Contacts of the helix formed by residues 235 - 252 (chain B) in PDB entry 1XV9
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 GLN 235 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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233B GLY 3.2 4.8 + - - +
234B PHE* 1.3 79.1 - - - +
236B VAL* 1.3 69.7 + - + +
237B GLU* 3.6 5.2 - - + +
238B PHE* 3.5 7.2 + - + +
239B LEU* 3.5 12.6 + - - +
328B TYR* 3.7 17.8 + - - -
329B GLN* 2.9 34.2 + - - +
332B HIS* 3.3 37.3 + - + -
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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
----------------------------------------------------------
230B ALA* 6.3 0.7 - - - -
234B PHE 3.4 1.9 + - - -
235B GLN* 1.3 73.8 - - + +
237B GLU* 1.3 79.7 + - + +
239B LEU* 2.9 13.9 + - - +
240B GLU* 2.8 45.6 + - + +
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Residues in contact with GLU 237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381A LYS* 3.9 26.9 - - + +
235B GLN* 3.6 3.4 - - + +
236B VAL* 1.3 90.8 - - + +
238B PHE* 1.3 54.5 + - - +
240B GLU* 3.3 11.3 - - - +
241B LEU* 2.6 39.1 + - - +
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Residues in contact with PHE 238 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203B HIS* 5.5 2.5 - - - -
234B PHE* 3.7 33.0 - + + -
235B GLN* 3.5 10.1 + - + +
236B VAL 3.2 0.6 + - - -
237B GLU* 1.3 77.7 - - - +
239B LEU* 1.3 55.1 + - + +
241B LEU* 3.6 9.9 - - + +
242B LEU* 2.8 54.2 + - + +
322B ILE* 4.6 9.4 - - + -
325B ALA* 4.0 18.2 - - + -
326B TYR* 3.7 37.2 - + + -
329B GLN* 3.7 24.5 - - + +
1001D CI2 3.6 34.5 - - + -
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Residues in contact with LEU 239 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226B ILE* 3.9 22.7 - - + +
229B GLY* 3.8 16.4 - - - -
230B ALA* 3.4 31.0 - - + +
234B PHE* 3.2 39.0 - - + +
235B GLN 3.7 7.9 - - - +
236B VAL* 2.9 9.5 + - - +
238B PHE* 1.3 77.4 - - + +
240B GLU* 1.3 61.1 + - - +
242B LEU* 4.0 21.8 - - + -
243B PHE* 2.9 40.6 + - + +
1001D CI2 4.6 8.1 - - + -
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Residues in contact with GLU 240 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381A LYS* 3.7 22.1 - - - +
226B ILE* 4.6 9.6 - - + -
236B VAL* 2.8 36.6 + - + +
237B GLU* 3.3 13.2 - - - +
239B LEU* 1.3 74.4 - - - +
241B LEU* 1.3 66.0 + - - +
243B PHE* 3.8 3.1 - - - +
244B HIS* 3.1 22.7 + - - +
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Residues in contact with LEU 241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379A ASP 5.1 10.5 - - - +
381A LYS* 3.5 23.7 - - + +
237B GLU 2.6 20.7 + - - +
238B PHE* 3.6 9.6 - - + +
240B GLU* 1.3 73.0 - - - +
242B LEU* 1.3 64.1 + - - +
244B HIS* 2.9 21.7 + - + +
245B PHE* 3.1 11.7 + - + +
318B GLU* 5.1 10.1 - - - +
321B SER* 5.5 9.6 - - - -
322B ILE* 5.1 15.5 - - + -
325B ALA* 5.1 15.3 - - + -
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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
----------------------------------------------------------
203B HIS* 3.5 31.2 - - + +
217B PHE* 5.4 5.4 - - + -
238B PHE* 2.8 40.8 + - + +
239B LEU* 4.0 19.3 - - + +
241B LEU* 1.3 74.8 - - - +
243B PHE* 1.3 71.2 + - + +
245B PHE* 3.4 12.2 - - - +
246B HIS* 3.3 23.2 + - + +
322B ILE* 4.6 11.0 - - + -
1001D CI2 3.6 33.9 - - + -
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Residues in contact with PHE 243 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210B PHE* 3.6 24.7 - + - -
215B GLN* 3.2 52.5 + - + +
217B PHE* 3.8 25.6 - + - -
225B THR* 4.2 5.2 - - - -
226B ILE* 3.3 58.1 - - + -
239B LEU* 2.9 25.9 + - + +
240B GLU* 3.8 3.8 - - - +
241B LEU 3.1 0.2 - - - -
242B LEU* 1.3 85.8 - - + +
244B HIS* 1.3 68.4 + - - +
246B HIS* 3.4 6.0 + - - +
247B GLY 3.2 14.2 + - - -
1001D CI2 6.1 5.2 - - + -
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Residues in contact with HIS 244 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378A PRO 5.0 2.7 - - - -
379A ASP* 4.0 39.4 + - + +
380A SER 5.6 1.9 + - - -
386A PRO* 5.5 8.3 - - + -
215B GLN* 5.6 0.7 - - - +
240B GLU 3.1 10.8 + - - +
241B LEU* 2.9 15.3 + - + +
243B PHE* 1.3 75.7 - - - +
245B PHE* 1.3 67.7 + - - +
247B GLY* 2.8 14.2 + - - -
248B THR* 2.9 32.0 + - - -
251B LYS* 5.7 6.0 + - - -
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Residues in contact with PHE 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203B HIS* 4.1 7.0 - - + -
204B ILE 5.5 0.2 - - - -
241B LEU* 3.1 7.5 + - + +
242B LEU 3.4 10.8 - - - +
244B HIS* 1.3 79.4 - - - +
246B HIS* 1.3 85.6 + + - +
248B THR* 3.3 7.6 - - - +
249B LEU* 2.8 54.7 + - + +
315B LEU* 3.5 40.2 - - + -
318B GLU* 4.3 10.1 - - + -
319B LEU* 3.3 44.9 - - + -
322B ILE* 3.8 22.7 - - + -
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Residues in contact with HIS 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203B HIS* 3.3 45.0 + - + -
206B LEU* 4.0 2.0 - - - +
207B ASN* 2.9 47.2 + - + +
210B PHE* 3.7 22.7 - + + -
217B PHE* 3.7 25.4 - + - -
242B LEU* 3.3 22.2 + - + +
243B PHE* 3.4 4.6 + - - +
244B HIS 3.2 0.8 - - - -
245B PHE* 1.3 93.9 - + - +
247B GLY* 1.3 71.4 + - - +
250B ARG* 2.8 22.5 + - - +
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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
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210B PHE* 4.2 14.1 - - - -
212B LEU* 4.2 2.9 - - - +
215B GLN* 4.6 5.4 - - - -
243B PHE 3.2 10.0 + - - -
244B HIS* 2.8 11.9 + - - -
246B HIS* 1.3 77.1 - - - +
248B THR* 1.3 60.7 + - - +
250B ARG* 3.8 1.2 - - - +
251B LYS* 2.9 43.8 + - - +
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Residues in contact with THR 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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379A ASP* 4.3 13.3 + - - +
390A GLU* 6.2 0.4 - - - +
244B HIS* 2.9 34.9 + - - -
245B PHE* 3.3 10.9 - - - -
247B GLY* 1.3 75.8 - - - +
249B LEU* 1.3 63.3 + - - +
251B LYS* 3.4 23.9 + - - +
252B LEU* 3.6 16.3 + - + +
311B LYS* 6.4 1.8 - - - -
315B LEU* 3.8 26.9 - - + -
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Residues in contact with LEU 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204B ILE* 4.5 15.3 - - + +
207B ASN* 3.3 38.6 - - + +
245B PHE* 2.8 44.0 + - + +
248B THR* 1.3 73.6 - - - +
250B ARG* 1.3 62.8 + - - +
252B LEU* 3.4 16.6 + - + +
253B GLN 4.2 1.0 + - - -
254B LEU* 4.2 15.4 - - + +
259B TYR* 3.7 22.4 + - + -
262B LEU* 4.7 9.4 - - + -
312B LEU* 5.3 0.2 - - + -
315B LEU* 4.0 25.4 - - + -
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Residues in contact with ARG 250 (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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207B ASN* 3.3 33.5 + - - +
208B THR* 3.2 27.6 + - - +
209B THR 5.0 0.6 - - - -
210B PHE* 3.5 31.4 + - + +
212B LEU* 3.9 30.4 - - + +
246B HIS 2.8 21.5 + - - +
247B GLY 3.8 2.0 - - - +
249B LEU* 1.3 73.1 - - - +
251B LYS* 1.3 62.6 + - - +
253B GLN* 3.1 17.9 + - - +
259B TYR* 3.7 16.8 + - - -
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Residues in contact with LYS 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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212B LEU* 3.8 22.2 - - + -
244B HIS* 5.7 5.3 + - - -
247B GLY* 2.9 41.1 + - - +
248B THR* 3.5 12.9 + - - +
250B ARG* 1.3 75.1 - - - +
252B LEU* 1.3 66.3 + - + +
253B GLN* 3.1 23.4 + - - +
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Residues in contact with LEU 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248B THR* 3.6 16.8 - - + +
249B LEU 3.6 7.0 - - - +
250B ARG 3.2 0.6 - - - -
251B LYS* 1.3 77.5 - - + +
253B GLN* 1.3 74.2 + - - +
254B LEU* 3.2 17.4 - - + +
304B ARG* 3.5 19.3 - - - +
305B ASP* 2.9 30.3 - - - +
308B LEU* 3.7 8.5 - - + +
311B LYS* 4.7 22.4 - - + +
312B LEU* 3.5 31.4 - - + -
315B LEU* 4.2 17.7 - - + -
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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
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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