Contacts of the helix formed by residues 288 - 299 (chain C) in PDB entry 3C6Q
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 ASN 288 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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283C VAL* 3.2 23.0 + - - +
284C VAL* 3.5 6.4 - - - +
285C THR* 2.6 43.1 + - - +
287C GLU* 1.3 76.8 - - + +
289C LEU* 1.3 64.3 + - - +
290C ASP 3.4 2.2 - - - -
291C GLU* 3.4 13.7 + - + +
292C TYR* 3.2 20.8 + - - +
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Residues in contact with LEU 289 (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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222C LEU* 4.2 28.0 - - + +
225C VAL* 4.3 11.0 - - + -
226C LYS* 4.1 38.8 - - + +
284C VAL* 3.9 20.4 - - + -
285C THR 2.9 12.9 + - - +
286C PRO* 4.0 12.3 - - + +
287C GLU 3.3 3.2 - - - -
288C ASN* 1.3 78.9 - - - +
290C ASP* 1.3 69.4 + - - +
292C TYR* 2.9 27.5 + - + +
293C LEU* 3.2 23.3 + - + +
305C PHE* 5.7 5.2 - - + -
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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
----------------------------------------------------------
226C LYS* 5.6 5.7 + - - -
286C PRO 5.2 1.9 - - - +
287C GLU 4.6 4.1 + - - +
288C ASN 3.4 0.4 - - - -
289C LEU* 1.3 88.6 - - - +
291C GLU* 1.3 63.2 + - - +
292C TYR 3.3 0.3 + - - -
293C LEU* 3.6 15.4 + - - +
294C LYS* 3.4 20.1 + - - +
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Residues in contact with GLU 291 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287C GLU 5.5 0.2 + - - -
288C ASN* 3.4 16.2 + - + +
289C LEU 3.2 0.6 - - - -
290C ASP* 1.3 79.6 - - - +
292C TYR* 1.3 57.9 + - - +
294C LYS* 3.8 28.3 + - - +
295C LYS* 3.3 22.9 + - - +
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Residues in contact with TYR 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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217C THR* 3.0 39.9 + - + +
222C LEU* 5.0 4.0 - - + -
235C GLY* 4.9 0.6 - - - -
236C GLN 4.7 5.4 + - - -
282C ASP* 3.6 31.5 + - + -
283C VAL 5.6 1.1 - - - -
284C VAL* 3.6 32.8 - - + -
288C ASN* 3.2 14.0 + - - +
289C LEU* 2.9 16.3 + - + +
291C GLU* 1.3 76.4 - - - +
293C LEU* 1.3 81.4 + - + +
294C LYS 3.1 1.3 - - - -
295C LYS* 2.9 21.3 + - + +
296C MET* 2.9 46.6 + - + +
303C ILE* 4.5 8.4 - - + +
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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
----------------------------------------------------------
222C LEU* 4.3 17.3 - - + -
289C LEU* 3.2 29.4 + - + +
290C ASP* 3.6 19.0 + - - +
292C TYR* 1.3 84.2 - - + +
294C LYS* 1.3 63.8 + - - +
296C MET* 3.2 9.0 + - - +
297C GLU* 3.2 20.5 + - - +
303C ILE* 4.0 27.3 - - + +
305C PHE* 5.0 15.3 - - + -
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Residues in contact with LYS 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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290C ASP 3.4 14.2 + - - +
291C GLU* 3.8 30.9 + - - +
292C TYR 3.1 0.2 - - - -
293C LEU* 1.3 78.7 - - - +
295C LYS* 1.3 64.3 + - - +
297C GLU* 3.1 19.3 + - - +
298C GLU* 3.1 33.9 + - - +
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Residues in contact with LYS 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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237C ARG* 4.2 10.8 - - - +
282C ASP* 3.8 23.6 - - - +
291C GLU 3.3 13.6 + - - +
292C TYR* 2.9 16.0 + - + +
294C LYS* 1.3 80.0 - - - +
296C MET* 1.3 65.3 + - + +
297C GLU 3.3 0.2 + - - -
298C GLU* 3.3 8.6 + - - +
299C LEU* 3.0 35.0 + - + +
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Residues in contact with MET 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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236C GLN 5.8 1.3 - - - +
237C ARG* 3.9 25.1 - - - +
282C ASP* 4.1 2.5 - - - +
292C TYR* 2.9 50.5 + - + +
293C LEU* 3.5 8.7 - - - +
295C LYS* 1.3 96.7 - - + +
297C GLU* 1.3 59.1 + - - +
299C LEU* 3.4 5.4 + - + +
300C GLY 3.3 2.6 + - - -
301C ILE* 2.9 63.2 + - + +
303C ILE* 3.6 31.2 - - + -
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Residues in contact with GLU 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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293C LEU 3.2 10.3 + - - +
294C LYS* 3.1 13.7 + - + +
296C MET* 1.3 72.5 - - - +
298C GLU* 1.3 66.2 + - - +
299C LEU 3.0 4.5 - - - -
300C GLY* 2.8 21.9 + - - -
301C ILE 4.6 3.6 - - - +
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Residues in contact with GLU 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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258B GLN* 5.0 5.4 - - - +
294C LYS* 3.1 44.0 + - - +
295C LYS* 3.3 9.4 + - - +
297C GLU* 1.3 84.3 - - - +
299C LEU* 1.3 63.6 - - + +
300C GLY 3.4 0.4 - - - -
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Residues in contact with LEU 299 (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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258B GLN* 3.6 46.1 + - - +
259B ASN* 4.8 5.5 - - - +
262B MET* 5.2 7.6 - - + -
237C ARG* 4.1 27.4 - - - +
240C MET* 5.4 4.3 - - + +
295C LYS* 3.0 24.1 + - + +
296C MET* 3.8 10.3 - - + +
297C GLU 3.0 1.2 - - - -
298C GLU* 1.3 82.1 - - + +
300C GLY* 1.3 61.0 + - - +
301C ILE* 3.5 28.8 + - + +
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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