Contacts of the helix formed by residues 286 - 304 (chain C) in PDB entry 5Y3R
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 LEU 286 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243C GLN* 5.0 6.5 - - + +
246C ARG* 3.2 46.7 - - - +
283C SER* 2.4 25.9 + - - +
285C CYS* 1.3 83.1 - - + +
287C LEU* 1.3 49.9 + - - -
288C ASP* 3.6 4.7 - - - -
289C ASN* 3.1 23.5 - - + +
290C TYR* 2.5 34.3 + - + -
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Residues in contact with LEU 287 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283C SER* 2.1 29.4 + - - +
284C THR* 4.1 11.0 + - - +
285C CYS 3.4 3.2 + - - -
286C LEU* 1.3 66.5 - - - +
288C ASP* 1.3 60.8 + - - +
290C TYR* 2.1 57.1 + - + -
291C VAL* 2.7 29.5 + - + +
323C VAL* 3.8 28.9 - - + -
334C HIS* 4.9 12.3 - - + -
337C LYS 5.4 1.6 - - - +
341C PHE* 3.6 35.0 - - + -
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Residues in contact with ASP 288 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285C CYS 4.8 3.7 - - - +
286C LEU 3.8 6.6 - - - +
287C LEU* 1.3 76.8 - - - +
289C ASN* 1.3 82.1 + - - +
291C VAL* 3.4 17.7 - - - +
292C SER* 3.9 6.2 + - - -
337C LYS* 4.2 23.9 - - + +
340C TYR* 4.3 33.8 - - + -
341C PHE 5.7 0.7 - - - +
344C GLN* 4.1 4.6 + - - -
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Residues in contact with ASN 289 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286C LEU* 3.1 26.8 + - + +
287C LEU 2.8 3.1 - - - -
288C ASP* 1.3 82.9 + - - +
290C TYR* 1.3 64.6 + - - +
292C SER* 3.1 24.2 + - - -
293C LEU* 3.8 19.1 + - - +
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Residues in contact with TYR 290 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246C ARG* 6.0 5.4 - - + +
250C ASN* 5.4 4.5 - - - -
272C LEU* 4.9 14.0 - - - +
282C PHE* 5.9 6.1 - + - -
283C SER* 3.9 22.7 - - - +
286C LEU* 2.5 21.8 + - + +
287C LEU* 2.1 36.1 + - + +
289C ASN* 1.3 69.8 - - - +
291C VAL* 1.3 58.3 + - - +
292C SER 2.6 0.5 + - - -
293C LEU* 2.1 62.3 + - + -
294C PHE* 2.8 62.0 + + + -
297C LEU* 5.9 1.3 - - + +
319C PHE* 5.2 10.8 - + + +
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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
----------------------------------------------------------
287C LEU* 2.7 28.3 + - + +
288C ASP* 3.4 13.2 - - - +
290C TYR* 1.3 71.4 - - - +
292C SER* 1.3 66.5 + - - +
294C PHE* 3.0 17.7 - - + +
295C GLU* 2.9 25.2 + - - +
341C PHE* 3.3 40.4 - - + -
344C GLN* 3.3 42.8 - - + +
345C PHE* 4.9 2.5 - - + +
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Residues in contact with SER 292 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288C ASP 3.9 3.8 + - - -
289C ASN* 3.1 17.7 + - - -
290C TYR 2.6 2.6 + - - -
291C VAL* 1.3 81.5 - - - +
293C LEU* 1.3 66.6 + - - -
295C GLU* 3.0 13.9 - - - +
296C VAL* 2.8 28.0 + - - +
344C GLN* 3.3 13.7 + - - +
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Residues in contact with LEU 293 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246C ARG* 5.6 6.3 - - + -
250C ASN* 4.5 29.2 - - + +
253C LEU* 5.6 3.6 - - + +
289C ASN* 4.3 20.6 - - - +
290C TYR* 2.1 48.9 + - + +
292C SER* 1.3 75.8 - - - +
294C PHE* 1.3 64.2 + - - +
296C VAL* 2.9 15.1 + - + +
297C LEU* 2.8 22.0 + - - +
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Residues in contact with PHE 294 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290C TYR* 2.8 51.9 + + + -
291C VAL* 3.0 29.6 - - + +
293C LEU* 1.3 80.8 - - - +
295C GLU* 1.3 73.2 + - + +
297C LEU* 3.0 5.2 + - - +
298C LEU* 2.9 43.2 + - + +
315C ALA* 4.1 4.0 - - + -
316C LEU* 3.2 48.7 - - + -
319C PHE* 4.2 6.5 - + + -
320C LEU* 3.9 20.6 - - + -
323C VAL* 6.0 0.2 - - + -
341C PHE* 4.5 13.9 - + - -
345C PHE* 6.4 3.8 - + + -
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Residues in contact with GLU 295 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291C VAL* 2.9 16.8 + - + +
292C SER* 3.0 19.1 - - - +
294C PHE* 1.3 81.0 - - + +
296C VAL* 1.3 56.4 + - + +
298C LEU* 3.4 21.8 - - + -
299C LYS* 2.7 54.1 + - + +
344C GLN* 3.6 32.7 + - - +
345C PHE* 4.6 0.9 + - - -
348C ILE* 3.2 31.9 - - + +
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Residues in contact with VAL 296 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253C LEU* 4.9 14.1 - - + -
292C SER* 2.8 28.1 + - - +
293C LEU* 2.9 19.5 + - + +
295C GLU* 1.3 78.3 - - + +
297C LEU* 1.3 58.1 + - - +
299C LYS* 3.1 18.3 - - - +
300C TRP* 2.8 29.3 + - + +
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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
----------------------------------------------------------
249C PHE* 4.1 26.5 - - + +
250C ASN* 5.6 1.3 - - - +
252C VAL* 4.5 2.0 - - + -
253C LEU* 3.5 27.6 - - + +
268C PRO* 5.0 4.3 - - + -
272C LEU* 4.5 19.3 - - + -
290C TYR* 5.9 0.7 - - - +
293C LEU 2.8 9.8 + - - +
294C PHE* 3.6 8.1 - - - +
296C VAL* 1.3 75.9 - - - +
298C LEU* 1.3 72.6 + - + +
300C TRP* 2.9 49.4 - - + +
301C CYS* 2.9 9.8 + - + +
312C ALA* 5.2 13.4 - - + +
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Residues in contact with LEU 298 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294C PHE* 2.9 34.5 + - + +
295C GLU* 3.3 24.0 - - + +
297C LEU* 1.3 79.5 - - + +
299C LYS* 1.3 59.1 + - + +
302C ALA* 2.5 41.9 + - + +
312C ALA* 4.1 14.9 - - + +
316C LEU* 3.5 57.7 - - + +
345C PHE* 6.2 3.6 - - + -
363C ILE* 5.8 5.2 - - + -
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Residues in contact with LYS 299 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295C GLU* 2.7 61.2 + - + +
296C VAL* 3.0 21.8 - - - +
298C LEU* 1.3 75.0 - - + +
300C TRP* 1.3 66.7 + - - +
302C ALA* 4.2 0.4 - - - -
303C HIS* 2.8 49.6 + - + +
348C ILE* 6.5 2.0 - - + -
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Residues in contact with TRP 300 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252C VAL* 3.0 39.0 - - + -
253C LEU* 2.8 43.5 + - + -
254C LYS* 4.6 0.6 - - - +
265C TYR* 3.2 42.0 + + - -
268C PRO* 4.0 12.8 - - + -
296C VAL* 2.8 22.5 + - + +
297C LEU* 2.9 45.4 + - + +
299C LYS* 1.3 75.0 - - - +
301C CYS* 1.3 78.4 + - + +
303C HIS* 3.6 0.3 - - - +
304C THR* 2.1 47.0 + - - -
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Residues in contact with CYS 301 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265C TYR* 3.4 25.8 - - + -
297C LEU* 2.9 6.4 + - + +
300C TRP* 1.3 100.4 - - + +
302C ALA* 1.3 61.9 + - - +
304C THR* 2.6 35.4 - - - +
306C VAL* 3.6 9.2 - - - -
308C LEU 3.3 26.0 - - - -
309C LYS* 3.1 5.1 + - - +
311C ALA* 6.4 0.7 - - - -
312C ALA* 4.8 10.1 - - + -
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Residues in contact with ALA 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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298C LEU* 2.5 27.1 + - + +
299C LYS* 4.1 2.9 - - - +
301C CYS* 1.3 75.5 - - - +
303C HIS* 1.3 59.3 + - + +
309C LYS* 2.3 42.6 + - - +
312C ALA* 4.6 12.9 - - + +
313C LEU* 5.4 8.3 - - + -
360C SER* 5.3 8.7 - - - +
363C ILE* 5.7 3.8 - - + -
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Residues in contact with HIS 303 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299C LYS* 2.8 55.0 + - + +
300C TRP 4.1 0.2 - - - +
302C ALA* 1.3 77.8 - - + +
304C THR* 1.3 66.1 + - - +
305C ASN* 3.0 6.6 + - - +
309C LYS* 3.8 1.4 + - - -
357C LYS* 6.2 5.8 - - + -
360C SER* 5.9 2.9 - - - -
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Residues in contact with THR 304 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265C TYR* 3.1 29.4 + - + +
300C TRP* 2.1 42.8 + - - -
301C CYS* 2.6 19.5 + - - +
303C HIS* 1.3 71.1 - - - +
305C ASN* 1.3 60.1 + - - +
306C VAL* 3.0 20.8 + - + +
309C LYS* 2.1 26.7 + - - -
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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