Contacts of the helix formed by residues 285 - 310 (chain C) in PDB entry 3L0I
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 PRO 285 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282C ASN* 5.5 1.3 - - - +
283C LEU 4.9 0.2 - - - +
284C LEU* 1.3 93.9 - - + +
286C GLU* 1.3 66.5 + - - +
287C GLU* 4.3 8.5 - - + +
288C GLN* 2.9 31.4 + - + +
289C ILE* 3.2 9.0 + - - +
335C LEU* 6.3 0.2 - - + -
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Residues in contact with GLU 286 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279C ARG* 2.5 49.5 + - + +
282C ASN* 5.7 1.0 - - - +
284C LEU 3.5 3.3 + - - -
285C PRO* 1.3 70.9 - - - +
287C GLU* 1.3 54.7 + - - +
289C ILE* 3.0 6.4 + - - +
290C ALA* 2.7 48.0 + - - +
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Residues in contact with GLU 287 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285C PRO* 4.3 7.4 - - + +
286C GLU* 1.3 76.9 - - - +
288C GLN* 1.3 61.9 + - + +
290C ALA* 3.8 6.1 + - - +
291C ARG* 3.3 47.1 + - - +
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Residues in contact with GLN 288 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284C LEU* 4.5 9.4 - - + -
285C PRO* 2.9 29.8 + - + +
287C GLU* 1.3 77.9 - - + +
289C ILE* 1.3 66.5 + - - +
291C ARG* 2.8 37.7 + - - +
292C ILE* 3.2 27.0 + - - +
331C LYS 4.6 3.3 + - - +
332C ILE* 5.2 2.2 - - - +
335C LEU* 3.3 53.5 - - + +
338C GLN* 4.0 8.5 + - - -
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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
----------------------------------------------------------
275C ILE* 3.6 32.9 - - + +
278C LEU* 3.8 41.7 - - + +
279C ARG* 3.9 25.8 - - + +
282C ASN* 5.6 0.7 - - - +
284C LEU* 3.3 39.7 - - + +
285C PRO 3.6 9.0 - - - +
286C GLU* 3.0 9.5 + - - +
288C GLN* 1.3 74.2 - - - +
290C ALA* 1.3 61.6 + - - +
292C ILE* 3.2 10.8 + - + +
293C GLU* 3.1 21.7 + - - +
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Residues in contact with ALA 290 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279C ARG* 4.1 14.0 - - - +
286C GLU* 2.7 34.9 + - - +
287C GLU* 3.8 7.2 - - - +
289C ILE* 1.3 72.0 - - - +
291C ARG* 1.3 51.7 + - - +
293C GLU* 3.1 7.3 + - - +
294C SER* 2.7 37.1 + - - -
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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
----------------------------------------------------------
287C GLU* 3.3 41.7 + - - +
288C GLN* 2.8 44.7 + - - +
290C ALA* 1.3 77.9 - - - +
292C ILE* 1.3 57.3 + - - +
294C SER* 3.6 6.2 - - - -
295C VAL* 2.6 37.7 + - - +
328C GLU* 3.9 32.5 - - + +
331C LYS* 3.6 54.1 + - - +
332C ILE* 4.2 9.4 - - + -
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Residues in contact with ILE 292 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248C ILE* 4.3 15.3 - - + +
251C MSE 5.6 1.3 - - + -
252C LEU* 3.6 29.2 - - + -
255C LEU* 3.8 26.2 - - + -
275C ILE* 4.7 9.4 - - + -
278C LEU* 5.1 3.6 - - + -
284C LEU* 4.8 4.0 - - + -
288C GLN 3.2 18.2 + - - +
289C ILE* 3.2 10.3 + - - +
291C ARG* 1.3 75.1 - - - +
293C GLU* 1.3 63.8 + - - +
295C VAL* 4.0 1.0 - - - +
296C TYR* 3.0 24.5 + - + +
332C ILE* 4.0 31.4 - - + -
335C LEU* 4.2 16.6 - - + -
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Residues in contact with GLU 293 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275C ILE* 3.8 26.2 - - + +
279C ARG* 2.7 38.8 + - - -
289C ILE 3.1 12.6 + - - +
290C ALA* 3.4 7.6 - - - +
292C ILE* 1.3 77.8 - - - +
294C SER* 1.3 64.7 + - - +
296C TYR* 3.8 2.4 - - - +
297C ASN* 3.1 27.5 + - + +
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Residues in contact with SER 294 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290C ALA 2.7 21.0 + - - -
291C ARG* 3.3 8.0 + - - -
293C GLU* 1.3 76.7 - - - +
295C VAL* 1.3 57.6 + - - +
297C ASN* 3.5 5.0 - - - +
298C GLN* 3.0 38.0 + - - +
328C GLU* 3.0 19.8 + - - -
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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
----------------------------------------------------------
244C ILE* 4.2 3.6 - - + -
248C ILE* 3.8 19.3 - - + -
291C ARG 2.6 28.0 + - - +
292C ILE 4.3 0.4 - - - +
294C SER* 1.3 70.9 - - - +
296C TYR* 1.3 62.7 + - - +
297C ASN 3.2 1.3 - - - -
298C GLN* 3.7 5.8 - - - -
299C ALA* 2.8 33.9 + - - +
325C MSE 3.8 31.6 - - + +
328C GLU* 3.3 40.4 - - + +
329C VAL* 4.2 4.0 - - + -
332C ILE* 3.8 10.3 - - + -
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Residues in contact with TYR 296 (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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245C MSE 3.3 29.9 - - + +
248C ILE* 3.7 22.0 - - + +
249C ASP* 3.5 17.3 + - - -
252C LEU* 4.0 15.3 - - + -
271C ALA* 3.6 27.9 - - + +
272C PRO* 5.8 0.9 - - + -
275C ILE* 5.4 6.3 - - + -
292C ILE* 3.0 20.7 + - + +
293C GLU* 3.8 5.4 - - - +
295C VAL* 1.3 74.9 - - - +
297C ASN* 1.3 57.9 + - - +
299C ALA* 3.6 5.0 - - - +
300C MSE 2.9 58.6 + - + +
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Residues in contact with ASN 297 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293C GLU* 3.1 21.1 + - + +
294C SER* 3.5 5.8 - - - +
296C TYR* 1.3 75.5 - - - +
298C GLN* 1.3 68.3 + - - +
300C MSE 3.3 17.1 + - - +
301C SER* 3.0 38.7 + - - -
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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
----------------------------------------------------------
294C SER* 3.0 34.0 + - - +
295C VAL 3.7 3.8 - - - +
297C ASN* 1.3 77.0 - - + +
299C ALA* 1.3 56.8 + - - +
301C SER* 3.7 6.6 - - - -
302C LYS* 3.1 20.4 + - - +
324C ALA* 5.1 10.5 - - - +
325C MSE 3.4 37.4 - - + +
328C GLU* 2.9 27.7 + - - +
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Residues in contact with ALA 299 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240C VAL* 4.0 7.2 - - + +
244C ILE* 3.8 27.1 - - + -
245C MSE 4.1 23.3 - - + -
295C VAL 2.8 16.9 + - - +
296C TYR* 3.6 4.0 - - - +
298C GLN* 1.3 74.4 - - - +
300C MSE 1.3 65.2 + - - +
301C SER 3.2 1.6 - - - -
302C LYS* 3.2 3.6 + - - +
303C ARG* 2.9 25.9 + - - +
325C MSE 3.9 7.8 - - - -
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Residues in contact with MSE 300 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245C MSE 4.5 10.2 - - - -
296C TYR* 2.9 46.6 + - + +
297C ASN* 3.6 17.0 - - - +
299C ALA* 1.3 74.7 - - - +
301C SER* 1.3 65.1 + - - +
303C ARG* 3.4 6.8 + - - +
304C PHE* 3.0 23.3 + - - +
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Residues in contact with SER 301 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297C ASN* 3.0 28.4 + - - -
298C GLN* 3.7 7.9 - - - -
299C ALA 3.2 0.2 - - - -
300C MSE 1.3 79.4 - - - +
302C LYS* 1.3 51.7 + - - +
304C PHE* 3.0 12.7 + - - +
305C GLU* 2.8 34.5 + - - +
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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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240C VAL* 4.9 1.3 - - + -
298C GLN 3.1 15.5 + - - +
299C ALA* 3.2 4.5 + - - +
301C SER* 1.3 76.1 - - - +
303C ARG* 1.3 60.6 + - - +
305C GLU* 3.4 32.7 + - - +
306C LEU* 2.8 47.0 + - + +
317C MSE 3.1 42.6 - - + -
321C ASP* 3.8 28.8 + - - +
325C MSE 3.9 17.7 - - + +
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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
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240C VAL* 4.3 12.0 - - + +
241C LYS* 4.9 18.4 - - - +
245C MSE 5.5 12.1 - - - +
299C ALA 2.9 16.3 + - - +
300C MSE 3.6 7.4 - - - +
302C LYS* 1.3 77.0 - - - +
304C PHE* 1.3 58.4 + - - +
306C LEU* 3.8 3.0 - - - -
307C HIS* 2.8 57.4 + - + -
314C HIS 4.9 0.7 - - - -
315C ASP* 3.3 39.1 + - - +
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Residues in contact with PHE 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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300C MSE 3.0 12.4 + - - +
301C SER* 3.0 14.0 + - - +
303C ARG* 1.3 77.2 - - - +
305C GLU* 1.3 66.4 + - + +
307C HIS* 3.4 6.2 + - + +
308C ALA* 3.2 35.1 + - + +
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Residues in contact with GLU 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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301C SER 2.8 16.1 + - - +
302C LYS* 3.4 43.9 + - - +
304C PHE* 1.3 80.0 - - + +
306C LEU* 1.3 62.7 + - - +
308C ALA* 3.1 4.6 + - - -
309C GLU* 3.0 66.7 + - - +
310C HIS* 5.6 1.0 - - - -
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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
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240C VAL* 3.4 32.8 - - + -
302C LYS* 2.8 34.9 + - + +
303C ARG 4.0 0.7 - - - +
305C GLU* 1.3 79.4 - - - +
307C HIS* 1.3 60.4 + - - +
308C ALA 3.4 0.7 + - - -
310C HIS* 3.5 55.9 + - + +
313C GLU 3.8 5.3 - - - +
314C HIS* 3.3 21.5 - - - +
316C GLU 3.7 24.7 - - - +
317C MSE 3.8 15.9 - - + -
318C PRO* 6.1 1.1 - - + -
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Residues in contact with HIS 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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303C ARG* 2.8 65.3 + - + +
304C PHE* 3.8 8.5 - - + +
305C GLU 3.3 0.2 - - - -
306C LEU* 1.3 75.9 - - - +
308C ALA* 1.3 57.8 + - + +
310C HIS 4.5 3.6 - - - +
314C HIS* 3.4 50.6 + + + +
315C ASP* 3.8 7.0 + - - -
551C CL 3.9 22.7 - - + -
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Residues in contact with ALA 308 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304C PHE* 3.2 30.8 + - + +
305C GLU* 3.1 5.4 + - - +
307C HIS* 1.3 79.8 - - - +
309C GLU* 1.3 64.1 + - + +
310C HIS 3.6 1.8 - - - -
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Residues in contact with GLU 309 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305C GLU* 3.0 49.9 + - - +
308C ALA* 1.3 83.5 - - + +
310C HIS* 1.3 79.5 + - + +
311C LYS* 4.5 3.3 + - - -
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Residues in contact with HIS 310 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305C GLU* 5.6 0.9 - - - -
306C LEU* 3.5 43.1 + - + +
307C HIS 4.5 4.0 - - - +
308C ALA 3.6 1.1 - - - -
309C GLU* 1.3 98.3 + - + +
311C LYS* 1.3 87.5 + - + +
312C LYS 3.6 0.4 + - - -
313C GLU* 3.3 25.0 + - + +
314C HIS* 3.8 13.7 + - - -
316C GLU 5.8 0.4 - - - -
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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