Contacts of the helix formed by residues 249 - 268 (chain F) in PDB entry 4XLN
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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109F LEU 4.6 11.1 + - - -
110F THR* 5.4 1.9 - - - +
111F LEU* 4.0 24.3 - - + +
114F GLU* 3.2 34.3 - - - +
242F PHE* 4.7 0.5 - - - -
247F ARG 4.0 0.6 + - - -
248F PHE* 1.3 72.3 - - - +
250F PHE* 1.3 63.8 + - - +
251F SER* 3.0 12.3 + - - +
252F THR* 3.1 19.6 + - - -
253F TYR 4.2 1.2 + - - -
28O A 2.9 30.6 + - - +
29O C 3.2 24.5 + - - +
30O T 3.3 32.6 + - - +
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Residues in contact with PHE 250 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114F GLU* 3.2 28.6 + - + +
202F LEU* 3.6 18.6 - - + -
206F ASN* 3.5 27.4 - - + -
235F LEU* 3.7 14.4 - - + -
238F ALA 3.2 26.2 - - - -
239F VAL* 3.5 24.2 - - + -
242F PHE* 3.4 44.4 - + + -
248F PHE 3.3 3.0 + - - -
249F LYS* 1.3 70.9 - - - +
251F SER* 1.3 55.3 + - - +
252F THR 3.0 1.3 + - - -
253F TYR 3.4 0.8 + - - +
254F ALA* 2.9 57.0 + - + +
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Residues in contact with SER 251 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209F LEU* 3.8 16.8 - - - -
249F LYS* 3.3 6.4 - - - +
250F PHE* 1.3 77.7 - - - +
252F THR* 1.3 51.7 + - - +
254F ALA* 4.7 0.2 - - - -
255F THR* 2.4 38.3 + - - +
28O A 3.4 9.2 - - - +
29O C 2.4 42.3 + - - -
30O T 3.8 28.0 + - - -
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Residues in contact with THR 252 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248F PHE* 5.7 0.7 - - - -
249F LYS 3.4 11.6 + - - -
250F PHE 3.0 0.6 - - - -
251F SER* 1.3 73.8 - - - +
253F TYR* 1.3 66.4 + - - +
254F ALA 3.1 1.1 - - - -
255F THR* 2.5 19.8 + - - -
256F TRP* 3.0 18.4 + - + +
26O A 3.8 33.9 - - - +
27O T 4.7 2.9 - - + +
28O A 3.2 44.8 + - + +
29O C 3.3 19.2 + - - +
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Residues in contact with TYR 253 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238F ALA 3.3 27.4 - - - -
241F LYS* 3.2 50.6 + - + +
242F PHE* 3.6 31.4 - + + -
249F LYS 4.2 0.6 + - - +
250F PHE* 3.4 2.3 + + + +
252F THR* 1.3 80.1 - - - +
254F ALA* 1.3 59.4 + - - +
256F TRP* 3.8 5.9 + - + +
257F TRP* 3.1 45.7 + + - -
25O T 2.9 30.8 + - + -
26O A 3.4 54.4 + + - +
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Residues in contact with ALA 254 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206F ASN* 5.6 0.7 - - + -
209F LEU* 4.7 9.4 - - + -
235F LEU* 3.7 13.7 - - + -
238F ALA* 3.6 10.5 - - - +
250F PHE* 2.9 46.9 + - + +
251F SER 4.6 2.0 - - - +
253F TYR* 1.3 75.5 - - - +
255F THR* 1.3 60.3 + - - +
257F TRP* 2.8 22.2 + - - +
258F ILE* 2.9 17.8 + - + +
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Residues in contact with THR 255 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209F LEU* 3.6 18.4 - - + -
213F ILE* 3.5 24.8 - - + +
251F SER 2.4 32.9 + - - +
252F THR 2.5 15.1 + - - -
254F ALA* 1.3 76.5 - - - +
256F TRP* 1.3 55.8 + - - +
258F ILE* 3.8 7.0 - - - +
259F ARG* 2.9 41.3 + - - +
29O C 2.9 34.8 + - + +
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Residues in contact with TRP 256 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252F THR* 3.0 26.6 + - + +
253F TYR* 4.1 7.2 - - + +
254F ALA 3.1 0.2 - - - -
255F THR* 1.3 77.1 - - - +
257F TRP* 1.3 61.4 + - + +
259F ARG* 3.9 31.7 + - + +
260F GLN 3.3 8.7 + - - -
25O T 3.0 73.8 - + + +
26O A 3.6 34.3 - - - -
27O T 4.8 12.6 + - + +
28O A 5.2 8.5 - - - -
29O C 4.2 12.9 - - - +
24P A 4.6 10.3 - + - -
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Residues in contact with TRP 257 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234F GLY* 3.5 17.8 - - - +
237F ARG* 4.1 33.9 - - + -
238F ALA* 3.5 15.5 - - + -
241F LYS* 3.8 19.1 - - + -
253F TYR* 3.1 46.2 - + - -
254F ALA 2.8 7.8 + - - +
256F TRP* 1.3 77.3 - - + +
258F ILE* 1.3 62.7 + - - +
260F GLN* 3.0 34.9 - - + +
261F ALA* 2.9 29.1 + - - +
23O G 4.6 3.4 - - + -
24O C 3.4 53.2 - + + -
25O T 3.7 17.6 + - + +
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Residues in contact with ILE 258 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210F VAL* 3.6 29.6 - - + -
213F ILE* 3.5 42.8 - - + -
231F GLY* 3.2 30.1 - - - +
234F GLY 3.8 0.2 - - - -
235F LEU* 3.3 33.2 - - + +
254F ALA* 2.9 18.5 + - + +
255F THR 3.8 0.7 - - - +
257F TRP* 1.3 74.9 - - - +
259F ARG* 1.3 66.4 + - - +
260F GLN 3.0 2.0 + - - -
261F ALA* 3.1 1.3 + - - -
262F ILE* 2.9 35.2 + - + +
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Residues in contact with ARG 259 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361C MET* 6.1 4.4 - - - +
213F ILE* 4.5 14.4 - - + +
216F LYS* 5.2 16.7 - - - +
217F TYR* 3.7 36.3 + - + +
255F THR* 2.9 26.4 + - - +
256F TRP* 4.0 32.0 - - + +
258F ILE* 1.3 76.9 - - - +
260F GLN* 1.3 59.0 + - - +
263F ASN* 3.5 21.3 + - - +
28O A 5.7 1.2 - - - +
29O C 3.5 29.7 + - - -
24P A 3.5 15.0 + - - +
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Residues in contact with GLN 260 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234F GLY* 4.9 1.4 - - - -
256F TRP 3.3 3.1 + - - +
257F TRP* 3.0 47.9 - - + +
258F ILE 3.0 1.0 - - - -
259F ARG* 1.3 75.9 - - - +
261F ALA* 1.3 85.9 + - - +
262F ILE 3.1 1.8 - - - -
263F ASN* 2.9 6.7 + - - +
264F ARG* 2.8 37.3 + - - +
23O G 4.8 7.1 + - - -
24O C 3.3 26.1 - - - +
25O T 3.0 29.4 - - + +
24P A 3.2 7.0 - - - +
25P G 5.0 0.9 - - - +
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Residues in contact with ALA 261 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230F GLU* 3.4 28.3 - - - +
231F GLY* 4.3 3.4 - - - +
233F GLN* 5.6 0.7 - - + -
234F GLY* 3.6 18.2 - - - +
257F TRP 2.9 22.2 + - - +
258F ILE 3.1 3.1 + - - +
260F GLN* 1.3 84.5 - - - +
262F ILE* 1.3 57.9 + - - +
264F ARG* 3.7 5.2 - - - +
265F ALA* 2.9 27.4 + - - +
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Residues in contact with ILE 262 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213F ILE* 4.2 3.4 - - + -
214F ALA* 3.8 29.8 - - + -
217F TYR* 3.6 36.3 - - + -
220F ARG* 5.1 1.1 - - - +
227F LEU* 3.8 33.0 - - + +
230F GLU 5.2 0.4 - - - -
231F GLY* 4.0 17.3 - - - +
258F ILE* 2.9 33.2 + - + +
261F ALA* 1.3 73.2 - - - +
263F ASN* 1.3 56.1 + - - +
264F ARG 3.1 4.7 - - - -
265F ALA* 2.9 8.7 + - + +
266F ILE* 2.9 32.8 + - + +
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Residues in contact with ASN 263 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217F TYR* 4.0 4.7 + - - +
220F ARG* 2.9 28.9 + - - +
259F ARG 3.5 17.6 + - - +
260F GLN* 2.9 4.7 + - - +
262F ILE* 1.3 79.2 - - - +
264F ARG* 1.3 58.2 + - - +
266F ILE* 3.1 27.7 - - - +
267F ALA* 3.7 8.3 + - - +
284F ASN* 5.5 6.1 - - - +
24P A 3.2 46.6 + - - +
25P G 4.8 7.3 + - - +
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Residues in contact with ARG 264 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230F GLU* 5.8 2.0 - - - +
260F GLN* 2.8 24.6 + - - +
261F ALA* 3.7 9.4 - - - +
263F ASN* 1.3 74.7 - - - +
265F ALA* 1.3 60.6 + - - +
266F ILE 3.1 2.0 - - - -
267F ALA* 2.9 19.2 + - - +
268F ASP* 2.9 33.4 + - - +
277F VAL* 4.1 17.7 - - - +
22O T 3.3 45.8 + - - +
23O G 2.9 41.8 + - - -
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Residues in contact with ALA 265 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222F LEU* 4.8 9.6 - - + +
227F LEU* 5.7 4.7 - - + +
230F GLU* 3.6 35.4 - - + +
261F ALA 2.9 19.7 + - - +
262F ILE* 2.9 10.1 + - + +
264F ARG* 1.3 76.0 - - - +
266F ILE* 1.3 63.5 + - + +
268F ASP* 3.6 5.8 + - - +
269F GLN* 3.2 27.9 + - - +
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Residues in contact with ILE 266 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220F ARG* 3.4 71.1 - - + +
221F GLY 5.2 2.7 - - - +
222F LEU* 6.0 2.2 - - + -
227F LEU* 4.7 5.6 - - + -
262F ILE* 2.9 18.8 + - + +
263F ASN* 3.1 33.0 - - - +
265F ALA* 1.3 76.8 - - + +
267F ALA* 1.3 63.6 + - - +
268F ASP 3.1 0.2 - - - -
269F GLN* 5.0 0.4 - - - -
270F ALA* 3.0 38.5 + - + +
280F VAL* 5.4 9.9 - - + -
284F ASN* 6.2 1.1 - - - +
24P A 4.6 1.6 - - - +
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Residues in contact with ALA 267 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263F ASN 3.9 10.5 - - - +
264F ARG* 2.9 11.7 + - - +
266F ILE* 1.3 82.7 - - + +
268F ASP* 1.3 60.4 + - - +
269F GLN 3.7 1.4 + - - -
270F ALA* 5.0 3.8 - - - +
274F ARG* 5.4 1.6 + - - -
275F ILE 3.2 23.6 + - - +
277F VAL* 4.1 26.0 + - + -
280F VAL* 4.2 26.1 - - + +
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Residues in contact with ASP 268 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29D PRO* 5.4 5.5 - - - +
545D ARG* 4.9 2.1 + - - -
549D ASN* 5.0 5.9 + - - +
264F ARG* 2.9 37.4 + - + +
265F ALA* 3.6 5.8 + - - +
266F ILE 3.1 0.2 - - - -
267F ALA* 1.3 80.2 - - - +
269F GLN* 1.3 60.3 + - - +
274F ARG* 3.3 27.5 + - - +
277F VAL* 5.4 2.3 - - - +
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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