Contacts of the helix formed by residues 279 - 301 (chain C) in PDB entry 4UQJ
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 279 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C GLN* 3.4 21.8 + - - +
25C GLU* 5.0 1.8 - - - +
229C ASP* 3.2 16.6 - - + +
278C ILE* 1.3 78.1 - - - +
280C TYR* 1.3 61.6 + - + +
281C THR* 3.1 16.6 - - + +
282C SER* 2.9 5.7 + - - +
283C ALA* 2.9 24.4 + - - +
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Residues in contact with TYR 280 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99C PRO 5.4 1.8 - - - -
114C ARG* 5.4 4.5 - - + -
141C ARG* 4.9 13.2 - - - -
197C GLU* 6.1 1.2 - - - -
198C ARG* 6.0 6.3 - - + -
224C ASN* 4.8 13.6 - - + +
225C LEU* 3.7 39.9 - - + +
226C GLY* 3.6 18.4 - - - -
229C ASP* 2.9 22.1 + - + +
246C GLN* 5.9 0.2 - - - +
247C ILE* 3.5 24.4 - - + +
248C VAL* 4.2 14.1 - - + -
278C ILE 3.5 1.2 + - - -
279C LYS* 1.3 72.7 - - + +
281C THR* 1.3 80.3 + - + +
283C ALA* 3.7 1.2 - - - +
284C LEU* 3.0 45.9 + - + +
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Residues in contact with THR 281 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C GLU* 2.8 31.3 + - - +
76C PHE* 4.9 7.6 - - + -
99C PRO* 3.9 11.3 - - + +
100C SER* 6.5 0.2 - - - -
279C LYS* 3.8 10.7 - - + +
280C TYR* 1.3 111.4 - - + +
282C SER* 1.3 58.8 + - - +
284C LEU* 3.5 8.1 + - - +
285C THR* 3.0 25.2 + - - -
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Residues in contact with SER 282 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C GLN* 3.3 40.3 + - - +
25C GLU* 3.3 22.9 + - - +
28C ALA* 3.4 7.8 - - - +
278C ILE* 3.6 19.1 - - - -
279C LYS* 2.9 9.6 + - - +
281C THR* 1.3 78.3 + - - +
283C ALA* 1.3 65.3 + - - +
285C THR* 3.1 17.9 + - - -
286C TYR* 3.1 9.9 + - - +
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Residues in contact with ALA 283 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248C VAL* 3.6 30.5 - - + -
278C ILE* 3.6 14.8 - - + +
279C LYS 2.9 11.9 + - - +
280C TYR 3.7 3.6 - - - +
282C SER* 1.3 76.1 - - - +
284C LEU* 1.3 59.1 + - + +
286C TYR* 3.4 4.4 + - - +
287C ASP* 3.1 32.3 + - - +
341C LEU* 4.0 23.0 - - + +
342C SER* 5.5 1.1 - - - +
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Residues in contact with LEU 284 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99C PRO* 3.7 27.6 - - + +
113C MET* 3.3 29.3 - - + +
114C ARG* 3.6 31.4 - - + +
115C PRO* 4.8 4.3 - - + -
225C LEU* 5.3 0.7 - - + -
247C ILE* 5.4 2.9 - - + -
280C TYR* 3.0 39.5 + - + +
281C THR* 3.8 1.1 - - - +
282C SER 3.2 0.2 - - - -
283C ALA* 1.3 75.0 - - + +
285C THR* 1.3 55.8 + - - +
287C ASP* 3.2 5.3 + - + +
288C ALA* 2.8 34.4 + - - +
342C SER* 3.5 33.0 - - - +
353C ARG* 3.9 1.8 - - - +
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Residues in contact with THR 285 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C PHE* 4.4 0.7 - - + -
25C GLU* 3.3 27.7 + - - +
29C PHE* 3.6 20.4 - - + -
74C PHE* 3.4 28.3 - - + -
76C PHE* 3.7 9.2 - - - -
99C PRO* 3.7 11.4 - - - +
281C THR 3.0 14.1 + - - -
282C SER* 3.1 11.0 + - - -
284C LEU* 1.3 79.3 - - - +
286C TYR* 1.3 63.2 + - - +
288C ALA* 3.1 15.6 + - - +
289C VAL* 3.3 10.6 + - - +
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Residues in contact with TYR 286 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C ALA* 3.9 19.4 + - + +
31C VAL* 4.2 7.4 - - + -
32C GLY* 3.7 26.2 - - - -
35C GLN* 3.3 25.8 - - + +
36C PHE* 3.4 32.3 - + - -
254C LEU* 5.8 4.6 - - + +
258C PHE* 3.4 34.6 - + + -
282C SER 3.1 8.2 + - - +
283C ALA 3.6 7.0 - - - +
284C LEU 3.3 0.2 - - - -
285C THR* 1.3 79.2 - - - +
287C ASP* 1.3 77.5 + - - +
288C ALA 3.3 0.7 + - - -
289C VAL* 3.3 15.4 + - - +
290C GLN* 3.5 9.0 + - - -
340C GLY* 5.8 0.4 - - - -
341C LEU* 3.7 24.7 - - + -
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Residues in contact with ASP 287 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113C MET* 4.3 3.8 - - - -
283C ALA 3.1 16.9 + - - +
284C LEU* 3.2 7.8 + - + +
286C TYR* 1.3 86.9 - - - +
288C ALA* 1.3 64.5 + - - +
290C GLN* 3.4 9.6 + - - +
291C VAL* 3.1 28.6 + - - +
340C GLY* 3.3 12.9 - - - -
341C LEU* 2.8 20.3 + - - -
342C SER* 2.9 38.6 + - - +
345C ILE* 3.7 15.3 - - + +
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Residues in contact with ALA 288 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74C PHE* 3.4 33.0 - - + -
97C ILE* 3.9 5.6 - - + +
113C MET* 3.7 19.3 - - + -
284C LEU 2.8 13.3 + - - +
285C THR 3.1 11.9 + - - +
287C ASP* 1.3 74.5 - - - +
289C VAL* 1.3 66.2 + - + +
291C VAL* 3.1 4.8 + - - +
292C MET* 3.0 30.0 + - - +
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Residues in contact with VAL 289 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C PHE* 3.8 43.1 - - + +
32C GLY* 3.4 34.1 - - - +
33C MET* 3.8 15.7 - - - +
36C PHE* 4.1 4.0 - - + -
43C LEU* 5.1 4.5 - - + -
285C THR 3.3 14.1 + - - +
286C TYR 3.6 7.9 - - - +
287C ASP 3.3 0.2 - - - -
288C ALA* 1.3 76.7 - - - +
290C GLN* 1.3 57.0 + - - +
292C MET* 3.3 10.8 + - - +
293C THR* 3.0 38.7 + - - +
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Residues in contact with GLN 290 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C PHE* 3.4 50.9 - - + -
286C TYR* 3.5 4.9 + - - +
287C ASP* 3.4 14.4 + - - +
288C ALA 3.2 0.4 - - - -
289C VAL* 1.3 78.8 - - - +
291C VAL* 1.3 57.7 + - - +
293C THR* 3.4 2.8 + - - -
294C GLU* 3.0 28.2 + - + +
338C VAL* 3.4 35.7 - - + +
339C GLU 3.2 27.3 + - - +
340C GLY* 4.0 9.5 - - - -
345C ILE* 5.3 0.3 - - - +
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Residues in contact with VAL 291 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97C ILE* 5.8 1.8 - - + -
111C ILE* 5.0 3.4 - - + -
113C MET* 4.3 14.4 - - + -
287C ASP 3.1 17.2 + - - +
288C ALA* 3.1 9.2 + - - +
290C GLN* 1.3 77.9 - - - +
292C MET* 1.3 57.7 + - + +
294C GLU 3.5 0.3 + - - -
295C ALA* 3.0 27.7 + - - +
333C LEU* 4.2 19.5 - - + +
336C VAL* 3.5 33.8 - - + +
338C VAL* 4.7 3.4 - - + -
345C ILE* 4.2 28.5 - - + -
347C PHE* 4.2 9.9 - - + -
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Residues in contact with MET 292 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C ILE* 3.7 43.3 - - + -
29C PHE* 5.4 4.0 - - - -
43C LEU* 4.5 12.4 - - + +
72C ALA* 4.1 20.2 - - + -
74C PHE* 4.1 25.6 - - + +
97C ILE* 4.3 26.9 - - + -
288C ALA 3.0 20.6 + - - +
289C VAL* 3.3 8.3 + - - +
291C VAL* 1.3 76.9 - - + +
293C THR* 1.3 61.5 + - - +
295C ALA* 3.7 1.2 - - - +
296C PHE* 3.1 25.5 + - - +
333C LEU* 4.0 11.0 - - + -
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Residues in contact with THR 293 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C PHE* 3.7 37.9 + - + +
38C THR* 5.4 4.0 - - + -
41C PHE* 3.5 25.1 - - + -
43C LEU* 4.2 15.0 - - + +
289C VAL* 3.0 19.1 + - - +
290C GLN* 3.7 5.6 - - - -
292C MET* 1.3 74.7 - - - +
294C GLU* 1.3 61.3 + - - +
296C PHE 3.3 1.0 + - - -
297C ARG* 3.0 31.7 + - + +
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Residues in contact with GLU 294 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290C GLN* 3.0 17.9 + - + +
293C THR* 1.3 77.0 - - - +
295C ALA* 1.3 56.4 + - - +
297C ARG* 3.7 8.2 - - - +
298C ASN* 3.1 59.1 + - - +
336C VAL* 3.9 19.5 - - + -
337C GLN 5.1 1.3 - - - +
338C VAL* 3.9 26.2 - - + +
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Residues in contact with ALA 295 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291C VAL 3.0 19.8 + - - +
292C MET 3.7 2.9 - - - +
294C GLU* 1.3 74.3 - - - +
296C PHE* 1.3 65.1 + - - +
297C ARG 3.1 2.3 + - - -
298C ASN* 3.3 11.8 + - - +
299C LEU* 3.4 21.5 + - - +
332C ALA* 3.9 7.7 - - + +
333C LEU* 3.5 34.5 - - + +
336C VAL* 3.6 16.1 - - + +
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Residues in contact with PHE 296 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C ILE* 3.6 33.7 - - + +
41C PHE* 4.1 11.9 - - + -
43C LEU* 5.6 1.8 - - + -
292C MET 3.1 14.7 + - - +
293C THR 4.0 2.7 - - - +
295C ALA* 1.3 78.8 - - - +
297C ARG* 1.3 61.3 + - - +
299C LEU* 3.6 14.3 + - - +
300C ARG* 3.5 18.0 + - - +
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Residues in contact with ARG 297 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41C PHE* 3.7 22.0 - - + -
293C THR* 3.0 19.4 + - + +
294C GLU* 3.7 13.0 - - - +
295C ALA 3.1 0.2 - - - -
296C PHE* 1.3 75.7 - - - +
298C ASN* 1.3 63.8 + - - +
299C LEU 3.1 4.7 - - - -
300C ARG* 3.3 5.6 + - - +
301C LYS* 3.2 24.1 + - - +
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Residues in contact with ASN 298 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294C GLU* 3.1 47.2 + - - +
295C ALA* 3.3 7.8 + - - +
297C ARG* 1.3 76.9 - - - +
299C LEU* 1.3 64.6 + - + +
301C LYS* 4.2 7.1 - - - +
302C GLN* 3.0 25.9 + - - +
332C ALA* 5.3 4.9 + - + +
335C GLN* 5.4 4.9 + - - +
336C VAL* 5.0 10.5 - - - +
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Residues in contact with LEU 299 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295C ALA 3.4 10.7 + - - +
296C PHE* 3.8 14.6 - - - +
297C ARG 3.1 0.8 - - - -
298C ASN* 1.3 86.6 - - + +
300C ARG* 1.3 61.7 + - - +
302C GLN* 3.5 2.1 + - - -
303C ARG 3.4 2.6 + - - -
304C ILE* 3.1 60.0 + - + +
306C ILE* 3.9 29.6 - - + -
328C GLU* 4.6 6.7 - - + +
329C ILE* 4.5 15.7 - - + +
332C ALA* 3.4 32.1 - - + -
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Residues in contact with ARG 300 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C ASN* 5.8 3.4 - - - +
41C PHE* 5.4 8.5 - - + -
296C PHE 3.5 10.2 + - - +
297C ARG* 3.3 10.4 + - - +
299C LEU* 1.3 79.0 - - - +
301C LYS* 1.3 60.5 + - - +
302C GLN 3.1 1.6 - - - -
303C ARG* 3.3 13.0 + - - +
304C ILE 5.5 0.4 - - - -
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Residues in contact with LYS 301 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297C ARG 3.2 14.2 + - - +
298C ASN* 4.3 6.5 - - - +
300C ARG* 1.3 77.7 - - - +
302C GLN* 1.3 56.9 + - - +
303C ARG* 3.3 2.2 + - - +
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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) + - + + + + + -
------------------------------------------------------------
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