Contacts of the helix formed by residues 235 - 253 (chain D) in PDB entry 3ENM
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 235 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176D ILE* 4.3 1.6 - - - -
233D GLY 3.9 4.4 + - - -
234D TYR* 1.3 84.7 - - - +
236D VAL* 1.3 59.2 + - - +
237D LYS* 3.3 23.7 + - - +
238D SER* 2.7 39.2 + - - -
299D SER* 5.6 0.5 + - - -
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Residues in contact with VAL 236 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170D HIS* 3.6 51.1 - - + +
176D ILE* 3.8 23.4 - - + +
235D SER* 1.3 75.4 - - - +
237D LYS* 1.3 79.3 + - + +
239D ASP* 2.8 18.1 + - - +
240D ILE* 2.9 17.2 + - + +
304D THR* 6.0 3.4 - - + -
305D TYR* 3.7 22.4 - - + +
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Residues in contact with LYS 237 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235D SER* 3.0 14.8 + - - +
236D VAL* 1.3 84.8 - - + +
238D SER* 1.3 61.2 + - - +
240D ILE* 3.2 8.2 + - + +
241D TRP 3.1 14.7 + - - -
299D SER* 3.3 38.7 + - - +
300D LYS* 3.4 14.1 + - - +
302D ARG* 2.7 52.4 + - + +
303D PRO 3.9 12.3 - - - +
304D THR* 4.0 26.4 - - - +
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Residues in contact with SER 238 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221D ALA* 4.3 6.5 + - - +
223D GLU* 3.0 21.5 + - - +
224D ARG* 4.0 16.0 + - - +
234D TYR* 3.6 26.4 + - - -
235D SER* 2.7 20.6 + - - -
237D LYS* 1.3 77.1 - - - +
239D ASP* 1.3 62.8 + - - -
240D ILE 3.3 0.3 + - - -
241D TRP* 3.5 4.9 + - - +
242D SER* 3.3 20.8 + - - -
302D ARG* 4.0 5.2 - - - +
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Residues in contact with ASP 239 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166D LEU* 4.7 0.7 - - + -
176D ILE* 2.7 29.3 - - - +
177D HIS* 3.0 15.1 + - - +
178D ARG* 2.9 20.7 + - - -
180D VAL* 3.8 20.4 + - + +
234D TYR* 2.8 22.2 + - - -
235D SER 3.8 0.6 + - - -
236D VAL 2.8 9.6 + - - +
238D SER* 1.3 73.0 - - - +
240D ILE* 1.3 58.4 + - - +
242D SER* 2.8 10.7 + - - -
243D LEU* 2.8 27.3 + - - +
305D TYR* 3.4 21.2 + - - +
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Residues in contact with ILE 240 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236D VAL* 2.9 23.1 + - + +
237D LYS* 3.6 13.0 - - + +
238D SER 3.1 0.4 - - - -
239D ASP* 1.3 77.4 - - - +
241D TRP* 1.3 56.7 + - - +
243D LEU* 3.2 8.9 - - + +
244D GLY 3.0 22.2 + - - -
294D CYS* 3.4 33.7 - - - +
302D ARG* 4.8 2.9 - - + -
303D PRO* 3.1 35.7 - - + +
304D THR* 4.1 8.3 - - - -
305D TYR* 3.4 42.8 - - + +
308D LEU* 4.0 12.6 - - + -
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Residues in contact with TRP 241 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218D PRO 5.5 0.8 + - - -
219D TYR 3.5 17.5 + - - -
220D MSE 3.6 11.1 + - - -
221D ALA* 3.5 14.1 - - + -
222D PRO* 3.6 30.7 - - + -
237D LYS 3.1 5.5 + - - -
238D SER 3.5 8.7 - - - +
240D ILE* 1.3 74.1 - - - +
242D SER* 1.3 67.4 + - - +
244D GLY* 2.9 4.0 + - - -
245D ILE* 2.9 40.4 + - + +
257D TYR* 3.5 19.9 - + - -
270D VAL* 4.1 9.4 - - + +
275D SER* 3.7 20.6 - - - -
294D CYS 3.4 13.3 + - - -
295D LEU* 3.4 43.6 - - + +
296D LYS 4.2 2.9 - - - -
297D LYS* 4.0 8.7 - - + -
302D ARG* 3.7 30.7 - - - +
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Residues in contact with SER 242 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178D ARG 5.7 0.5 + - - -
179D ASP* 5.6 1.0 - - - -
180D VAL* 3.5 29.2 + - - -
219D TYR* 2.7 27.7 + - - +
220D MSE 4.5 2.8 - - - -
234D TYR* 4.9 2.4 + - - -
238D SER 3.3 10.1 + - - -
239D ASP* 2.8 17.7 + - - -
241D TRP* 1.3 75.2 - - - +
243D LEU* 1.3 53.8 + - - +
245D ILE* 3.2 5.2 + - - +
246D THR* 2.7 40.2 + - - +
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Residues in contact with LEU 243 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162D ILE* 4.1 11.0 - - + -
163D VAL* 3.4 30.1 - - + -
166D LEU* 4.8 11.9 - - + -
180D VAL* 3.9 14.4 - - + +
239D ASP 2.8 11.1 + - - +
240D ILE* 3.2 11.9 - - + +
242D SER* 1.3 76.1 - - - +
244D GLY* 1.3 62.5 + - - +
246D THR* 3.3 2.0 + - - +
247D MSE 2.6 67.3 + - + +
290D PHE* 4.6 5.6 - - + -
294D CYS* 4.3 9.9 - - - -
305D TYR* 5.3 0.7 - - + -
308D LEU* 4.0 19.1 - - + -
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Residues in contact with GLY 244 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240D ILE 3.0 8.1 + - - -
241D TRP 2.9 8.3 + - - -
243D LEU* 1.3 76.7 - - - +
245D ILE* 1.3 62.9 + - - +
247D MSE 3.3 5.6 + - - +
248D ILE* 3.0 29.1 + - - +
291D THR* 4.7 4.9 - - - +
294D CYS* 3.8 22.7 - - - -
295D LEU* 3.8 12.8 - - - -
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Residues in contact with ILE 245 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218D PRO 4.7 1.6 - - - +
219D TYR* 3.6 29.6 - - + +
241D TRP* 2.9 37.9 + - + +
242D SER* 3.7 7.4 - - - +
244D GLY* 1.3 75.7 - - - +
246D THR* 1.3 56.6 + - - +
248D ILE* 3.4 3.0 + - + +
249D GLU* 2.9 28.2 + - - +
255D PHE* 3.8 21.1 - - + -
256D PRO* 4.1 15.8 - - + +
257D TYR* 3.8 30.5 - - + +
276D PRO* 4.7 2.9 - - + -
295D LEU* 3.7 19.3 - - + +
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Residues in contact with THR 246 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162D ILE* 4.4 6.4 - - - +
180D VAL* 3.7 11.9 - - + +
181D LYS* 3.4 28.7 - - - +
182D PRO* 3.4 24.1 - - + +
185D VAL* 5.6 0.5 - - - +
219D TYR* 4.4 2.9 - - + -
242D SER 2.7 36.9 + - - +
243D LEU* 4.0 3.3 + - - -
244D GLY 3.2 0.2 - - - -
245D ILE* 1.3 77.4 - - - +
247D MSE 1.3 75.4 + - - +
249D GLU* 3.5 7.6 - - - +
250D LEU* 3.0 34.5 + - - +
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Residues in contact with MSE 247 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155D LEU* 4.5 7.7 - - - +
158D ILE* 4.2 11.4 - - - -
159D ALA* 3.7 35.0 - - + -
162D ILE* 3.0 30.3 - - + -
243D LEU* 2.6 60.3 + - + +
244D GLY* 3.3 4.2 + - - +
246D THR* 1.3 82.0 - - - +
248D ILE* 1.3 58.2 + - - +
250D LEU* 3.3 12.2 + - - +
251D ALA* 3.0 28.6 + - - +
287D PHE* 4.4 14.0 - - + -
290D PHE* 4.8 9.2 - - + -
291D THR* 4.1 16.6 - - + -
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Residues in contact with ILE 248 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244D GLY 3.0 20.1 + - - +
245D ILE* 3.8 3.8 - - - +
247D MSE 1.3 71.6 - - - +
249D GLU* 1.3 67.8 + - - +
251D ALA* 3.1 1.2 + - - +
252D ILE* 2.9 35.3 + - + +
256D PRO* 3.9 26.2 - - + -
276D PRO* 3.5 34.3 - - + +
277D GLN 4.0 2.2 - - - +
278D LEU* 3.8 37.9 - - + +
291D THR* 4.2 14.6 - - - -
295D LEU* 3.9 12.6 - - + -
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Residues in contact with GLU 249 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137D ASP* 5.9 0.5 - - - +
140D TYR* 2.5 43.7 + - + +
182D PRO* 3.4 11.9 - - + +
219D TYR* 2.5 39.1 + - - -
245D ILE 2.9 17.4 + - - +
246D THR 3.5 6.3 - - - +
248D ILE* 1.3 77.2 - - - +
250D LEU* 1.3 57.4 + - - +
253D LEU* 2.8 27.9 + - - -
254D ARG 3.2 25.0 + - - +
255D PHE* 3.9 15.9 + - - +
256D PRO* 4.1 5.8 - - + +
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Residues in contact with LEU 250 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136D LEU* 3.8 39.9 - - + -
140D TYR* 3.8 35.0 - - + -
150D ILE* 3.9 18.1 + - + +
155D LEU* 3.6 18.5 - - + +
158D ILE* 3.8 17.7 - - + -
182D PRO* 4.6 7.9 - - + -
246D THR* 3.0 29.5 + - - +
247D MSE 3.6 14.8 - - - +
249D GLU* 1.3 75.5 - - - +
251D ALA* 1.3 61.6 + - - +
253D LEU* 3.5 20.4 - - - +
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Residues in contact with ALA 251 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149D THR* 5.7 1.0 + - - -
150D ILE* 5.7 1.8 + - - +
155D LEU* 4.1 11.6 - - + +
247D MSE 3.0 17.3 + - - +
248D ILE 3.1 4.4 + - - +
250D LEU* 1.3 81.3 - - - +
252D ILE* 1.3 62.0 + - - +
253D LEU* 4.5 4.3 - - - +
278D LEU* 4.1 10.8 - - + -
283D PHE* 3.6 34.2 - - + -
287D PHE* 4.1 16.8 - - + -
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Residues in contact with ILE 252 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248D ILE* 2.9 32.5 + - + +
251D ALA* 1.3 79.6 - - + +
253D LEU* 1.3 72.3 + - - +
254D ARG* 3.7 58.6 + - + +
256D PRO* 4.4 8.7 - - + -
277D GLN 5.9 0.4 - - - +
278D LEU* 4.2 18.8 - - + -
279D PRO* 4.6 9.0 - - + -
283D PHE* 4.5 11.0 - - + -
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Residues in contact with LEU 253 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140D TYR* 3.6 40.7 - - + +
143D VAL* 4.5 4.3 - - + -
144D ILE* 3.8 32.7 - - + +
148D GLN 3.9 21.5 - - - +
149D THR* 4.3 13.2 - - - +
150D ILE* 4.4 13.0 - - + +
249D GLU 2.8 11.4 + - - -
250D LEU 3.5 17.9 - - - +
251D ALA 3.3 3.8 - - - +
252D ILE* 1.3 81.2 - - - +
254D ARG* 1.3 64.3 + - - +
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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) + - + + + + + -
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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