20.9 - - - -
239R PHE 4.1 2.7 - - - +
240R ALA* 3.3 33.7 - - - +
241R PHE* 3.6 12.6 - - - +
243R MET* 1.3 89.2 - - + +
245R VAL* 1.3 60.5 + - - +
247R ILE* 3.3 10.5 - - + +
248R ILE* 2.9 36.0 + - + +
289R PHE* 4.2 15.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 245 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241R PHE* 3.3 39.1 + - + +
242R ILE* 4.1 2.0 - - + +
244R PRO* 1.3 76.4 - - - +
246R LEU* 1.3 59.1 + - - +
248R ILE* 4.0 6.5 - - + +
249R THR* 2.9 40.2 + - + +
286R VAL* 6.2 0.7 - - + -
289R PHE* 3.6 27.8 - - + -
290R ILE* 4.5 22.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 246 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242R ILE* 2.9 26.2 + - + +
243R MET* 3.9 10.8 - - + +
245R VAL* 1.3 77.3 - - - +
247R ILE* 1.3 59.5 + - - +
249R THR* 4.4 5.8 - - - -
250R VAL* 3.8 22.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 247 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159R CYS* 3.8 22.9 - - + +
163R VAL* 4.3 21.8 - - + -
243R MET* 2.9 25.5 + - + +
244R PRO* 3.3 16.2 - - + +
246R LEU* 1.3 80.1 - - - +
248R ILE* 1.3 60.0 + - + +
249R THR 3.4 0.4 - - - -
250R VAL* 3.6 1.3 + - - +
251R CYS* 2.7 48.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 248 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158R LEU* 4.4 8.7 - - + +
159R CYS* 4.3 13.5 - - - +
162R SER* 3.8 31.6 - - - +
244R PRO* 2.9 24.7 + - + +
245R VAL* 4.0 5.6 - - - +
247R ILE* 1.3 83.1 - - + +
249R THR* 1.3 66.5 + - - +
251R CYS* 4.1 1.6 - - - -
252R TYR* 3.4 31.4 - - + +
285R VAL* 5.6 1.6 - - + +
286R VAL* 4.0 22.6 - - + +
289R PHE* 4.1 37.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 249 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245R VAL* 2.9 28.6 + - + +
246R LEU* 4.3 5.6 - - - +
248R ILE* 1.3 81.8 - - - +
250R VAL* 1.3 70.9 + - + +
252R TYR* 4.4 0.8 - - - +
253R GLY* 2.9 27.2 + - - -
286R VAL* 4.8 17.5 - - - +
290R ILE* 6.2 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 250 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246R LEU 3.8 17.9 - - - +
247R ILE* 3.6 3.2 + - - +
249R THR* 1.3 83.4 - - + +
251R CYS* 1.3 58.4 + - - +
252R TYR 3.1 1.3 - - - -
253R GLY* 4.9 0.4 - - - -
254R LEU* 2.9 42.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 251 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162R SER* 3.1 46.4 - - - +
163R VAL* 3.7 16.2 - - - -
166R TYR* 3.5 40.5 - - - +
247R ILE* 2.7 27.6 + - + +
248R ILE* 4.1 0.2 - - - -
250R VAL* 1.3 76.1 - - - +
252R TYR* 1.3 64.3 + - - +
254R LEU 4.7 0.4 - - - -
255R MET* 4.0 3.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 252 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158R LEU 4.9 1.4 + - - -
161R MET* 4.3 1.7 - - - +
162R SER* 3.3 41.7 + - - -
165R ARG* 3.3 43.4 + - + -
248R ILE* 3.4 27.7 + - + +
249R THR* 4.4 1.1 - - - +
250R VAL 3.1 0.4 - - - -
251R CYS* 1.3 83.5 - - - +
253R GLY* 1.3 59.3 + - - +
254R LEU 3.3 1.8 - - - -
255R MET* 3.2 19.9 + - + +
256R ILE* 2.9 33.2 + - - +
282R VAL* 3.7 22.4 - - + -
285R VAL* 4.3 18.8 - - + -
286R VAL* 3.8 18.2 - - + -
336R TYR* 4.4 7.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 253 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249R THR 2.9 20.2 + - - -
250R VAL* 3.8 1.3 - - - -
252R TYR* 1.3 76.6 - - - +
254R LEU* 1.3 57.5 + - - +
256R ILE* 3.3 10.4 + - - +
257R LEU* 2.9 38.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 254 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166R TYR* 3.3 39.3 - - + +
170R CYS* 4.6 9.6 - - - +
250R VAL* 2.9 24.6 + - + +
253R GLY* 1.3 73.3 - - - +
255R MET* 1.3 60.8 + - - +
257R LEU* 4.3 12.6 - - + +
258R ARG* 2.9 28.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 255 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353A LEU* 4.2 16.8 - - + -
165R ARG* 3.9 24.2 - - - +
166R TYR* 4.5 8.3 - - + -
169R VAL* 3.7 38.1 - - + -
170R CYS* 5.5 0.9 - - - -
251R CYS 4.0 10.1 + - - +
252R TYR* 3.2 37.4 + - + +
254R LEU* 1.3 75.7 - - - +
256R ILE* 1.3 61.2 + - + +
258R ARG* 3.3 5.9 + - - +
259R LEU* 2.9 38.8 + - + +
278R ILE* 5.3 0.7 - - + -
282R VAL* 3.8 25.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 256 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252R TYR 2.9 18.5 + - - +
253R GLY* 3.3 10.5 + - - +
255R MET* 1.3 79.2 - - + +
257R LEU* 1.3 60.9 + - + +
259R LEU* 3.2 9.7 + - + +
260R LYS* 2.9 51.9 + - + +
275R LEU* 5.7 0.2 - - - +
278R ILE* 6.1 1.3 - - + -
279R THR* 3.9 29.4 - - + -
282R VAL* 3.7 35.4 - - + -
283R LEU* 5.0 15.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 257 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253R GLY* 2.9 28.0 + - - +
254R LEU* 3.5 16.1 + - + +
256R ILE* 1.3 83.9 - - + +
258R ARG* 1.3 60.5 + - - +
260R LYS* 3.9 22.5 + - + +
261R SER* 4.0 13.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 258 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337A ASP* 5.9 1.0 + - - -
340A THR* 4.6 11.9 - - - +
341A ASP* 5.8 1.2 + - - +
344A ILE* 3.5 23.6 - - + +
169R VAL* 4.0 23.9 + - + +
170R CYS* 4.2 28.5 + - + +
172R PRO* 5.4 1.8 - - - +
254R LEU* 2.9 18.1 + - + +
255R MET* 3.6 5.4 - - - +
256R ILE 3.2 0.2 - - - -
257R LEU* 1.3 77.6 - - - +
259R LEU* 1.3 60.7 + - - +
260R LYS 3.2 0.2 - - - -
261R SER* 3.1 34.0 + - - -
262R VAL* 3.3 18.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 259 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344A ILE* 4.0 4.9 - - + -
348A LEU* 3.8 33.9 - - + -
169R VAL* 3.8 17.9 - - + -
255R MET* 2.9 34.7 + - + +
256R ILE* 3.2 7.1 + - - +
258R ARG* 1.3 76.3 - - - +
260R LYS* 1.3 60.9 + - - +
261R SER 3.2 0.6 + - - -
262R VAL* 3.5 34.5 + - + +
265R LEU* 4.7 5.1 - - + +
275R LEU* 3.6 29.0 - - + +
278R ILE* 3.9 31.9 - - + -
279R THR* 6.4 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 260 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256R ILE* 2.9 38.1 + - + +
257R LEU* 4.1 26.0 - - + +
258R ARG 3.2 0.6 - - - -
259R LEU* 1.3 78.2 - - - +
261R SER* 1.3 58.5 + - - +
262R VAL 3.5 2.2 + - - +
266R SER* 5.1 8.4 + - - -
275R LEU* 4.4 19.3 - - + +
279R THR* 4.9 8.9 - - + +
----------------------------------------------------------
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