Contacts of the helix formed by residues 249 - 269 (chain L) in PDB entry 4XLR
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 LYS 249 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109L LEU* 5.5 5.2 - - - -
110L THR 5.8 0.2 - - - -
111L LEU* 3.6 32.7 - - + +
114L GLU* 3.1 36.6 - - - +
242L PHE* 4.8 0.7 - - - -
247L ARG 4.2 0.2 + - - -
248L PHE* 1.3 72.6 - - - +
250L PHE* 1.3 66.8 + - - +
251L SER* 3.0 16.1 + - - +
252L THR* 3.1 18.7 + - - -
253L TYR 4.4 0.7 + - - -
28R A 3.0 30.6 + - - +
29R C 2.7 33.2 + - - +
30R T 3.3 22.1 - - - +
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Residues in contact with PHE 250 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114L GLU* 3.5 27.1 + - + +
202L LEU* 3.5 15.9 - - + -
206L ASN* 3.1 48.5 - - + -
235L LEU* 4.1 5.2 - - + -
238L ALA 3.4 23.1 - - - -
239L VAL* 3.8 26.7 - - + -
242L PHE* 3.6 42.6 - + + -
248L PHE 3.2 3.6 + - - -
249L LYS* 1.3 71.4 - - - +
251L SER* 1.3 62.5 + - - +
252L THR 3.0 0.7 + - - -
253L TYR* 3.5 1.8 + + - -
254L ALA* 3.0 41.5 + - + +
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Residues in contact with SER 251 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114L GLU* 4.5 0.6 + - - -
206L ASN* 4.4 3.6 + - - -
209L LEU* 3.7 23.7 - - - +
249L LYS* 3.3 14.8 - - - +
250L PHE* 1.3 80.0 - - - +
252L THR* 1.3 50.1 + - - +
254L ALA* 4.3 0.2 - - - -
255L THR* 2.4 42.5 + - - +
28R A 3.6 6.8 - - - +
29R C 3.1 36.6 + - - -
30R T 4.1 14.1 - - - -
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Residues in contact with THR 252 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248L PHE* 5.5 1.6 - - - -
249L LYS 3.1 8.4 + - - -
250L PHE 3.0 0.2 + - - -
251L SER* 1.3 73.0 + - - +
253L TYR* 1.3 69.1 + - - +
255L THR* 2.3 26.0 + - - -
256L TRP* 2.9 16.4 - - - +
26R A 3.6 38.6 - - - +
27R T 4.9 1.1 - - + -
28R A 3.3 47.0 + - + +
29R C 3.3 19.3 - - - +
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Residues in contact with TYR 253 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238L ALA* 3.5 30.7 - - + -
241L LYS* 3.0 49.2 + - + +
242L PHE* 3.6 29.6 - - + -
249L LYS 4.4 0.6 + - - +
250L PHE* 3.5 6.5 + + + +
252L THR* 1.3 81.5 - - - +
254L ALA* 1.3 64.1 + - - +
256L TRP* 3.2 5.7 + - - +
257L TRP* 3.0 38.9 + + - -
25R T 3.4 19.8 + - + -
26R A 3.4 63.0 + + - +
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Residues in contact with ALA 254 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209L LEU* 4.3 4.0 - - + -
235L LEU* 3.5 28.4 - - + -
238L ALA* 4.0 12.6 - - - -
250L PHE* 3.0 32.9 + - + +
251L SER* 3.9 4.9 - - - +
253L TYR* 1.3 80.6 - - - +
255L THR* 1.3 56.9 + - - +
257L TRP* 3.2 5.0 + - - +
258L ILE* 2.9 33.5 + - - +
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Residues in contact with THR 255 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209L LEU* 3.9 14.4 - - + -
213L ILE* 3.5 26.1 - - + +
251L SER 2.4 24.0 + - - +
252L THR 2.3 26.5 + - - -
254L ALA* 1.3 68.8 - - - +
256L TRP* 1.3 65.5 + - - +
258L ILE* 2.8 20.0 + - - +
259L ARG* 3.0 19.2 + - - +
29R C 3.0 39.8 + - + +
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Residues in contact with TRP 256 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252L THR* 2.9 40.9 + - + +
253L TYR* 3.7 7.2 - - - +
255L THR* 1.3 77.3 - - - +
257L TRP* 1.3 64.7 + - + +
259L ARG* 3.2 37.4 + - - +
260L GLN 3.0 17.2 + - - -
86N TRP* 5.1 5.6 - + - -
87N ALA* 4.6 12.3 - - + -
91N ARG* 3.7 26.2 - - - +
25R T 3.2 71.9 - + + +
26R A 4.4 9.4 - - - -
27R T 5.6 0.4 - - + -
28R A 4.9 10.6 + - - +
29R C 2.9 25.4 - - - +
24S A 5.8 1.8 - + - -
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Residues in contact with TRP 257 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234L GLY* 3.8 13.5 - - - +
237L ARG* 3.5 39.5 - - + -
238L ALA* 3.5 26.9 - - + -
241L LYS* 3.8 17.3 - - + -
253L TYR* 3.0 36.0 + + - -
254L ALA 3.5 8.3 - - - +
256L TRP* 1.3 78.4 - - + +
258L ILE* 1.3 58.2 + - - +
260L GLN* 3.1 38.4 - - + +
261L ALA 2.9 23.7 + - - -
23R G 4.7 2.0 - - + -
24R C 3.1 48.5 - + + -
25R T 3.6 31.3 + + + +
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Residues in contact with ILE 258 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210L VAL* 3.5 27.4 - - + +
213L ILE* 3.6 41.7 - - + -
231L GLY 3.2 21.5 - - - +
235L LEU* 3.2 35.9 - - + +
254L ALA 2.9 18.8 + - - +
255L THR 2.8 8.1 + - - +
257L TRP* 1.3 72.3 - - - +
259L ARG* 1.3 64.2 + - - +
260L GLN 2.9 4.6 + - - -
261L ALA* 3.2 3.6 + - - +
262L ILE* 2.9 34.9 + - + +
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Residues in contact with ARG 259 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361I MET* 6.3 0.8 - - - +
213L ILE* 4.4 13.7 - - + -
217L TYR* 3.4 35.0 + - + +
255L THR* 3.0 14.5 + - - +
256L TRP* 3.8 49.8 - - - +
258L ILE* 1.3 77.3 - - - +
260L GLN* 1.3 57.6 + - - +
262L ILE* 3.9 6.7 - - - -
263L ASN* 2.9 38.7 + - - +
28R A 6.0 0.8 - - - +
29R C 5.9 2.7 + - - +
24S A 4.1 10.4 + - + +
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Residues in contact with GLN 260 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234L GLY* 4.6 1.7 - - - -
256L TRP 3.0 7.2 + - - +
257L TRP* 3.1 36.6 - - + +
258L ILE 2.9 0.4 - - - -
259L ARG* 1.3 78.1 - - - +
261L ALA* 1.3 80.7 + - - +
263L ASN* 3.8 1.0 - - - +
264L ARG* 2.9 45.3 + - - +
23R G 5.4 2.2 + - - -
24R C 3.2 39.8 + - + +
25R T 3.1 17.3 - - + +
24S A 3.6 9.6 + - - +
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Residues in contact with ALA 261 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230L GLU* 3.5 23.5 - - - +
231L GLY* 4.0 3.4 - - - +
233L GLN* 5.6 0.4 - - + -
234L GLY* 3.4 31.6 - - - +
257L TRP 2.9 6.3 + - - -
258L ILE 3.8 4.7 - - - +
260L GLN* 1.3 86.1 + - - +
262L ILE* 1.3 56.3 + - - +
264L ARG* 3.9 1.5 - - - +
265L ALA* 2.9 32.5 + - - +
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Residues in contact with ILE 262 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213L ILE* 4.8 0.2 - - + -
214L ALA* 3.6 29.2 - - + +
217L TYR* 3.5 42.8 - - + -
220L ARG* 5.5 3.6 - - + +
227L LEU* 3.8 21.5 - - + -
230L GLU* 5.5 0.4 - - - -
231L GLY* 3.6 18.4 - - - +
258L ILE* 2.9 33.7 + - + +
259L ARG 3.9 3.4 - - - +
261L ALA* 1.3 75.4 - - - +
263L ASN* 1.3 61.8 + - - +
265L ALA* 3.1 7.2 + - - +
266L ILE* 3.0 35.1 + - + +
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Residues in contact with ASN 263 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217L TYR* 4.0 20.0 + - - -
220L ARG* 3.3 26.2 - - - +
259L ARG* 2.9 27.5 + - - +
260L GLN 4.0 1.1 - - - +
262L ILE* 1.3 77.9 - - - +
264L ARG* 1.3 58.2 + - - +
266L ILE* 3.1 13.5 - - - +
267L ALA* 3.0 29.1 + - - +
284L ASN* 6.2 0.2 - - - +
24S A 3.0 45.1 + - + +
25S G 5.7 2.0 - - - +
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Residues in contact with ARG 264 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260L GLN* 2.9 34.5 + - - +
261L ALA* 3.9 2.9 - - - +
263L ASN* 1.3 77.3 - - - +
265L ALA* 1.3 58.3 + - - +
267L ALA* 3.3 2.2 + - - +
268L ASP* 2.9 35.5 + - - +
277L VAL* 3.6 31.1 - - - +
21R G 5.8 0.2 - - - +
22R T 3.3 47.5 + - - +
23R G 2.9 44.6 + - - -
24R C 4.0 6.6 - - - +
25S G 4.1 5.1 + - - -
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Residues in contact with ALA 265 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222L LEU* 5.7 2.2 - - + -
230L GLU* 3.7 38.8 - - + +
261L ALA 2.9 19.9 + - - +
262L ILE* 3.5 4.9 - - - +
264L ARG* 1.3 77.2 - - - +
266L ILE* 1.3 59.4 + - + +
268L ASP* 3.1 6.7 + - - +
269L GLN* 2.9 34.1 + - - +
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Residues in contact with ILE 266 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220L ARG* 3.5 72.5 - - + +
222L LEU* 3.9 16.2 - - + -
227L LEU* 5.1 3.6 - - + -
262L ILE* 3.0 23.1 + - + +
263L ASN* 3.1 24.2 - - - +
265L ALA* 1.3 74.4 - - + +
267L ALA* 1.3 77.8 + - + +
269L GLN* 4.4 1.8 - - - +
270L ALA* 3.0 35.7 + - + +
280L VAL* 5.0 3.3 - - + +
284L ASN* 5.0 8.7 - - - +
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Residues in contact with ALA 267 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263L ASN 3.0 20.1 + - - +
264L ARG* 3.5 6.3 - - - +
266L ILE* 1.3 78.0 - - + +
268L ASP* 1.3 61.1 + - - +
269L GLN 3.7 0.3 + - - +
270L ALA* 4.8 0.9 - - - +
271L ARG* 4.6 3.3 + - - -
275L ILE* 3.3 20.1 + - - +
277L VAL* 4.2 22.9 - - + +
280L VAL* 3.4 38.1 - - + +
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Residues in contact with ASP 268 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29J PRO 5.6 1.6 - - - +
30J GLU* 5.3 2.3 - - - +
549J ASN* 5.7 0.5 - - - +
264L ARG* 2.9 23.8 + - + +
265L ALA* 3.1 6.0 + - - +
267L ALA* 1.3 78.3 - - - +
269L GLN* 1.3 57.5 + - - +
274L ARG* 4.1 35.2 + - - +
275L ILE 4.7 4.0 - - - -
277L VAL* 3.6 25.8 - - - +
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Residues in contact with GLN 269 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29J PRO 6.0 0.9 - - - +
545J ARG* 3.6 20.6 + - - +
546J ARG* 3.4 16.8 - - - +
549J ASN* 3.0 43.5 + - - +
553J ARG* 6.0 1.2 - - - +
222L LEU* 3.3 36.2 - - + +
226L ASP* 4.1 3.0 + - - +
230L GLU* 5.9 4.2 - - - +
265L ALA* 2.9 17.9 + - - +
266L ILE* 3.4 1.8 + - - -
267L ALA 4.9 0.4 - - - +
268L ASP* 1.3 81.2 - - - +
270L ALA* 1.3 73.8 + - - +
271L ARG 2.8 14.4 + - - +
273L ILE 4.5 2.9 - - - +
274L ARG* 5.4 2.6 - - - -
275L ILE 5.7 0.7 + - - -
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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
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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