Contacts of the helix formed by residues 231 - 248 (chain B) in PDB entry 3DAE
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 231 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169B HIS* 3.3 42.2 - - + +
174B VAL* 4.0 16.8 - - + -
228B TYR* 5.0 3.1 - - + +
230B GLY* 1.3 81.5 - - - +
232B GLU* 1.3 69.8 + - + +
233B VAL 2.8 6.3 - - - -
234B ASP* 2.8 17.4 + - - +
235B VAL* 3.4 9.4 + - - +
297B ILE* 5.8 0.7 - - + -
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Residues in contact with GLU 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221B GLU* 4.2 3.6 - - - +
228B TYR* 4.8 5.1 - - - +
230B GLY* 2.9 34.7 + - - -
231B PRO* 1.3 83.3 - - + +
233B VAL* 1.3 61.3 + - - +
235B VAL* 3.0 21.0 + - - +
236B TRP 3.1 6.9 + - - -
291B PRO* 3.7 34.4 - - + +
292B LEU* 6.0 1.8 - - - +
294B ARG* 3.1 30.5 + - + +
295B ILE 5.9 0.4 - - - -
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Residues in contact with VAL 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B VAL* 4.1 4.0 - - + -
176B ARG* 4.0 22.4 - - + -
219B ALA* 3.7 9.4 + - + +
221B GLU* 3.5 24.5 - - + +
222B VAL* 3.0 35.7 - - + -
229B ALA* 4.1 8.3 - - + -
230B GLY 3.4 18.4 + - - +
231B PRO 2.8 0.4 - - - -
232B GLU* 1.3 81.1 - - - +
234B ASP* 1.3 73.4 + - - +
236B TRP* 3.5 4.9 + - - +
237B SER* 3.3 23.0 + - - -
294B ARG* 4.2 4.3 - - - +
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Residues in contact with ASP 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B VAL* 4.1 9.0 - - + +
168B CYS* 6.0 0.3 - - - +
169B HIS* 3.1 26.5 + - + +
174B VAL* 3.8 4.5 - - - -
175B HIS* 2.7 30.8 + - - +
176B ARG* 2.9 28.1 + - - -
178B LEU* 3.8 20.4 - - + +
231B PRO 2.8 10.0 + - - +
233B VAL* 1.3 78.5 - - - +
235B VAL* 1.3 58.6 + - - +
237B SER* 3.5 4.8 + - - +
238B CYS* 3.0 33.6 + - - +
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Residues in contact with VAL 235 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231B PRO 3.4 7.5 + - - +
232B GLU* 3.0 12.8 + - - +
234B ASP* 1.3 74.3 - - - +
236B TRP* 1.3 67.3 + - - +
238B CYS* 3.0 7.7 + - - +
239B GLY* 2.9 21.3 + - - -
286B MET* 3.7 31.9 - - + +
294B ARG* 4.0 6.5 - - - -
295B ILE* 3.5 30.3 - - + +
296B SER* 5.0 0.7 - - - -
297B ILE* 3.7 37.2 - - + +
300B ILE* 4.3 5.8 - - + -
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Residues in contact with TRP 236 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216B ASN 5.1 0.4 + - - -
217B TYR 3.6 8.6 + - - -
218B ALA 3.4 10.9 + - - -
219B ALA* 3.4 27.6 - - + -
220B PRO* 3.5 27.8 - - + -
232B GLU 3.1 8.1 + - - +
233B VAL 3.6 8.5 - - - +
235B VAL* 1.3 81.1 - - - +
237B SER* 1.3 65.2 + - - +
239B GLY 3.0 7.3 + - - -
240B VAL* 3.2 21.7 + - + +
252B PHE* 3.4 33.6 - + - -
264B ILE* 3.8 20.0 - - + -
267B GLY* 4.6 1.3 - - - -
286B MET 3.8 15.0 - - - -
287B LEU* 3.5 33.8 - - + +
288B ILE 3.8 11.0 - - - -
289B VAL* 3.9 5.4 - - + -
294B ARG* 3.4 26.2 - - - +
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Residues in contact with SER 237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176B ARG 5.3 4.2 + - - -
177B ASP* 5.3 0.9 + - - -
178B LEU* 3.8 36.9 + - - +
217B TYR* 2.7 29.5 + - - -
218B ALA* 4.5 2.8 - - - -
219B ALA 4.9 0.7 + - - -
233B VAL* 3.3 11.5 + - - +
234B ASP* 3.8 9.1 + - - -
235B VAL 3.3 0.2 - - - -
236B TRP* 1.3 78.7 - - - +
238B CYS* 1.3 56.0 + - - +
240B VAL* 3.0 18.9 + - - +
241B ILE* 3.1 18.6 + - - +
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Residues in contact with CYS 238 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B PHE* 3.5 15.2 - - + -
161B ILE* 3.8 28.7 - - - -
162B ILE* 3.9 26.2 - - + -
165B VAL* 4.0 8.3 - - - -
178B LEU* 3.9 17.3 - - - -
234B ASP 3.0 22.6 + - - +
235B VAL* 3.0 7.4 + - - +
237B SER* 1.3 74.8 - - - +
239B GLY* 1.3 60.8 + - - +
241B ILE* 3.4 8.9 + - - +
242B LEU 2.9 22.2 + - - -
286B MET* 5.0 1.6 - - - -
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Residues in contact with GLY 239 (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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235B VAL 2.9 12.4 + - - -
236B TRP 3.6 4.0 - - - -
238B CYS* 1.3 75.2 - - - +
240B VAL* 1.3 60.0 + - - +
242B LEU* 3.8 2.0 - - - +
243B TYR* 3.1 25.8 + - - +
283B ILE* 4.2 4.4 - - - +
286B MET* 3.8 33.1 - - - -
287B LEU* 4.2 11.5 - - - +
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Residues in contact with VAL 240 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216B ASN 3.7 17.5 - - - +
217B TYR* 3.6 26.5 - - + -
236B TRP* 3.4 37.0 - - + +
237B SER 3.0 8.3 + - - +
239B GLY* 1.3 77.0 - - - +
241B ILE* 1.3 59.9 + - - +
243B TYR* 3.5 1.4 + - - +
244B VAL* 2.8 36.0 + - + +
250B LEU* 4.5 1.8 - - + -
251B PRO* 3.5 29.2 - - + -
252B PHE* 4.6 3.6 - - + -
287B LEU* 3.8 13.2 - - + -
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Residues in contact with ILE 241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B LEU* 4.7 3.8 - - + -
158B PHE* 5.7 0.7 - - + -
161B ILE* 3.9 27.1 - - + -
178B LEU* 4.0 29.2 - - + -
180B PRO* 4.6 6.1 - - + -
183B LEU* 3.7 31.0 - - + -
217B TYR* 4.1 16.2 - - + -
237B SER 3.1 14.3 + - - +
238B CYS* 3.6 17.7 - - - +
240B VAL* 1.3 74.7 - - - +
242B LEU* 1.3 66.1 + - - +
244B VAL* 3.3 5.5 + - - +
245B MET* 3.1 37.5 + - + +
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Residues in contact with LEU 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B ALA* 4.0 10.1 - - + +
158B PHE* 3.8 37.0 - - + -
238B CYS 2.9 16.9 + - - +
239B GLY* 3.9 6.7 - - - +
241B ILE* 1.3 79.8 - - - +
243B TYR* 1.3 64.8 + - - +
245B MET* 3.3 7.5 + - + +
246B LEU* 3.1 40.1 + - + +
279B ALA* 4.8 1.6 - - - +
282B LEU* 4.5 6.3 - - + -
283B ILE* 3.7 14.4 - - + -
286B MET* 3.5 24.9 - - + -
305B TRP* 4.0 22.0 - - + -
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Residues in contact with TYR 243 (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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239B GLY 3.1 16.1 + - - +
240B VAL 3.6 4.5 - - - +
242B LEU* 1.3 80.0 - - - +
244B VAL* 1.3 51.9 + - - +
246B LEU* 3.3 1.6 + - - -
247B CYS* 2.7 60.4 + - + +
249B ARG* 3.0 32.6 - - + +
250B LEU 3.7 3.5 + - - -
251B PRO* 3.3 41.4 + - + +
269B TYR* 4.0 13.7 - + - -
270B THR* 2.4 34.7 + - - +
271B LEU* 4.2 9.2 - - + -
272B PRO* 3.8 6.3 - - + +
283B ILE* 4.0 30.7 - - + +
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Residues in contact with VAL 244 (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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143B ILE* 4.2 29.2 - - + +
180B PRO* 5.5 1.1 - - + -
217B TYR* 4.0 14.8 - - + +
240B VAL 2.8 25.1 + - - +
241B ILE* 3.8 6.3 - - - +
242B LEU 3.2 0.2 - - - -
243B TYR* 1.3 72.6 - - - +
245B MET* 1.3 60.0 + - - +
248B ARG* 2.7 30.7 + - - -
249B ARG 3.7 13.5 - - - +
250B LEU* 3.3 33.4 - - + -
251B PRO* 4.1 8.1 - - + -
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Residues in contact with MET 245 (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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139B LEU* 4.1 13.7 - - - -
143B ILE* 4.2 23.1 - - + +
149B MET* 3.4 37.2 + - + +
154B ALA* 3.4 32.5 - - + +
157B PHE* 3.6 33.7 - - + -
158B PHE* 4.1 13.0 - - + +
161B ILE* 4.6 1.1 - - + -
241B ILE* 3.1 33.0 + - + +
242B LEU* 3.8 14.1 - - + +
244B VAL* 1.3 80.9 - - - +
246B LEU* 1.3 64.2 + - - +
248B ARG* 4.0 6.9 + - - +
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Residues in contact with LEU 246 (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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148B LYS* 3.3 22.9 - - - +
149B MET 4.6 4.5 - - - +
150B SER 4.4 2.0 - - - +
151B GLU* 3.9 30.1 - - + +
154B ALA* 3.1 29.2 - - + -
242B LEU* 3.1 35.3 + - + +
243B TYR* 3.7 3.4 - - - +
245B MET* 1.3 82.3 - - - +
247B CYS* 1.3 64.9 + - - +
274B PHE* 3.8 9.1 - - - -
275B LEU* 4.7 10.3 - - + -
279B ALA* 3.8 28.0 - - + -
283B ILE* 4.2 8.7 - - + -
305B TRP* 4.7 3.6 - - + -
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Residues in contact with CYS 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B LYS* 4.0 8.4 - - - +
243B TYR* 2.7 43.3 + - + +
246B LEU* 1.3 76.1 - - - +
248B ARG* 1.3 72.3 + - - +
249B ARG* 2.9 22.1 + - + +
272B PRO* 3.8 20.0 - - + -
274B PHE* 4.2 9.6 - - + -
275B LEU* 3.8 29.2 - - - -
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Residues in contact with ARG 248 (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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143B ILE* 3.8 23.8 + - + +
144B VAL* 3.5 25.2 + - - +
146B ARG 2.3 34.7 + - - -
147B ASP* 3.3 11.4 - - - +
148B LYS* 3.4 36.6 - - + +
149B MET* 4.9 0.7 - - + +
244B VAL* 2.7 22.0 + - - +
245B MET 4.5 4.5 - - - +
246B LEU 3.6 0.2 - - - -
247B CYS* 1.3 79.8 - - - +
249B ARG* 1.3 64.4 + - - +
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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