Contacts of the helix formed by residues 289 - 311 (chain C) in PDB entry 3U8Z
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 289 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70C ASP* 5.5 9.1 + - - +
71C THR* 4.9 6.2 + - - +
287C SER* 3.5 2.2 + - - +
288C SER* 1.4 86.1 + - - +
290C LEU* 1.3 63.4 + - - +
291C ARG* 3.4 26.7 - - - +
292C VAL* 3.5 29.1 + - + +
293C ASN* 2.9 28.8 + - - +
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Residues in contact with LEU 290 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266C TYR* 3.6 20.9 - - + +
268C ASP* 5.3 3.8 - - - +
269C LYS* 4.3 30.3 - - + +
288C SER 3.9 3.8 + - - +
289C LYS* 1.3 69.1 - - - +
291C ARG* 1.4 76.5 + - + +
293C ASN* 3.3 8.1 + - - +
294C LYS* 3.2 20.8 + - - +
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Residues in contact with ARG 291 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68C ILE* 4.4 32.8 + - + -
69C LYS* 5.1 16.1 - - - +
71C THR* 3.5 28.9 + - + +
72C VAL 5.1 1.2 - - - +
289C LYS* 3.4 40.0 - - - +
290C LEU* 1.4 84.2 - - + +
292C VAL* 1.3 63.8 + - - +
294C LYS* 3.5 11.2 + - - +
295C LEU* 3.3 20.6 + - - +
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Residues in contact with VAL 292 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71C THR* 3.7 23.8 - - + +
222C PHE* 3.5 33.4 - - + -
223C ALA 5.9 0.7 - - - +
287C SER* 4.3 8.1 - - - +
289C LYS* 3.5 40.3 + - + +
290C LEU 3.3 0.2 - - - -
291C ARG* 1.3 76.7 - - - +
293C ASN* 1.4 55.3 - - - +
295C LEU* 3.2 8.4 + - + +
296C ILE* 2.9 35.3 + - + +
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Residues in contact with ASN 293 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266C TYR* 2.8 39.4 + - + +
269C LYS* 3.9 1.8 - - - +
271C PHE* 3.7 22.5 - - + -
287C SER* 2.7 47.8 + - - -
289C LYS 2.9 12.6 + - - +
290C LEU* 3.3 13.5 + - - +
292C VAL* 1.4 73.0 - - - +
294C LYS* 1.3 63.7 + - - +
296C ILE* 3.4 4.3 + - - +
297C LEU* 3.2 30.6 + - - +
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Residues in contact with LYS 294 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A ARG* 5.2 3.8 + - - +
76C LYS* 4.2 23.3 - - - +
290C LEU 3.2 11.6 + - - +
291C ARG* 3.7 12.6 - - - +
293C ASN* 1.3 74.4 - - - +
295C LEU* 1.3 62.4 + - - +
297C LEU* 3.5 9.3 + - - +
298C GLN* 3.1 51.3 + - + +
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Residues in contact with LEU 295 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71C THR* 4.9 5.2 - - + -
72C VAL* 3.7 39.0 - - + +
74C TRP* 3.5 35.0 - - + +
99C LYS* 4.8 0.2 - - - -
222C PHE* 4.2 18.2 - - + -
291C ARG 3.3 10.2 + - - +
292C VAL* 3.2 11.3 + - - +
294C LYS* 1.3 75.9 - - - +
296C ILE* 1.4 65.2 + - - +
298C GLN* 3.2 14.4 + - - +
299C LEU* 3.0 45.9 + - + +
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Residues in contact with ILE 296 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222C PHE* 3.7 46.9 - - + -
224C ILE* 5.1 2.2 - - + -
234C LEU* 3.8 23.3 - - + -
236C VAL* 4.5 2.5 - - + +
271C PHE* 3.7 33.9 - - + -
285C PHE* 5.2 0.2 - - + -
287C SER* 4.3 7.4 - - - +
292C VAL* 2.9 32.4 + - + +
293C ASN* 3.4 14.3 + - - +
295C LEU* 1.4 70.0 - - - +
297C LEU* 1.3 57.1 + - - +
299C LEU* 3.2 6.0 + - - +
300C CYS* 2.9 43.5 + - - -
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Residues in contact with LEU 297 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A GLN 5.2 2.9 - - - +
179A MET* 3.5 43.7 - - + -
184A TRP* 5.7 0.2 - - + -
187A ARG* 4.3 13.9 - - - +
264C ILE* 4.2 8.1 - - + -
266C TYR* 3.9 30.1 - - + -
271C PHE* 3.6 25.1 - - + -
293C ASN 3.2 18.8 + - - +
294C LYS* 3.8 8.1 - - - +
295C LEU 3.3 0.4 - - - -
296C ILE* 1.3 70.9 - - - +
298C GLN* 1.3 65.3 + - - +
300C CYS* 3.2 9.1 + - + +
301C ILE* 3.0 31.1 + - - +
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Residues in contact with GLN 298 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187A ARG* 4.6 10.0 - - - +
191A TRP* 5.3 1.7 + - - -
74C TRP* 4.0 24.0 + - - +
76C LYS* 4.3 15.5 - - - +
99C LYS* 3.2 30.7 + - - +
100C PHE* 4.0 8.5 - - - -
294C LYS* 3.1 47.2 + - + +
295C LEU* 3.4 14.1 - - - +
297C LEU* 1.3 75.8 - - - +
299C LEU* 1.3 60.6 + - - +
301C ILE* 3.5 8.4 + - - +
302C GLY 3.2 18.4 + - - -
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Residues in contact with LEU 299 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74C TRP* 5.1 0.9 - - + +
99C LYS* 3.8 43.7 - - + +
100C PHE* 4.0 8.7 - - + -
220C ASN* 3.7 27.4 - - + +
222C PHE* 3.6 32.3 - - + -
236C VAL* 3.9 13.2 - - + -
295C LEU* 3.0 31.1 + - + +
296C ILE* 3.6 6.3 - - - +
298C GLN* 1.3 72.4 - - - +
300C CYS* 1.3 64.5 + - - +
303C ASN* 2.8 33.3 + - - +
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Residues in contact with CYS 300 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184A TRP* 4.0 15.7 - - + -
236C VAL* 4.2 3.4 - - - -
241C LEU* 3.7 32.5 - - - -
258C TRP* 3.4 17.6 - - + -
264C ILE* 4.6 6.5 - - + -
271C PHE* 6.2 0.2 - - - -
296C ILE* 2.9 37.8 + - - -
297C LEU* 3.5 16.8 - - + +
299C LEU* 1.3 77.0 - - - +
301C ILE* 1.4 56.0 + - - +
304C HIS* 3.0 32.2 + - - +
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Residues in contact with ILE 301 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A MET* 4.6 7.9 - - - -
184A TRP* 3.7 23.8 - - + -
187A ARG* 3.1 74.0 - - + +
188A ILE* 4.3 5.8 - - + +
191A TRP* 3.7 22.2 - - + -
297C LEU 3.0 23.7 + - - +
298C GLN* 3.9 5.2 - - - +
299C LEU 3.4 0.2 - - - -
300C CYS* 1.4 75.1 - - - +
302C GLY* 1.3 63.7 + - - +
304C HIS* 3.4 1.3 + - - +
305C ASP* 3.1 28.8 + - - +
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Residues in contact with GLY 302 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191A TRP* 3.6 25.2 - - - +
100C PHE* 3.6 23.3 - - - -
298C GLN 3.2 7.5 + - - -
301C ILE* 1.3 79.0 - - - +
303C ASN* 1.3 56.7 + - - +
305C ASP* 3.3 2.4 + - - +
306C LEU* 3.0 34.4 + - - +
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Residues in contact with ASN 303 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100C PHE* 3.7 28.1 - - - +
101C TYR 4.9 3.8 + - - +
220C ASN* 4.6 6.9 - - - +
236C VAL* 3.9 12.3 - - - +
237C ASP* 3.4 35.3 + - - +
238C ALA* 3.7 11.2 + - - +
258C TRP* 3.6 11.7 + - + +
299C LEU* 2.8 33.2 + - - +
302C GLY* 1.3 71.5 - - - +
304C HIS* 1.3 65.9 + - - +
306C LEU* 4.2 5.7 - - - +
307C PHE* 3.0 25.5 + - - +
310C ARG* 4.9 1.1 + - - +
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Residues in contact with HIS 304 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184A TRP* 4.0 22.4 + + + -
188A ILE* 3.7 31.3 - - + +
192A TYR* 4.3 0.9 - - - -
258C TRP* 3.7 47.1 + + + -
261C ILE* 5.4 4.6 + - + -
300C CYS 3.0 20.7 + - - +
301C ILE 3.5 4.0 - - - +
303C ASN* 1.3 76.7 - - - +
305C ASP* 1.3 76.1 + - - +
307C PHE* 3.3 4.5 - - - +
308C MET* 3.1 54.0 + - + +
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Residues in contact with ASP 305 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A ILE* 2.6 38.2 - - - +
191A TRP* 3.1 38.4 - - + +
192A TYR* 3.3 33.7 + - + -
301C ILE 3.1 15.4 + - - +
302C GLY 3.8 0.7 - - - +
304C HIS* 1.3 93.7 + - - +
306C LEU* 1.3 63.8 + - - +
308C MET 3.4 0.9 + - - -
309C ARG* 3.1 21.5 + - - +
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Residues in contact with LEU 306 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191A TRP* 3.7 24.5 - - + -
60C TRP* 3.6 32.5 - - + +
61C PHE* 4.8 1.3 - - + -
100C PHE* 3.7 35.2 - - + -
101C TYR 5.3 0.4 - - - +
302C GLY 3.0 21.2 + - - +
303C ASN* 4.2 4.9 - - - +
305C ASP* 1.3 72.2 - - - +
307C PHE* 1.3 64.1 + - - +
309C ARG* 3.5 19.1 + - + +
310C ARG* 3.2 54.0 + - - +
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Residues in contact with PHE 307 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103C GLU* 4.0 1.3 - - - -
238C ALA 3.3 18.8 - - - +
239C LEU* 3.6 20.6 - - + -
257C PRO* 5.1 1.6 - - + -
258C TRP* 3.6 21.8 - + + -
259C ASN* 3.3 45.8 - - + -
303C ASN 3.0 19.5 + - - +
304C HIS 3.3 4.5 - - - +
306C LEU* 1.3 76.7 - - - +
308C MET* 1.3 73.5 + - - +
310C ARG* 3.4 14.5 + - - +
311C ARG* 2.9 74.0 + - - +
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Residues in contact with MET 308 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192A TYR* 3.2 27.4 - - + +
259C ASN* 4.8 13.7 - - + -
304C HIS* 3.1 34.6 + - + +
305C ASP 3.4 1.3 + - - +
306C LEU 3.3 0.2 - - - -
307C PHE* 1.3 93.3 - - - +
309C ARG* 1.3 63.8 + - - +
311C ARG* 3.1 20.9 + - + +
312C LYS 3.4 13.9 + - - +
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Residues in contact with ARG 309 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191A TRP* 4.1 5.8 - - - -
192A TYR* 2.6 58.7 + - + +
195A HIS 2.8 25.0 + - - -
196A ARG* 3.7 20.6 - - - +
60C TRP* 4.7 9.3 - - - -
305C ASP 3.1 19.0 + - - +
306C LEU* 3.8 28.3 - - + +
308C MET* 1.3 75.0 - - - +
310C ARG* 1.3 58.0 + - + +
312C LYS* 3.2 27.3 + - - +
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Residues in contact with ARG 310 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61C PHE* 4.1 8.5 - - - -
101C TYR 3.2 21.4 + - - -
102C PRO* 3.7 1.2 - - - +
103C GLU* 2.9 38.6 + - - -
108C GLU* 3.0 41.1 + - + +
238C ALA* 3.8 15.8 + - - +
303C ASN* 4.9 0.4 + - - -
306C LEU* 3.2 44.8 + - - +
307C PHE* 3.6 11.1 - - - +
308C MET 3.3 0.4 - - - -
309C ARG* 1.3 76.7 - - + +
311C ARG* 1.3 66.9 + - - +
312C LYS* 3.3 7.9 + - - +
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Residues in contact with ARG 311 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103C GLU* 2.6 37.0 + - - -
239C LEU* 4.6 5.1 - - - +
259C ASN* 5.5 2.5 - - - -
307C PHE* 2.9 64.5 + - - +
308C MET* 3.1 17.5 + - + +
310C ARG* 1.3 88.0 - - - +
312C LYS* 1.4 69.0 + - - +
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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) + - + + + + + -
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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