Contacts of the helix formed by residues 287 - 299 (chain C) in PDB entry 3QN3
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 287 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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246C PHE* 4.5 11.4 - - + -
251C TYR* 2.7 28.1 + - - +
260C SER* 2.5 31.0 + - - -
283C LEU* 3.9 5.6 - - + +
284C ALA* 3.1 19.0 + - + +
285C GLU 3.6 0.2 - - - -
286C ASN* 1.3 74.4 + - - +
288C PHE* 1.3 63.5 + - - +
289C GLU* 4.1 2.1 + - - +
290C GLY* 3.1 17.6 + - - -
291C TRP* 3.1 21.4 + - - -
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Residues in contact with PHE 288 (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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46C LYS* 6.6 0.4 - - - -
285C GLU 3.4 19.7 - - - -
286C ASN* 3.1 32.7 + - + -
287C ASP* 1.3 72.5 - - - +
289C GLU* 1.3 71.9 + - + +
291C TRP* 3.2 5.7 + - - +
292C ILE* 3.1 25.6 + - - +
309C LEU* 4.5 11.0 - - + -
316C ILE* 6.6 0.2 - - + -
325C MET* 3.5 34.9 - - + +
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Residues in contact with GLU 289 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287C ASP* 3.3 2.2 + - - +
288C PHE* 1.3 83.8 - - + +
290C GLY* 1.3 63.8 + - - +
292C ILE* 3.3 23.9 + - - +
293C LYS* 3.1 36.2 + - - +
325C MET* 5.5 0.2 - - - +
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Residues in contact with GLY 290 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260C SER* 4.3 10.8 - - - -
261C GLU* 5.9 0.4 - - - -
264C ILE* 3.7 1.8 - - - +
283C LEU* 3.2 21.5 - - - +
287C ASP* 3.1 20.9 + - - -
289C GLU* 1.3 78.4 - - - +
291C TRP* 1.4 51.5 + - - +
293C LYS* 3.1 10.8 + - - +
294C LEU 2.7 31.4 + - - -
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Residues in contact with TRP 291 (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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279C ILE 5.4 0.9 - - - -
281C ASP* 3.8 23.3 - - - -
282C GLY 4.2 4.0 - - - -
283C LEU* 3.2 33.2 + - + +
284C ALA 3.0 24.7 + - - -
287C ASP 3.1 27.1 + - - -
288C PHE* 3.6 7.4 - - - +
290C GLY* 1.4 73.9 - - - +
292C ILE* 1.3 54.7 + - - +
294C LEU* 3.6 20.8 - - + +
295C THR* 2.7 40.1 + - - -
304C LEU* 4.5 8.7 - - + -
305C VAL 3.6 23.1 - - - -
306C GLY* 4.2 0.2 - - - -
309C LEU* 3.6 39.9 - - + +
325C MET* 4.0 16.2 - - + -
326C ALA* 3.9 30.7 - - + -
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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
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288C PHE 3.1 15.8 + - - +
289C GLU* 3.6 29.6 - - - +
291C TRP* 1.3 75.4 - - - +
293C LYS* 1.3 59.2 + - + +
295C THR* 3.6 2.1 + - - -
296C GLU* 3.1 45.8 + - + +
323C LYS* 3.4 31.6 - - + +
324C LYS* 4.0 12.5 - - + +
325C MET* 3.8 16.8 - - + -
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Residues in contact with LYS 293 (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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261C GLU* 2.5 42.6 + - + +
264C ILE* 3.8 12.8 - - + -
289C GLU* 3.1 23.0 + - - +
290C GLY* 3.1 9.7 + - - +
292C ILE* 1.3 76.0 - - + +
294C LEU* 1.3 58.9 + - - +
296C GLU* 3.2 18.7 + - - +
297C LYS* 2.9 29.9 + - - +
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Residues in contact with LEU 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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264C ILE* 3.6 20.1 - - + +
267C TYR* 4.1 17.0 - - + -
279C ILE* 6.3 0.2 - - + -
282C GLY* 4.6 8.5 - - - -
283C LEU* 3.9 31.0 - - + +
290C GLY 2.7 19.3 + - - +
291C TRP* 3.6 29.6 - - + +
293C LYS* 1.3 72.4 - - - +
295C THR* 1.3 59.1 + - - +
297C LYS* 3.2 0.5 + - - -
298C LEU* 2.9 54.1 + - + -
304C LEU* 3.7 24.5 - - + +
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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
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291C TRP* 2.7 23.9 + - - -
292C ILE 3.9 0.7 - - - -
294C LEU* 1.3 77.2 - - - +
296C GLU* 1.3 58.1 + - - +
299C GLY* 2.9 33.1 + - - -
300C ASN* 4.6 0.9 + - - -
304C LEU* 3.7 12.8 - - + +
324C LYS* 3.4 24.2 - - + +
325C MET 3.6 0.2 - - - -
326C ALA* 2.7 44.3 + - - +
327C ASN* 4.9 2.7 - - + +
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Residues in contact with GLU 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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292C ILE* 3.1 32.8 + - + +
293C LYS* 3.2 24.2 + - - +
295C THR* 1.3 74.6 - - - +
297C LYS* 1.3 60.9 + - - +
299C GLY 4.6 0.7 + - - -
300C ASN* 4.8 10.7 + - - -
324C LYS* 6.5 0.9 - - + -
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Residues in contact with LYS 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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264C ILE* 3.9 16.4 - - + -
265C GLU* 3.2 26.2 + - - +
268C VAL* 3.7 26.9 - - + -
293C LYS 2.9 16.6 + - - +
294C LEU 3.7 3.6 - - - +
296C GLU* 1.3 80.8 - - - +
298C LEU* 1.3 64.3 + - + +
300C ASN* 6.1 0.6 - - - +
301C LYS* 5.4 5.4 - - - +
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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
----------------------------------------------------------
264C ILE* 4.4 2.2 - - + +
267C TYR* 3.8 24.9 - - + +
268C VAL* 4.1 31.4 - - + +
271C CYS* 4.9 10.8 - - + -
279C ILE* 5.1 0.2 - - + -
294C LEU* 2.9 36.9 + - + +
297C LYS* 1.3 83.4 - - + +
299C GLY* 1.3 57.9 + - - +
300C ASN* 3.2 5.4 - - - -
301C LYS* 2.9 33.3 + - + +
302C ILE* 2.9 36.8 + - + +
304C LEU* 4.2 6.5 - - + -
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Residues in contact with GLY 299 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295C THR* 2.9 25.7 + - - -
296C GLU 4.6 0.4 + - - -
297C LYS 3.8 0.4 - - - -
298C LEU* 1.3 75.3 - - - +
300C ASN* 1.3 61.1 + - - +
301C LYS 3.3 0.7 - - - -
302C ILE 4.0 1.9 - - - +
304C LEU* 3.7 10.5 - - - +
327C ASN* 2.9 33.5 + - - +
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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
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Atomic class I II III IV V VI VII VIII
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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