Contacts of the helix formed by residues 230 - 247 (chain B) in PDB entry 2V5Q
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 230 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168B HIS* 3.4 74.2 - + + +
171B ARG* 4.1 10.3 - - + -
172B VAL 4.0 7.9 - - - -
173B ILE* 3.8 20.8 - - + +
201B VAL* 3.6 31.2 - - + -
229B SER* 1.3 90.9 + - - +
231B GLU* 1.3 65.7 + - + +
233B ASP* 3.0 14.6 + - - +
234B VAL* 3.8 2.0 + - - +
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Residues in contact with GLU 231 (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 1.7 - - - +
228B HIS* 5.2 0.3 - - - -
229B SER* 3.3 31.7 + - - -
230B PHE* 1.3 79.2 - - + +
232B VAL* 1.3 60.2 + - - +
233B ASP 3.2 0.2 - - - -
234B VAL* 3.1 13.1 + - - +
235B TRP 3.0 18.5 + - - -
290B PRO* 3.4 38.1 - - + +
291B THR* 5.1 7.7 + - - +
293B ARG* 3.0 27.9 + - + +
294B PRO 6.0 1.3 - - - +
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Residues in contact with VAL 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173B ILE* 3.6 19.1 - - + -
175B ARG* 4.0 19.1 - - + -
217B TYR 5.0 0.2 - - - +
219B ALA* 4.0 14.8 - - + +
221B GLU* 3.6 11.0 - - - +
222B VAL* 3.7 18.6 - - + -
228B HIS* 3.5 34.3 - - + -
229B SER 3.4 12.1 - - - +
230B PHE 3.1 1.0 + - - -
231B GLU* 1.3 78.0 - - - +
233B ASP* 1.3 61.4 + - - +
235B TRP* 3.4 4.7 - - - +
236B SER* 3.1 29.2 + - - -
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Residues in contact with ASP 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164B CYS* 3.8 12.4 - - - -
167B LEU* 5.5 0.2 - - - +
168B HIS* 2.8 34.8 + - + +
173B ILE* 3.4 8.0 - - - +
174B HIS* 3.0 25.8 + - - +
175B ARG* 2.8 30.1 + - - -
177B LEU* 3.8 17.1 - - + +
230B PHE 3.0 3.9 + - - +
232B VAL* 1.3 75.2 - - - +
234B VAL* 1.3 61.2 + - - +
236B SER* 3.3 5.0 + - - -
237B ILE* 2.9 33.7 + - - +
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Residues in contact with VAL 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B HIS* 4.7 3.8 - - + -
230B PHE 4.6 6.7 - - - +
231B GLU* 3.1 14.3 + - - +
233B ASP* 1.3 75.3 - - - +
235B TRP* 1.3 65.5 + - - +
237B ILE* 3.2 5.6 + - - -
238B GLY* 2.9 19.4 + - - -
285B MET* 3.6 30.3 - - + +
293B ARG* 4.1 9.2 - - + -
294B PRO* 3.5 34.5 - - + +
295B THR* 4.4 1.3 - - - -
296B ILE* 4.1 31.2 - - + +
299B LEU* 4.2 5.6 - - + -
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Residues in contact with TRP 235 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217B TYR 3.6 15.4 + - - -
218B ILE 3.7 11.9 + - - -
219B ALA* 3.6 17.0 - - + -
220B PRO* 3.6 32.8 - - + -
231B GLU 3.0 5.9 + - - -
232B VAL 3.4 8.5 - - - +
234B VAL* 1.3 75.8 - - - +
236B SER* 1.3 58.7 + - - +
238B GLY 3.1 2.3 + - - -
239B CYS* 3.0 40.5 + - - -
251B PHE* 3.4 39.4 - + - -
263B ILE* 3.8 15.8 - - + +
266B ASN* 3.7 14.8 - - - -
285B MET 3.8 17.9 - - - -
286B LEU* 3.5 25.0 - - + +
287B GLN 3.7 20.2 - - - -
293B ARG* 3.8 18.3 - - - +
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Residues in contact with SER 236 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B ARG 5.3 4.9 + - - -
176B ASP* 5.5 0.2 - - - -
177B LEU* 3.8 35.6 + - - +
217B TYR* 3.4 28.7 + - - +
232B VAL 3.1 13.8 + - - -
233B ASP* 3.5 11.0 + - - -
234B VAL 3.3 0.2 - - - -
235B TRP* 1.3 73.8 - - - +
237B ILE* 1.3 60.3 + - - +
239B CYS* 3.1 3.5 + - - +
240B ILE* 2.9 34.3 + - - +
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Residues in contact with ILE 237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157B LEU* 4.3 15.0 - - + -
160B ILE* 4.0 20.9 - - + -
161B VAL* 4.1 15.7 - - + -
164B CYS* 4.0 19.1 - - + -
177B LEU* 4.1 8.5 - - + -
233B ASP 2.9 21.6 + - - +
234B VAL 3.2 4.5 + - - +
236B SER* 1.3 75.8 - - - +
238B GLY* 1.3 54.2 + - - +
240B ILE* 3.3 8.0 + - + +
241B MET* 2.8 33.4 + - - +
285B MET* 4.0 15.7 - - + -
296B ILE* 3.6 30.5 - - + -
299B LEU* 4.0 10.3 - - + -
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Residues in contact with GLY 238 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234B VAL 2.9 12.0 + - - -
235B TRP 3.1 6.0 + - - -
237B ILE* 1.3 76.5 - - - +
239B CYS* 1.3 56.2 + - - +
241B MET* 3.3 2.8 + - - +
242B TYR* 3.0 28.6 + - - +
282B ILE* 4.6 3.7 - - - +
285B MET* 3.5 32.2 - - - -
286B LEU* 3.8 12.2 - - - +
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Residues in contact with CYS 239 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217B TYR* 3.4 37.7 - - + -
235B TRP* 3.0 42.9 + - - -
236B SER 3.1 3.3 + - - +
238B GLY* 1.3 71.7 - - - +
240B ILE* 1.3 61.0 + - - +
242B TYR* 3.4 3.2 + - - +
243B THR* 2.8 33.7 + - - -
250B PRO* 3.9 26.3 - - + +
251B PHE* 4.2 6.5 - - - -
286B LEU* 3.9 7.4 - - - -
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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
----------------------------------------------------------
157B LEU* 4.2 4.3 - - + -
160B ILE* 4.2 18.8 - - + -
177B LEU* 4.0 26.2 - - + -
178B LYS* 4.0 3.1 - - - +
179B LEU* 4.0 17.7 - - + -
182B LEU* 3.9 19.5 - - + -
217B TYR* 3.7 18.2 - - + -
236B SER 2.9 24.2 + - - +
237B ILE* 3.6 13.2 - - + +
239B CYS* 1.3 72.9 - - - +
241B MET* 1.3 61.8 + - - +
243B THR* 3.2 6.6 + - - -
244B LEU* 2.9 49.1 + - + +
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Residues in contact with MET 241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157B LEU* 3.6 31.9 - - + -
237B ILE 2.8 20.9 + - - +
238B GLY 3.3 5.4 + - - +
240B ILE* 1.3 74.4 - - - +
242B TYR* 1.3 61.4 + - - +
244B LEU* 3.4 2.2 + - - +
245B LEU* 3.1 44.7 + - + +
278B ALA* 3.5 32.1 - - - +
281B LEU* 3.7 13.7 - - + -
282B ILE* 3.8 12.8 - - + -
285B MET* 3.6 25.6 - - + -
304B PHE* 3.8 24.2 - - + -
305B PHE* 6.1 0.4 - - - -
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Residues in contact with TYR 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238B GLY 3.0 12.8 + - - +
239B CYS 3.5 8.7 - - - +
241B MET* 1.3 77.1 - - - +
243B THR* 1.3 53.0 + - - +
245B LEU 3.2 0.9 + - - -
246B VAL* 2.7 69.4 + - + +
248B LYS* 3.1 22.9 - - + -
249B PRO 3.8 3.0 + - - -
250B PRO* 3.4 43.9 + - + +
268B TYR* 4.1 11.4 - + - -
269B SER 2.6 30.5 + - - -
270B ILE* 4.2 7.0 - - + -
271B PRO* 4.1 1.4 - - - +
282B ILE* 4.1 33.4 - - + +
286B LEU* 4.8 0.4 - - + -
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Residues in contact with THR 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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142B HIS* 3.5 33.3 + - + +
147B ALA* 4.7 0.3 - - - -
179B LEU* 4.0 17.3 - - + -
217B TYR* 3.5 14.9 + - - +
239B CYS 2.8 17.8 + - - -
240B ILE* 3.6 5.4 - - - -
242B TYR* 1.3 75.3 - - - +
244B LEU* 1.3 58.9 + - - +
247B GLY* 2.8 31.0 + - - -
248B LYS 3.4 17.3 - - - -
249B PRO* 3.5 21.6 - - + +
250B PRO* 3.9 0.7 - - - +
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Residues in contact with LEU 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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138B LEU* 4.7 11.9 - - + +
141B LEU* 5.5 2.9 - - + -
142B HIS* 5.1 10.1 - - + +
146B LYS 5.2 2.2 - - - +
147B ALA* 3.4 2.4 - - - -
148B LEU* 2.8 59.0 + - + +
153B ALA* 4.4 11.0 - - + +
156B TYR* 4.7 16.4 - - + -
157B LEU* 4.2 20.9 - - + -
160B ILE* 4.9 0.4 - - + -
179B LEU* 4.0 22.2 - - + -
240B ILE* 2.9 39.3 + - + +
241B MET* 3.8 4.0 - - - +
242B TYR 3.3 0.2 - - - -
243B THR* 1.3 77.3 - - - +
245B LEU* 1.3 58.5 - - - +
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Residues in contact with LEU 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B ALA* 3.4 15.1 - - - +
148B LEU 4.5 7.1 - - - +
150B GLU* 4.0 27.8 - - + +
153B ALA* 3.6 26.5 - - + -
241B MET* 3.1 52.5 + - + +
242B TYR* 4.0 1.6 - - - +
244B LEU* 1.3 76.1 - - - +
246B VAL* 1.3 63.0 + - + +
273B HIS* 4.6 3.1 + - - -
274B ILE* 3.5 26.5 - - + +
278B ALA* 3.8 17.3 - - + -
282B ILE* 4.4 6.5 - - + -
304B PHE* 4.5 4.9 - - + -
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Residues in contact with VAL 246 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B ALA* 3.7 8.2 - - - +
242B TYR* 2.7 64.6 + - + +
245B LEU* 1.3 77.9 - - + +
247B GLY* 1.3 55.9 + - - +
248B LYS* 3.4 9.2 + - + +
270B ILE* 4.9 2.2 - - + -
271B PRO* 3.8 33.0 - - + -
273B HIS* 5.1 6.4 + - + -
274B ILE* 4.0 14.4 - - + -
282B ILE* 5.2 1.3 - - + -
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Residues in contact with GLY 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B HIS* 3.1 20.7 + - - -
146B LYS* 4.0 16.1 + - - +
147B ALA 3.5 23.1 - - - -
243B THR 2.8 21.9 + - - -
245B LEU 3.7 0.8 - - - -
246B VAL* 1.3 74.6 - - - +
248B LYS* 1.3 65.5 + - - +
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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