Contacts of the helix formed by residues 282 - 290 (chain C) in PDB entry 6UZA
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 SER 282 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227C ALA* 3.2 28.2 + - - +
228C HIS* 5.5 0.2 - - - -
230C GLN* 3.5 13.0 - - - -
278C LYS 4.1 7.6 - - - -
279C GLY 3.5 13.7 + - - -
280C LEU 3.3 1.6 - - - -
281C ALA* 1.3 78.7 - - - +
283C PRO* 1.3 62.4 - - - +
284C ALA 3.8 1.8 + - - -
285C TYR* 3.5 14.9 + - - +
286C LEU* 2.9 31.6 + - - +
324C GLN* 3.9 2.9 - - - +
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Residues in contact with PRO 283 (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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230C GLN* 3.4 24.9 - - - +
232C TYR* 3.8 14.4 - - - +
281C ALA 4.4 2.7 - - - +
282C SER* 1.3 83.7 - - - +
284C ALA* 1.3 50.5 + - - +
286C LEU* 4.2 3.4 - - + -
287C SER* 2.3 40.8 + - - -
324C GLN* 4.9 12.1 - - + +
328C PHE* 4.0 22.2 - - + -
866C TYR* 3.7 24.9 - - + +
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Residues in contact with ALA 284 (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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227C ALA 4.9 1.6 - - - +
230C GLN* 3.8 33.6 + - - +
231C GLU 4.5 0.9 - - - +
232C TYR* 3.7 25.7 + - + -
235C VAL* 3.4 21.2 - - + +
282C SER* 3.3 5.7 + - - +
283C PRO* 1.3 80.1 - - - +
285C TYR* 1.3 58.9 + - - +
288C LEU* 3.3 30.0 + - - +
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Residues in contact with TYR 285 (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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223C ILE* 4.3 13.9 - - + -
227C ALA* 4.2 6.5 - - + -
235C VAL* 4.6 7.0 - - + -
239C LEU* 4.1 16.2 - - + -
244C ARG* 3.7 15.6 - - - +
245C ILE* 3.1 46.0 + - + +
279C GLY 3.8 11.0 - - - +
280C LEU* 3.7 37.4 - - + +
282C SER* 3.3 17.0 + - - +
283C PRO 3.2 0.2 - - - -
284C ALA* 1.3 79.2 - - - +
286C LEU* 1.3 58.8 + - + +
287C SER 3.3 0.4 - - - -
289C SER* 2.7 64.4 + - - -
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Residues in contact with LEU 286 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280C LEU 3.8 17.5 - - - +
281C ALA 4.5 3.8 - - - +
282C SER 2.9 25.1 + - - +
283C PRO* 4.2 4.0 - - + +
285C TYR* 1.3 78.7 - - + +
287C SER* 1.3 62.2 + - - +
289C SER* 4.4 2.9 - - - +
290C SER* 3.2 23.4 + - - -
293C PRO* 3.3 10.5 - - + +
296C THR* 4.0 28.7 - - + -
297C ALA* 4.1 25.1 - - + +
300C LEU* 4.2 8.5 - - + -
325C CYS* 4.4 19.7 - - - -
328C PHE* 4.2 24.2 - - + -
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Residues in contact with SER 287 (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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232C TYR* 3.8 15.9 - - - -
283C PRO 2.3 26.7 + - - -
284C ALA 4.0 1.9 + - - -
286C LEU* 1.3 78.1 - - - +
288C LEU* 1.3 62.3 + - - +
290C SER 4.5 3.7 - - - +
293C PRO* 4.5 3.8 - - - +
328C PHE* 4.0 20.2 - - - -
863C ILE* 3.4 40.3 - - - +
866C TYR* 4.3 11.9 - - - -
867C VAL* 4.4 4.8 - - - +
88D PHE* 4.3 2.3 - - - +
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Residues in contact with LEU 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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232C TYR* 3.6 38.1 - - + +
235C VAL* 3.8 9.9 - - + -
236C HIS* 4.2 19.1 - - + +
239C LEU* 3.8 16.3 - - + +
284C ALA 3.3 20.3 + - - +
285C TYR 3.6 1.6 + - - -
287C SER* 1.3 83.6 + - - +
289C SER* 1.3 62.2 + - - +
290C SER 3.5 2.8 + - - +
867C VAL* 4.3 13.9 - - + -
87D MET* 3.6 7.8 - - - +
88D PHE* 3.4 54.8 + - + +
132D MET* 5.2 4.3 - - + -
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Residues in contact with SER 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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239C LEU* 4.1 11.0 - - - -
244C ARG* 3.5 9.7 + - - +
285C TYR* 2.7 61.7 + - - -
286C LEU* 4.4 2.9 - - - +
287C SER 3.7 0.2 - - - -
288C LEU* 1.3 78.6 - - - +
290C SER* 1.3 65.3 + - - +
86D TYR* 3.1 21.7 + - - +
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Residues in contact with SER 290 (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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286C LEU* 3.2 18.8 + - - -
287C SER 4.5 9.2 - - - +
288C LEU 4.7 0.7 - - - -
289C SER* 1.3 84.5 + - - +
291C GLU* 1.3 62.3 + - - +
292C ASP 4.5 1.3 - - - -
293C PRO* 3.6 20.4 - - - +
296C THR* 4.0 24.0 + - - +
863C ILE* 4.9 2.6 - - - +
86D TYR* 3.3 18.8 - - - -
88D PHE* 6.0 0.5 - - - +
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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