Contacts of the helix formed by residues 269 - 282 (chain C) in PDB entry 5UHG
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 GLY 269 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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239C LYS* 4.3 9.0 - - - +
268C VAL* 1.3 86.6 - - - +
270C THR* 1.3 60.8 + - - -
271C ASP 3.3 2.7 - - - -
272C GLU* 3.4 6.5 + - - -
273C ALA* 3.0 30.5 + - - +
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Residues in contact with THR 270 (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 LYS 3.3 20.9 + - - +
240C ALA 4.4 7.4 - - - +
242C GLY* 4.4 21.9 + - - -
243C TRP 5.6 0.7 + - - -
269C GLY* 1.3 70.2 - - - +
271C ASP* 1.3 66.7 + - - +
273C ALA* 4.0 1.4 - - - +
274C LEU* 3.4 31.2 + - + +
293C GLN* 5.5 2.5 - - - +
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Residues in contact with ASP 271 (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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269C GLY* 3.3 0.6 - - - -
270C THR* 1.3 80.6 - - - +
272C GLU* 1.3 73.4 + - + +
274C LEU* 3.5 9.4 + - - +
275C LEU* 3.1 32.5 + - + +
289C LYS* 3.4 47.2 - - + +
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Residues in contact with GLU 272 (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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267C THR* 4.3 17.7 + - + +
268C VAL 3.5 27.4 - - - +
269C GLY* 3.4 5.5 + - - +
270C THR 3.4 0.4 - - - -
271C ASP* 1.3 87.9 - - + +
273C ALA* 1.3 57.4 + - - +
275C LEU* 4.2 14.4 - - - +
276C ASP* 3.1 27.5 + - - +
279C ARG* 3.8 10.3 + - - +
289C LYS* 6.1 0.2 - - - -
209F SER* 4.5 14.4 + - - -
211F ALA* 4.0 21.7 - - - +
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Residues in contact with ALA 273 (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 VAL* 3.4 28.5 - - + +
239C LYS* 3.7 9.0 - - + +
240C ALA* 3.6 20.0 - - - +
267C THR* 5.2 4.5 - - - +
269C GLY 3.0 17.8 + - - +
270C THR 4.0 0.7 - - - +
271C ASP 3.2 0.2 - - - -
272C GLU* 1.3 75.6 - - - +
274C LEU* 1.3 64.7 + - - +
276C ASP* 3.2 7.1 + - - +
277C ILE* 3.0 28.9 + - - +
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Residues in contact with LEU 274 (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 ALA* 3.3 29.2 - - + +
270C THR* 3.4 26.3 + - + +
271C ASP* 3.9 9.6 - - - +
273C ALA* 1.3 78.6 - - - +
275C LEU* 1.3 58.6 + - + +
277C ILE* 3.4 4.0 + - - +
278C TYR* 2.9 30.8 + - - +
289C LYS* 4.9 6.1 - - - +
292C ALA* 3.6 24.5 - - + +
293C GLN* 3.2 39.5 - - + +
296C LEU* 3.6 28.6 - - + +
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Residues in contact with LEU 275 (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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271C ASP* 3.1 32.6 + - + +
272C GLU* 3.9 19.5 - - - +
274C LEU* 1.3 76.8 - - + +
276C ASP* 1.3 57.2 + - - +
278C TYR* 3.4 5.1 + - - +
279C ARG* 2.9 53.1 + - - +
287C PRO* 4.0 33.2 - - + +
288C THR 4.3 13.2 - - - +
289C LYS* 4.8 6.5 - - + +
292C ALA* 5.0 2.5 - - + -
211F ALA 5.9 0.2 - - - -
212F LEU* 4.0 37.2 - - + +
215F ALA* 5.9 2.0 - - + -
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Residues in contact with ASP 276 (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 GLN* 3.3 29.3 + - - +
236C VAL* 3.5 14.4 - - + +
266C ASN* 6.0 1.4 - - - +
267C THR* 4.8 9.6 + - - +
272C GLU 3.1 19.7 + - - +
273C ALA* 3.2 8.3 + - - +
275C LEU* 1.3 77.1 - - - +
277C ILE* 1.3 62.4 + - - +
279C ARG* 3.3 25.9 + - - +
280C LYS* 3.3 27.9 + - - +
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Residues in contact with ILE 277 (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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226C ILE* 4.5 21.5 - - + -
232C GLN* 4.2 9.9 - - - +
236C VAL* 3.9 20.9 - - + +
237C LEU* 3.9 24.5 - - + -
240C ALA* 3.7 28.9 - - + -
273C ALA 3.0 11.0 + - - +
274C LEU 3.9 3.4 - - - +
276C ASP* 1.3 72.1 - - - +
278C TYR* 1.3 66.4 + - - +
280C LYS* 3.2 5.1 + - - +
281C LEU* 3.0 30.1 + - + +
296C LEU* 4.3 21.8 - - + -
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Residues in contact with TYR 278 (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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274C LEU 2.9 19.1 + - - +
275C LEU* 3.6 5.4 - - - +
277C ILE* 1.3 77.7 - - - +
279C ARG* 1.3 66.3 + - + +
281C LEU* 4.5 4.3 - - - -
282C ARG* 3.1 35.8 + - + +
285C GLU* 3.4 49.1 + - - +
286C PRO 3.4 9.5 + - - -
287C PRO* 3.8 21.3 - - + -
291C SER* 3.3 36.8 + - - -
292C ALA* 3.6 16.8 - - + -
295C LEU* 3.5 31.2 - - + -
296C LEU* 5.4 1.3 - - + +
219F ALA* 5.7 1.3 - - + -
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Residues in contact with ARG 279 (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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267C THR* 5.9 3.2 + - - +
272C GLU* 3.8 14.1 + - - +
275C LEU* 2.9 34.2 + - - +
276C ASP* 3.4 37.3 + - - +
277C ILE 3.2 0.2 - - - -
278C TYR* 1.3 83.8 - - + +
280C LYS* 1.3 66.3 + - + +
282C ARG 5.2 1.6 - - - -
283C PRO* 3.6 22.3 - - - +
287C PRO* 5.0 6.7 - - + -
211F ALA* 4.9 6.5 + - - +
215F ALA* 3.4 43.1 - - + +
218F ASP* 5.8 2.4 + - - -
219F ALA* 5.5 8.3 - - + -
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Residues in contact with LYS 280 (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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229C LYS* 4.3 17.9 - - + +
230C ARG* 5.8 10.5 - - + +
232C GLN* 3.1 35.0 - - + +
276C ASP* 3.3 19.1 - - - +
277C ILE* 3.2 4.6 + - - +
278C TYR 3.1 0.6 - - - -
279C ARG* 1.3 83.2 - - - +
281C LEU* 1.3 65.6 + - - +
283C PRO* 4.1 8.4 - - - +
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Residues in contact with LEU 281 (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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226C ILE* 4.6 19.7 - - + +
227C ASP* 6.1 2.2 - - + -
229C LYS* 3.9 33.2 - - + +
277C ILE* 3.0 27.5 + - + +
278C TYR* 3.2 4.5 + - - +
280C LYS* 1.3 80.1 - - - +
282C ARG* 1.3 81.4 + - + +
283C PRO* 3.4 7.6 - - - +
295C LEU* 3.8 20.0 - - + -
296C LEU* 5.6 0.7 - - + -
299C LEU* 3.6 31.4 - - + -
229F ARG* 5.7 0.2 + - - -
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Residues in contact with ARG 282 (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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278C TYR* 3.1 25.0 + - + +
279C ARG* 4.9 0.7 - - - +
281C LEU* 1.3 100.8 - - + +
283C PRO* 1.3 65.4 - - - +
284C GLY 3.7 1.4 + - - -
285C GLU* 3.4 41.4 + - - +
295C LEU* 4.5 22.6 - - + +
299C LEU* 5.0 5.7 - - - +
305C ARG* 3.2 29.3 - - - +
219F ALA* 5.3 0.9 - - - +
229F ARG* 3.1 37.7 - - - +
9H G 3.4 11.5 + - - -
10H A 4.1 9.3 - - - +
11H G 4.7 5.9 - - - +
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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