Contacts of the helix formed by residues 278 - 299 (chain C) in PDB entry 6S6A
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 ASP 278 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258C LYS* 5.5 0.4 - - - +
276C PRO 3.7 5.0 + - - +
277C VAL* 1.3 73.9 - - - +
279C MET* 1.3 67.5 + - - +
280C GLN* 3.1 38.7 + - - +
281C SER* 3.1 31.3 + - - +
282C TYR 3.4 3.5 + - - -
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Residues in contact with MET 279 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227C GLU* 3.1 38.0 - - - +
231C LYS* 5.0 16.8 - - - -
269C TYR* 4.4 12.8 - - + +
277C VAL* 3.6 34.2 + - + +
278C ASP* 1.3 74.4 + - - +
280C GLN* 1.3 59.4 + - + +
282C TYR* 3.3 17.2 + - - +
283C GLU* 2.9 33.2 + - - +
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Residues in contact with GLN 280 (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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244A LYS 4.3 12.0 - - - +
245A LEU* 3.4 48.5 + - + +
278C ASP* 3.1 24.8 + - - +
279C MET* 1.3 79.3 - - + +
281C SER* 1.3 56.7 + - - +
283C GLU* 3.3 8.0 + - - +
284C LEU* 2.9 29.9 + - - +
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Residues in contact with SER 281 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A LEU 5.3 0.6 + - - -
258C LYS* 5.4 2.7 - - - -
260C PHE* 4.5 6.3 - - - -
278C ASP* 3.1 23.2 + - - +
280C GLN* 1.3 74.8 - - - +
282C TYR* 1.3 65.4 + - - -
284C LEU* 3.3 8.4 + - - +
285C CYS* 3.0 30.1 + - - -
340C ILE* 3.8 26.2 - - - +
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Residues in contact with TYR 282 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223C HIS* 4.9 2.7 - + - -
226C PHE* 3.5 18.2 + - + +
227C GLU* 3.9 32.5 - - + -
230C SER* 2.8 20.1 + - - -
260C PHE* 4.0 22.5 - + + -
262C PHE* 3.6 16.2 - + - -
267C LYS 2.7 23.4 + - - -
269C TYR* 3.3 27.4 - + + -
277C VAL* 4.5 1.3 - - + -
278C ASP 3.4 3.0 + - - +
279C MET* 3.3 32.1 + - - +
281C SER* 1.3 79.7 - - - +
283C GLU* 1.3 66.1 + - + +
285C CYS* 3.3 2.0 + - - +
286C CYS* 3.0 43.6 + - - -
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Residues in contact with GLU 283 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A LEU* 3.3 32.1 - - + +
223C HIS* 3.3 53.7 + - + +
227C GLU* 5.0 4.6 - - - +
279C MET* 2.9 20.5 + - - +
280C GLN* 3.6 7.8 - - - +
282C TYR* 1.3 76.3 - - + +
284C LEU* 1.3 63.4 + - - +
286C CYS* 3.1 2.4 + - - +
287C ASP* 3.0 28.3 + - - +
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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
----------------------------------------------------------
238A PHE* 4.0 8.2 - - + -
241A SER* 4.0 14.1 - - - +
242A CYS* 3.9 36.8 - - - -
245A LEU* 3.5 10.7 - - + +
246A ALA* 4.1 22.0 - - + -
280C GLN 2.9 17.9 + - - +
281C SER* 3.3 10.1 + - - +
283C GLU* 1.3 76.6 - - - +
285C CYS* 1.3 57.9 + - - +
287C ASP* 3.1 7.3 + - - +
288C MET* 2.9 25.9 + - - +
320C LEU* 4.2 7.6 - - + -
324C THR* 5.9 0.2 - - + -
326C LEU* 3.5 30.5 - - + -
340C ILE* 6.1 1.3 - - + -
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Residues in contact with CYS 285 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260C PHE* 4.1 11.4 - - + -
262C PHE* 3.8 22.7 - - + -
281C SER 3.0 20.7 + - - +
282C TYR 3.6 4.9 - - - +
284C LEU* 1.3 74.1 - - - +
286C CYS* 1.3 64.1 + - - +
288C MET* 3.1 11.7 + - - +
289C ILE* 3.1 25.5 + - - +
326C LEU* 5.0 7.6 - - - -
338C VAL* 3.6 23.5 - - + +
340C ILE* 3.9 26.2 - - - -
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Residues in contact with CYS 286 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223C HIS* 3.5 25.4 - - - +
226C PHE* 5.1 1.8 - - + -
262C PHE* 3.8 3.1 - - - -
267C LYS* 3.5 29.0 - - + +
282C TYR* 3.0 50.1 + - - -
283C GLU 3.1 7.2 + - - +
285C CYS* 1.3 75.9 - - - +
287C ASP* 1.3 62.4 + - - +
289C ILE* 3.2 12.3 + - - +
290C ASP* 3.2 26.6 + - - +
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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
----------------------------------------------------------
238A PHE* 3.7 20.4 - - + +
241A SER* 2.8 35.7 + - - +
245A LEU* 4.3 5.9 - - - +
223C HIS* 3.3 23.7 + - - -
283C GLU* 3.0 19.4 + - - +
284C LEU 3.1 7.8 + - - +
286C CYS* 1.3 75.3 - - - +
288C MET* 1.3 63.1 + - - +
290C ASP* 3.7 14.9 - - - +
291C VAL* 3.2 17.8 + - - +
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Residues in contact with MET 288 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238A PHE* 3.6 12.3 - - + -
284C LEU 2.9 11.2 + - - +
285C CYS* 3.3 10.3 - - - +
287C ASP* 1.3 76.0 - - - +
289C ILE* 1.3 56.9 + - + +
291C VAL* 3.1 4.9 + - - +
292C VAL* 2.8 38.8 + - + +
316C ALA* 3.8 24.9 - - + -
318C ILE* 3.5 32.1 - - + -
326C LEU* 3.8 40.6 - - + +
328C LEU* 3.8 20.9 - - + +
338C VAL* 4.2 18.2 - - - -
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Residues in contact with ILE 289 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262C PHE* 3.4 55.0 - - + -
263C ASP 5.2 1.1 - - - +
264C VAL* 3.7 31.9 - - + +
267C LYS* 4.0 12.3 - - + -
285C CYS 3.1 11.6 + - - +
286C CYS* 3.2 8.0 + - - +
288C MET* 1.3 73.4 - - + +
290C ASP* 1.3 65.8 + - - +
292C VAL* 3.1 7.4 + - - +
293C ILE* 2.8 38.2 + - + +
328C LEU* 4.1 20.4 - - + -
336C ALA* 5.7 0.9 - - + -
338C VAL* 4.4 4.0 - - + -
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Residues in contact with ASP 290 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223C HIS* 5.9 0.5 + - - -
267C LYS* 2.9 37.8 + - - +
286C CYS* 3.2 17.3 + - - +
287C ASP* 3.7 18.7 - - - +
289C ILE* 1.3 74.6 - - - +
291C VAL* 1.3 57.5 + - + +
293C ILE* 3.3 2.6 + - - -
294C ASP* 2.8 46.4 + - - +
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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
----------------------------------------------------------
234A ILE* 3.8 29.6 - - + +
235A ILE* 4.8 1.8 - - + -
238A PHE* 3.5 33.7 - - + -
252A MET* 3.3 43.1 - - + -
287C ASP 3.2 9.0 + - - +
288C MET* 3.1 10.7 + - - +
290C ASP* 1.3 78.2 - - + +
292C VAL* 1.3 64.7 + - + +
294C ASP 4.0 0.3 - - - -
295C VAL* 3.1 31.0 + - + +
318C ILE* 5.1 2.7 - - + -
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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
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252A MET* 5.3 1.6 - - - -
254A VAL* 3.8 22.7 - - + +
255A ARG 5.4 2.0 - - - +
288C MET* 2.8 30.8 + - + +
289C ILE* 3.7 7.6 - - - +
291C VAL* 1.3 76.7 - - + +
293C ILE* 1.3 66.7 + - + +
295C VAL* 3.9 0.5 - - - -
296C SER* 2.8 41.4 + - - +
310C TYR* 5.9 0.9 - - + -
314C SER* 5.6 7.6 - - - +
315C MET 4.9 2.2 - - - +
316C ALA* 3.3 32.1 - - + -
328C LEU* 4.3 21.1 - - + -
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Residues in contact with ILE 293 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264C VAL* 3.8 26.9 - - + +
289C ILE* 2.8 38.5 + - + +
290C ASP* 4.0 3.6 - - - +
292C VAL* 1.3 80.5 - - + +
294C ASP* 1.3 63.2 + - - +
296C SER* 3.4 3.7 + - - -
297C CYS* 2.8 41.7 + - - -
309C ALA* 4.7 6.1 - - + +
310C TYR* 4.1 26.9 - - + +
314C SER* 5.9 0.2 - - - +
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Residues in contact with ASP 294 (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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234A ILE* 3.2 35.7 - - + +
290C ASP* 2.8 30.5 + - - +
291C VAL 4.4 1.6 - - - +
293C ILE* 1.3 82.8 - - - +
295C VAL* 1.3 60.4 + - - +
297C CYS* 3.8 8.1 + - - +
298C ILE* 3.2 29.9 + - - +
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Residues in contact with VAL 295 (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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231A ILE* 4.2 15.5 - - + -
234A ILE* 4.2 17.5 - - + -
235A ILE* 5.3 5.8 - - + -
252A MET* 5.6 0.2 - - - -
254A VAL* 4.3 16.8 - - + -
259A PHE* 4.0 22.0 - - + -
263A ILE* 5.4 2.5 - - + -
273A MET* 4.0 25.6 - - + -
291C VAL* 3.1 24.7 + - + +
292C VAL 4.1 2.0 - - - +
294C ASP* 1.3 76.1 - - - +
296C SER* 1.3 60.0 + - - +
298C ILE* 3.2 5.4 + - - +
299C TYR* 3.0 32.7 + - + +
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Residues in contact with SER 296 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254A VAL* 3.9 6.9 - - - +
255A ARG 4.7 3.6 + - - -
256A ASN* 4.6 0.7 + - - +
259A PHE* 3.7 21.4 - - - -
292C VAL* 2.8 28.6 + - - +
293C ILE* 3.6 6.3 - - - -
295C VAL* 1.3 73.8 - - - +
297C CYS* 1.3 60.6 + - - -
299C TYR 2.5 22.5 - - - +
300C GLY 3.5 9.2 - - - +
301C LEU* 3.8 5.0 - - - +
309C ALA* 3.5 28.2 + - - +
314C SER* 5.3 0.9 + - - -
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Residues in contact with CYS 297 (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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223A ARG* 4.1 4.0 + - - -
293C ILE* 2.8 34.7 + - - +
294C ASP* 4.0 9.9 - - - +
295C VAL 3.3 0.6 - - - -
296C SER* 1.3 72.4 - - - +
298C ILE* 1.3 63.2 + - + +
301C LEU* 3.3 29.4 - - + +
309C ALA* 3.6 18.6 - - - -
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Residues in contact with ILE 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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222A GLN* 5.2 2.1 - - - +
223A ARG* 4.6 9.1 + - - +
224A ASP* 4.2 23.6 - - + +
227A ARG* 4.0 20.5 - - + -
230A LYS* 4.1 25.6 - - + -
231A ILE* 3.6 22.0 - - + -
234A ILE* 4.5 4.5 - - + -
294C ASP* 3.2 18.3 + - + +
295C VAL 3.2 6.5 + - - +
296C SER 3.2 0.4 - - - -
297C CYS* 1.3 82.2 - - + +
299C TYR* 1.3 96.1 + - + +
301C LEU* 5.5 1.4 - - - +
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Residues in contact with TYR 299 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A GLU* 2.8 31.2 + - - -
204A LEU* 3.6 19.9 - - - +
222A GLN* 3.9 20.2 - - - -
227A ARG* 3.8 13.6 + - - +
231A ILE* 4.1 15.3 - - + +
259A PHE* 3.6 24.9 - + + -
273A MET* 4.3 8.7 - - + -
275A VAL* 4.0 39.3 - - + -
295C VAL* 3.0 20.6 + - + -
296C SER* 2.5 34.5 - - - +
298C ILE* 1.3 100.5 - - + +
300C GLY* 1.3 60.4 + - - +
301C LEU 3.5 1.1 + - - -
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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