Contacts of the helix formed by residues 287 - 309 (chain C) in PDB entry 3PK1
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 ILE 287 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183C SER* 3.1 43.7 - - - +
186C LEU* 4.0 19.3 - - + +
187C ARG* 3.9 21.1 - - + +
190C ALA* 4.2 11.7 - - + -
275C ALA* 3.9 28.5 - - + +
278C LEU* 6.4 0.9 - - + -
279C LYS* 6.0 3.4 - - + +
285C SER 5.6 1.1 - - - +
286C CYS* 1.3 79.2 - - - +
288C GLU* 1.3 79.2 + - - +
289C PRO 3.4 1.3 - - - -
290C LEU* 3.0 10.7 + - + +
291C ALA* 2.7 30.5 + - + +
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Residues in contact with GLU 288 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C CD 2.8 9.5 - - - -
183C SER* 5.1 2.4 - - - +
187C ARG* 3.4 29.0 + - - +
286C CYS* 2.7 35.5 - - + -
287C ILE* 1.3 89.4 - - + +
289C PRO* 1.3 75.5 - - + +
291C ALA* 3.7 5.5 - - - +
292C GLU* 2.9 42.1 + - + +
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Residues in contact with PRO 289 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C CD 4.6 5.2 - - - -
240C GLU* 3.1 35.7 - - - +
241C ASP* 3.7 24.7 - - - +
243C VAL* 4.3 10.7 - - + +
286C CYS 4.0 7.9 - - - +
287C ILE 3.8 2.0 - - - -
288C GLU* 1.3 95.8 - - + +
290C LEU* 1.3 51.1 + - - +
292C GLU* 3.7 9.8 - - + +
293C SER* 2.8 34.0 + - - -
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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
----------------------------------------------------------
186C LEU* 4.0 9.6 - - + -
237C ILE* 4.9 3.1 - - + -
240C GLU 4.5 2.6 + - - +
243C VAL* 3.5 26.2 - - + -
246C LEU* 3.7 26.5 - - + -
271C GLY 3.3 26.2 - - - +
274C VAL* 4.2 14.1 - - + -
275C ALA* 3.7 25.6 - - + +
278C LEU* 4.9 8.5 - - + -
286C CYS 5.3 0.7 - - - +
287C ILE* 3.0 15.0 + - + +
289C PRO* 1.3 76.4 - - - +
291C ALA* 1.3 67.0 + - - +
293C SER* 3.2 2.9 + - - -
294C ILE* 3.1 31.1 + - + +
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Residues in contact with ALA 291 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179C LEU* 3.9 3.1 - - + -
182C ILE* 4.2 4.4 - - + +
183C SER* 3.2 44.2 - - - +
186C LEU* 3.8 14.4 - - + +
287C ILE* 2.7 21.0 + - + +
288C GLU* 3.7 4.3 - - - +
290C LEU* 1.3 73.0 - - - +
292C GLU* 1.3 54.5 + - - +
294C ILE* 3.3 2.1 + - - +
295C THR* 2.8 37.2 + - - -
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Residues in contact with GLU 292 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175C TYR* 3.7 10.2 + - + +
179C LEU* 3.7 27.8 - - + +
288C GLU* 2.9 38.1 + - + +
289C PRO* 3.7 8.1 - - + +
291C ALA* 1.3 71.5 - - + +
293C SER* 1.3 67.0 + - - +
296C ASP* 2.8 33.9 + - - +
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Residues in contact with SER 293 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243C VAL* 4.0 21.6 + - - +
246C LEU* 4.8 2.6 - - - +
247C SER* 2.9 24.6 + - - -
250C MET* 3.2 11.6 - - - +
289C PRO 2.8 18.7 + - - -
290C LEU* 3.3 12.3 - - - -
292C GLU* 1.3 76.5 - - - +
294C ILE* 1.3 64.9 + - - +
296C ASP* 3.2 18.8 - - - +
297C VAL* 3.3 12.6 + - - +
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Residues in contact with ILE 294 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182C ILE* 4.0 21.8 - - + -
186C LEU* 4.0 15.5 - - + -
246C LEU* 4.9 4.9 - - + -
250C MET* 3.7 29.1 - - + +
267C LEU* 4.2 9.4 - - + +
268C ILE* 4.0 20.4 - - + +
271C GLY* 3.6 31.4 - - - -
290C LEU* 3.1 17.6 + - + +
291C ALA 3.7 5.4 - - - +
293C SER* 1.3 71.6 - - - +
295C THR* 1.3 66.9 + - - +
297C VAL* 3.2 4.2 + - - +
298C LEU* 3.0 29.4 + - + +
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Residues in contact with THR 295 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175C TYR* 3.8 23.6 - - + +
178C SER* 3.8 3.1 - - - -
179C LEU* 3.5 36.3 - - - +
182C ILE* 3.5 19.7 - - - +
291C ALA 2.8 21.9 + - - -
292C GLU 3.9 3.4 - - - -
294C ILE* 1.3 73.3 - - - +
296C ASP* 1.3 58.2 + - - +
298C LEU* 4.5 2.2 - - - +
299C VAL* 2.7 56.9 + - + +
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Residues in contact with ASP 296 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175C TYR* 2.5 30.2 + - - -
292C GLU* 2.8 27.7 + - - +
293C SER* 3.2 9.4 - - - +
295C THR* 1.3 77.3 - - - +
297C VAL* 1.3 60.3 + - + +
300C ARG* 2.9 65.1 + - - +
301C THR* 3.9 1.2 + - - +
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Residues in contact with VAL 297 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247C SER* 4.2 9.2 - - - +
250C MET* 4.0 42.0 - - + +
251C ILE* 3.7 29.6 - - + -
254C PHE* 4.5 8.1 - - + -
267C LEU* 5.1 0.2 - - + -
293C SER 3.3 9.6 + - - +
294C ILE 3.2 7.7 + - - +
295C THR 3.2 0.4 - - - -
296C ASP* 1.3 80.3 - - + +
298C LEU* 1.3 75.7 + - + +
301C THR* 2.7 42.6 + - + +
302C LYS* 4.2 0.3 - - - +
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Residues in contact with LEU 298 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178C SER* 6.5 0.2 - - - -
182C ILE* 4.1 23.1 - - + -
250C MET* 6.4 0.2 - - - -
254C PHE* 3.8 32.5 - - + -
264C ILE* 3.4 35.4 - - + +
267C LEU* 4.4 12.1 - - + -
268C ILE* 4.2 10.8 - - + -
294C ILE* 3.0 20.6 + - + +
295C THR* 4.0 3.8 - - - +
297C VAL* 1.3 77.9 - - + +
299C VAL* 1.3 61.6 + - + +
302C LYS* 2.8 40.0 + - + +
306C LEU* 3.5 13.0 - - + +
312C TRP* 5.5 4.7 - - + -
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Residues in contact with VAL 299 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174C LEU* 3.3 24.9 - - + -
175C TYR* 3.8 27.4 - - + +
178C SER* 3.5 27.4 - - - +
295C THR* 2.7 37.4 + - + +
298C LEU* 1.3 78.6 - - + +
300C ARG* 1.3 60.1 + - + +
303C ARG* 3.1 39.3 + - - +
306C LEU* 3.9 9.2 - - + -
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Residues in contact with ARG 300 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175C TYR* 4.1 17.2 - - + -
296C ASP* 2.9 53.0 + - - +
299C VAL* 1.3 80.0 - - + +
301C THR* 1.3 63.7 + - + +
303C ARG* 4.6 4.3 - - - +
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Residues in contact with THR 301 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251C ILE* 4.3 19.8 - - + +
254C PHE* 5.0 1.9 - - - -
296C ASP 4.2 1.3 - - - +
297C VAL* 2.7 37.2 + - + +
300C ARG* 1.3 80.9 - - + +
302C LYS* 1.3 83.2 + - - +
303C ARG* 3.6 1.3 - - - -
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Residues in contact with LYS 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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254C PHE* 3.6 46.4 + - + +
257C GLY* 5.1 6.7 + - - -
258C VAL 4.9 1.0 + - - -
259C THR* 3.0 38.5 + - + +
264C ILE* 5.5 0.7 - - + -
297C VAL 4.2 2.2 - - - +
298C LEU* 2.8 22.1 + - + +
301C THR* 1.3 97.6 + - - +
303C ARG* 1.3 67.2 + - - +
304C ASP 3.3 2.5 - - - -
305C TRP* 3.0 12.2 + - + +
306C LEU* 2.7 33.5 + - + +
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Residues in contact with ARG 303 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173C SER* 5.1 5.3 + - - +
174C LEU* 3.9 32.2 - - - +
175C TYR* 5.2 5.3 - - - +
299C VAL* 3.1 39.1 + - - +
300C ARG* 4.9 5.4 - - - +
301C THR 3.6 0.8 - - - -
302C LYS* 1.3 76.2 - - - +
304C ASP* 1.3 78.8 + - - +
306C LEU* 3.1 7.8 + - - +
307C VAL* 2.8 42.9 + - + +
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Residues in contact with ASP 304 (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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302C LYS 3.3 1.0 - - - -
303C ARG* 1.3 84.8 - - - +
305C TRP* 1.3 64.7 + - - +
307C VAL* 3.1 8.2 + - - +
308C LYS* 2.8 25.0 + - - +
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Residues in contact with TRP 305 (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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259C THR* 3.5 55.1 + - + +
260C ASN* 3.8 6.7 - - - -
261C TRP* 3.6 44.0 - + - -
264C ILE* 3.3 21.1 - - + -
302C LYS* 3.0 13.6 + - + +
304C ASP* 1.3 80.0 - - - +
306C LEU* 1.3 83.6 + - + +
308C LYS* 3.1 18.1 + - + +
309C GLN* 2.9 51.6 + - + +
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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
----------------------------------------------------------
174C LEU* 4.4 16.6 - - + -
178C SER* 5.4 1.6 - - - +
261C TRP* 3.7 24.6 - - + -
264C ILE* 3.9 12.6 - - + -
298C LEU* 3.5 38.1 - - + +
299C VAL* 3.9 15.7 - - + -
302C LYS* 2.7 22.6 + - + +
303C ARG* 3.4 5.8 - - - +
305C TRP* 1.3 93.5 - - + +
307C VAL* 1.3 61.6 + - - +
309C GLN* 3.1 10.2 + - - +
311C GLY* 3.1 26.8 + - - -
312C TRP* 6.5 1.3 - - + -
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Residues in contact with VAL 307 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174C LEU* 4.3 13.9 - - + -
303C ARG* 2.8 42.8 + - + +
304C ASP* 3.3 8.7 - - - +
306C LEU* 1.3 71.5 - - - +
308C LYS* 1.3 67.4 + - - +
309C GLN 2.9 1.6 - - - -
310C ARG* 2.8 16.8 + - - +
311C GLY 4.7 2.5 - - - +
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Residues in contact with LYS 308 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304C ASP 2.8 15.3 + - - +
305C TRP* 3.1 18.1 + - + +
307C VAL* 1.3 75.2 - - - +
309C GLN* 1.3 70.2 + - - +
310C ARG* 3.2 10.2 + - - +
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Residues in contact with GLN 309 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261C TRP* 4.0 20.2 + - + +
305C TRP* 2.9 72.8 + - + +
306C LEU 3.1 6.9 + - - +
307C VAL 2.9 1.6 + - - -
308C LYS* 1.3 88.9 - - - +
310C ARG* 1.3 76.7 + - - +
311C GLY 3.0 1.0 + - - -
314C GLY* 3.3 18.2 - - - -
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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) + - + + + + + -
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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