Contacts of the helix formed by residues 235 - 253 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176B ILE* 3.5 35.5 - - - +
178B ARG* 5.8 2.0 - - - +
232B LYS* 3.0 58.5 + - - +
236B VAL* 1.3 65.7 + - - +
237B LYS* 3.2 26.1 + - - +
238B SER* 3.2 23.8 + - - -
239B ASP 4.0 2.1 + - - -
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Residues in contact with VAL 236 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170B HIS* 3.5 43.7 - - + +
176B ILE* 4.2 7.9 - - + +
235B SER* 1.3 68.9 + - - +
237B LYS* 1.3 79.6 + - + +
238B SER 3.0 5.8 + - - -
239B ASP* 3.1 9.4 + - - +
240B ILE* 3.0 34.9 + - + +
304B THR* 5.2 6.3 - - + -
305B TYR* 3.5 32.0 + - + +
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Residues in contact with LYS 237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223B GLU* 5.3 0.7 - - - +
232B LYS* 4.4 8.3 - - - +
235B SER* 3.1 15.8 - - - +
236B VAL* 1.3 88.0 - - + +
238B SER* 1.3 53.6 - - - +
240B ILE* 3.8 4.5 - - + -
241B TRP 3.3 14.9 + - - -
299B SER* 2.9 42.2 + - - +
300B LYS* 3.6 14.3 + - - +
302B ARG* 2.5 58.0 + - + +
303B PRO 3.6 20.9 - - - +
304B THR* 4.1 14.3 - - - +
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Residues in contact with SER 238 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176B ILE* 6.2 0.4 - - - -
221B ALA* 4.0 5.8 + - - +
223B GLU* 3.3 18.9 + - - +
224B ARG* 3.6 30.9 + - - +
235B SER* 3.2 18.2 + - - -
236B VAL 3.0 0.6 - - - -
237B LYS* 1.3 79.3 - - - +
239B ASP* 1.3 64.8 - - - +
240B ILE 3.2 0.2 - - - -
241B TRP* 3.6 5.4 + - - +
242B SER* 3.3 23.4 + - - -
302B ARG* 4.2 3.4 - - - +
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Residues in contact with ASP 239 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B LEU* 3.9 4.4 - - + +
176B ILE* 3.6 14.5 - - - +
177B HIS* 2.8 34.5 + - - +
178B ARG* 2.8 30.3 + - - -
180B VAL* 4.0 16.6 + - + +
235B SER 4.0 1.1 + - - -
236B VAL* 3.1 7.6 + - - +
238B SER* 1.3 81.4 - - - +
240B ILE* 1.3 57.9 + - - +
242B SER* 3.1 7.5 + - - -
243B LEU* 2.9 27.6 + - - +
305B TYR* 3.4 19.5 + - - +
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Residues in contact with ILE 240 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236B VAL* 3.0 22.2 + - + +
237B LYS* 3.9 16.2 - - + +
239B ASP* 1.3 73.6 - - - +
241B TRP* 1.3 65.7 + - - +
243B LEU* 3.3 8.6 + - + +
244B GLY 3.0 16.3 + - - -
294B CYS* 3.4 35.4 - - - +
302B ARG* 4.7 3.4 - - + -
303B PRO* 2.9 39.3 - - + +
304B THR* 4.3 9.6 - - - -
305B TYR* 3.8 28.3 - - + -
308B LEU* 4.0 12.3 - - + -
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Residues in contact with TRP 241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218B PRO 5.7 0.6 + - - -
219B TYR 3.5 15.8 + - - -
220B MSE 3.6 12.1 + - - -
221B ALA* 3.6 12.6 - - + -
222B PRO* 3.6 31.6 - - + -
237B LYS 3.3 4.8 + - - -
238B SER 3.6 8.7 - - - +
240B ILE* 1.3 77.2 - - - +
242B SER* 1.3 65.4 + - - +
244B GLY* 2.9 11.6 + - - -
245B ILE* 2.9 32.3 + - + +
257B TYR* 3.3 21.9 - - - -
270B VAL* 4.2 4.7 - - + +
275B SER* 3.4 21.5 - - - -
294B CYS 3.5 11.7 + - - -
295B LEU* 3.2 40.2 - - + +
296B LYS 3.8 10.8 - - - -
297B LYS* 4.1 7.0 - - + -
302B ARG* 3.6 31.9 - - - +
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Residues in contact with SER 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178B ARG 6.1 1.0 - - - -
180B VAL* 3.3 32.5 + - - +
219B TYR* 2.8 27.7 + - - +
220B MSE 4.4 2.8 - - - -
238B SER 3.3 11.7 + - - -
239B ASP* 3.1 12.0 + - - -
241B TRP* 1.3 78.3 - - - +
243B LEU* 1.3 56.6 + - - +
245B ILE* 3.1 5.2 + - - +
246B THR* 2.8 34.8 + - - -
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Residues in contact with LEU 243 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159B ALA* 4.8 3.1 - - + -
162B ILE* 3.5 43.5 - - + -
163B VAL* 3.6 27.8 - - + -
166B LEU* 4.9 6.3 - - + -
180B VAL* 3.9 11.6 - - + +
239B ASP 2.9 12.7 + - - +
240B ILE* 3.4 11.4 - - + +
242B SER* 1.3 75.3 - - - +
244B GLY* 1.3 58.9 + - - +
246B THR* 3.0 5.1 + - - -
247B MSE 2.8 49.6 + - + +
290B PHE* 4.6 6.3 - - + -
294B CYS* 4.3 12.3 - - - -
305B TYR* 5.5 0.4 - - + -
308B LEU* 4.2 17.3 - - + -
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Residues in contact with GLY 244 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240B ILE 3.0 7.5 + - - -
241B TRP 2.9 8.1 + - - -
243B LEU* 1.3 78.6 - - - +
245B ILE* 1.3 61.4 + - - +
247B MSE 3.3 4.8 + - - +
248B ILE* 3.2 28.2 + - - +
291B THR* 4.9 4.3 - - - -
294B CYS* 3.8 22.9 - - - -
295B LEU* 4.0 13.5 - - - -
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Residues in contact with ILE 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218B PRO 5.2 0.7 - - - +
219B TYR* 3.6 35.9 - - + +
241B TRP* 2.9 39.1 + - + +
242B SER* 3.1 7.4 + - - +
244B GLY* 1.3 74.6 - - - +
246B THR* 1.3 62.5 + - - +
248B ILE* 4.0 2.3 - - - +
249B GLU* 3.1 22.9 + - - +
255B PHE* 3.8 18.4 - - + -
256B PRO* 4.1 10.9 - - + +
257B TYR* 3.8 28.0 - - + -
276B PRO* 4.0 14.4 - - + -
295B LEU* 3.7 17.3 - - + -
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Residues in contact with THR 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B LEU* 5.8 0.2 - - + -
162B ILE* 4.3 21.1 - - + -
180B VAL* 3.8 4.8 + - + +
181B LYS* 3.2 28.6 + - - -
182B PRO* 3.6 28.3 - - + +
185B VAL* 5.3 0.9 - - + -
219B TYR* 4.3 1.4 - - - -
242B SER 2.8 20.0 + - - -
243B LEU* 3.0 9.1 + - - +
245B ILE* 1.3 80.3 - - - +
247B MSE 1.3 59.1 + - - +
249B GLU* 3.5 3.5 - - - +
250B LEU* 3.1 46.0 + - + +
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Residues in contact with MSE 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155B LEU* 3.0 47.5 - - + +
158B ILE* 4.0 12.8 - - + -
159B ALA* 3.9 27.4 - - + +
162B ILE* 4.1 11.4 - - - -
243B LEU* 2.8 28.5 + - + +
244B GLY* 4.0 4.7 - - - +
246B THR* 1.3 76.0 - - - +
248B ILE* 1.3 66.1 + - - +
250B LEU* 3.5 19.0 + - + +
251B ALA* 3.0 23.1 + - - +
287B PHE* 4.2 17.0 - - + -
290B PHE* 4.9 6.7 - - + -
291B THR* 4.3 12.6 - - - +
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Residues in contact with ILE 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244B GLY 3.2 9.0 + - - +
245B ILE 4.0 2.5 - - - +
247B MSE 1.3 74.3 - - - +
249B GLU* 1.3 55.7 + - - +
251B ALA* 2.9 2.4 + - - +
252B ILE* 2.7 46.1 + - + +
256B PRO* 3.9 24.5 - - + -
276B PRO* 3.7 20.6 - - + +
277B GLN 5.0 4.3 - - - +
278B LEU* 3.8 29.8 - - + +
291B THR* 2.8 40.2 - - + +
295B LEU* 3.2 20.0 - - + -
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Residues in contact with GLU 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137B ASP* 5.9 0.5 - - - +
140B TYR* 2.7 37.4 + - + +
182B PRO* 3.5 13.9 - - + +
219B TYR* 2.4 42.4 + - - -
245B ILE 3.1 16.8 + - - +
246B THR 3.5 4.9 - - - +
248B ILE* 1.3 76.3 - - - +
250B LEU* 1.3 54.0 + - - +
253B LEU* 2.7 34.1 + - - -
254B ARG 3.4 20.1 + - - +
255B PHE* 3.8 17.4 + - - +
256B PRO* 4.2 4.4 - - + +
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Residues in contact with LEU 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B LEU* 4.1 28.7 - - + -
140B TYR* 3.9 31.9 - - + -
150B ILE* 3.8 16.7 + - + +
155B LEU* 3.6 17.5 - - + +
158B ILE* 3.9 32.5 - - + -
182B PRO* 4.5 6.7 - - + -
246B THR* 3.1 26.1 + - + +
247B MSE 3.8 16.4 - - + +
248B ILE 3.3 0.2 - - - -
249B GLU* 1.3 75.3 - - - +
251B ALA* 1.3 61.7 + - - +
253B LEU* 3.4 20.4 - - - +
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Residues in contact with ALA 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149B THR* 4.7 7.4 + - - -
150B ILE 5.5 1.9 + - - +
155B LEU* 3.8 23.8 - - + -
247B MSE 3.0 16.4 + - - +
248B ILE 2.9 5.2 + - - +
250B LEU* 1.3 80.0 - - - +
252B ILE* 1.3 62.0 + - - +
253B LEU* 4.3 5.2 - - - +
278B LEU* 4.0 14.4 - - + -
283B PHE* 3.7 30.4 - - + -
287B PHE* 4.1 3.8 - - + -
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Residues in contact with ILE 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248B ILE* 2.7 38.0 + - + +
251B ALA* 1.3 75.8 - - - +
253B LEU* 1.3 69.8 + - - +
254B ARG* 3.2 62.7 + - + +
256B PRO* 4.1 14.6 - - + -
277B GLN 5.8 0.2 - - - +
278B LEU* 4.4 17.9 - - + -
279B PRO* 4.4 16.4 - - + -
282B LYS* 6.5 0.4 - - - -
283B PHE* 4.4 6.3 - - + -
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Residues in contact with LEU 253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140B TYR* 3.6 40.1 - - + +
143B VAL* 4.3 3.8 - - + -
144B ILE* 3.3 37.6 - - + +
148B GLN 3.7 23.1 - - - +
149B THR* 4.2 13.9 - - - +
150B ILE* 4.2 14.6 - - + +
249B GLU 2.7 12.9 + - - -
250B LEU 3.4 20.4 - - - +
251B ALA 3.3 4.4 - - - +
252B ILE* 1.3 81.9 - - - +
254B ARG* 1.3 58.4 + - - +
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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