Contacts of the helix formed by residues 235 - 252 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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233D GLY 3.8 2.0 + - - -
234D PHE* 1.3 72.5 - - - +
236D VAL* 1.3 71.9 + - + +
237D GLU* 3.9 24.1 + - + +
238D PHE* 3.0 17.1 + - - +
239D LEU* 3.2 9.7 + - - +
328D TYR* 4.2 12.1 + - - -
329D GLN* 2.6 34.7 + - - +
332D HIS* 4.2 25.9 + - + -
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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
----------------------------------------------------------
234D PHE 3.5 3.6 + - - -
235D GLN* 1.3 76.0 - - + +
237D GLU* 1.3 80.3 + - + +
239D LEU* 3.2 16.7 + - - +
240D GLU* 2.9 42.8 + - - +
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Residues in contact with GLU 237 (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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235D GLN* 3.1 24.1 + - + +
236D VAL* 1.3 86.2 - - + +
238D PHE* 1.3 64.6 + - - +
240D GLU* 3.7 11.7 - - - +
241D LEU* 3.0 27.9 + - - +
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Residues in contact with PHE 238 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203D HIS* 5.8 2.2 - - - -
234D PHE* 3.9 41.5 - + + -
235D GLN* 3.0 11.0 + - - +
237D GLU* 1.3 78.8 - - - +
239D LEU* 1.3 60.2 + - + +
241D LEU* 3.5 10.9 - - + +
242D LEU* 2.8 60.8 + - + +
322D ILE* 4.5 15.9 - - + -
325D ALA* 4.1 18.6 - - + -
326D TYR* 3.9 38.4 - + + -
329D GLN* 3.9 24.9 - - + +
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Residues in contact with LEU 239 (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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226D ILE* 3.2 42.6 - - + +
229D GLY* 3.8 12.6 - - - -
230D ALA* 3.3 25.4 - - + +
234D PHE* 4.0 27.6 - - + +
235D GLN 3.2 7.4 + - - +
236D VAL* 3.2 13.1 + - - +
238D PHE* 1.3 78.8 - - + +
240D GLU* 1.3 69.4 + - - +
242D LEU* 2.8 27.6 + - + +
243D PHE* 2.8 23.0 + - + -
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Residues in contact with GLU 240 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381C LYS* 6.0 3.1 - - + -
226D ILE* 4.0 11.2 - - + +
236D VAL* 2.9 36.9 - - - +
237D GLU* 3.7 11.4 - - - +
239D LEU* 1.3 74.4 - - - +
241D LEU* 1.3 64.8 + - - +
243D PHE* 3.5 9.2 - - - +
244D HIS* 2.9 22.3 + - - +
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Residues in contact with LEU 241 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379C ASP* 5.3 5.4 - - + +
381C LYS* 4.6 31.8 - - + +
237D GLU 3.0 21.5 + - - +
238D PHE* 3.5 15.3 - - + +
240D GLU* 1.3 80.5 - - - +
242D LEU* 1.3 65.3 + - - +
243D PHE 3.0 0.3 + - - -
244D HIS* 3.1 15.9 + - + +
245D PHE* 3.3 10.6 + - - +
318D GLU* 4.8 13.7 - - - +
321D SER* 5.5 5.4 - - - +
322D ILE* 4.5 20.6 - - + -
325D ALA* 5.4 6.5 - - + -
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Residues in contact with LEU 242 (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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203D HIS* 3.6 26.9 - - + +
217D PHE* 6.3 1.3 - - + -
238D PHE* 2.8 47.3 + - + +
239D LEU* 2.8 20.2 + - + +
241D LEU* 1.3 74.8 - - - +
243D PHE* 1.3 65.0 + - + +
245D PHE* 3.6 2.0 - - - +
246D HIS* 3.5 38.1 + - + -
322D ILE* 4.3 21.3 - - + -
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Residues in contact with PHE 243 (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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210D PHE* 3.7 21.9 - + - -
215D GLN* 2.9 45.5 + - + -
217D PHE* 4.1 22.0 - + - -
225D THR* 4.2 3.6 - - - -
226D ILE* 3.6 50.7 - - + -
239D LEU* 2.8 26.0 + - + +
240D GLU* 3.5 11.4 - - - +
241D LEU 3.1 0.2 - - - -
242D LEU* 1.3 82.1 - - + +
244D HIS* 1.3 66.4 + - - +
245D PHE 3.1 1.6 - - - -
246D HIS* 3.2 7.0 + - - +
247D GLY* 2.9 21.0 + - - -
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Residues in contact with HIS 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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378C PRO 4.5 4.5 - - - -
379C ASP* 3.7 35.0 + - - +
381C LYS* 3.2 33.0 + - + +
386C PRO* 6.5 0.2 - - + -
240D GLU 2.9 11.0 + - - +
241D LEU* 3.5 14.1 - - + +
243D PHE* 1.3 74.8 - - - +
245D PHE* 1.3 65.6 + - - +
247D GLY* 3.2 2.5 + - - -
248D THR* 2.8 42.6 + - - -
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Residues in contact with PHE 245 (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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379C ASP* 6.1 0.2 - - - -
203D HIS* 4.2 7.9 - - + -
241D LEU 3.3 6.1 + - - +
242D LEU 3.6 9.6 - - - +
243D PHE 3.1 0.6 - - - -
244D HIS* 1.3 78.3 - - - +
246D HIS* 1.3 74.6 + + - +
248D THR* 2.9 11.7 + - - -
249D LEU* 2.8 55.4 + - + +
315D LEU* 3.5 46.0 - - + -
318D GLU* 4.0 17.5 - - + -
319D LEU* 3.4 38.8 - - + -
322D ILE* 3.8 23.8 - - + -
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Residues in contact with HIS 246 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203D HIS* 2.9 58.0 + - + +
206D LEU* 4.2 3.2 - - + +
207D ASN* 2.6 53.3 + - - +
210D PHE* 4.1 19.1 - - + -
217D PHE* 3.7 25.8 - + + -
242D LEU* 3.5 31.1 + - + +
243D PHE* 3.2 8.4 + - - +
245D PHE* 1.3 88.2 - + - +
247D GLY* 1.3 62.4 + - - +
250D ARG* 3.1 10.2 + - - +
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Residues in contact with GLY 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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210D PHE* 4.0 7.1 - - - -
212D LEU* 3.7 18.5 - - - +
215D GLN* 4.8 5.2 - - - -
243D PHE 2.9 14.3 + - - -
244D HIS* 3.6 3.6 - - - -
245D PHE 3.1 0.2 - - - -
246D HIS* 1.3 75.8 - - - +
248D THR* 1.3 62.2 + - - +
251D LYS* 3.1 36.3 + - - +
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Residues in contact with THR 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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379C ASP* 4.8 8.9 + - - +
244D HIS* 2.8 37.9 + - - -
245D PHE* 2.9 11.5 + - - -
247D GLY* 1.3 77.6 - - - +
249D LEU* 1.3 62.6 + - - +
251D LYS* 3.4 19.8 + - - +
252D LEU* 3.8 15.9 - - + +
315D LEU* 3.6 27.8 - - + -
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Residues in contact with LEU 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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203D HIS 4.0 5.8 - - - +
204D ILE* 4.1 14.8 - - + +
207D ASN* 3.2 36.8 - - + +
245D PHE* 2.8 40.1 + - + +
248D THR* 1.3 74.3 - - - +
250D ARG* 1.3 62.0 + - - +
252D LEU* 3.7 8.4 + - - +
254D LEU* 3.9 22.2 - - + +
259D TYR* 3.6 20.8 + - + -
262D LEU* 4.5 13.0 - - + -
312D LEU* 5.0 0.7 - - + -
315D LEU* 3.6 24.5 - - + -
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Residues in contact with ARG 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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207D ASN* 3.0 28.6 + - - +
208D THR* 3.0 39.2 + - - +
209D THR 4.7 1.2 + - - -
210D PHE* 3.2 24.6 + - + +
212D LEU* 4.0 24.6 - - + +
246D HIS 3.1 20.5 + - - +
247D GLY 4.0 2.7 - - - +
249D LEU* 1.3 76.9 - - - +
251D LYS* 1.3 56.8 + - - +
253D GLN* 3.0 23.6 + - - +
254D LEU 5.5 1.2 + - - -
259D TYR* 3.6 16.0 + - - -
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Residues in contact with LYS 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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212D LEU* 3.6 26.9 - - + -
247D GLY* 3.1 28.1 + - - +
248D THR* 3.5 10.1 - - - +
249D LEU 3.4 0.2 - - - -
250D ARG* 1.3 72.3 - - - +
252D LEU* 1.3 64.7 + - + +
253D GLN* 3.1 24.9 + - - +
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Residues in contact with LEU 252 (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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248D THR* 3.8 20.0 - - + +
249D LEU 4.1 2.7 - - - +
250D ARG 3.1 1.6 + - - -
251D LYS* 1.3 79.6 - - + +
253D GLN* 1.3 74.5 + - - +
254D LEU* 3.5 16.7 - - + +
304D ARG* 3.4 23.5 + - + +
305D ASP* 3.9 21.3 - - - +
308D LEU* 3.5 26.8 - - + +
311D LYS* 4.7 17.9 - - + -
312D LEU* 4.2 24.0 - - + -
315D LEU* 5.0 7.9 - - + -
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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