Contacts of the helix formed by residues 282 - 295 (chain C) in PDB entry 2HYE
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 THR 282 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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227C TYR* 3.0 23.2 + - - +
232C GLU* 2.8 28.9 + - - +
235C PHE* 3.7 30.7 - - + -
236C LEU* 4.5 4.7 - - + -
278C LEU* 4.0 13.9 - - + -
279C ASP 2.8 13.8 + - - -
281C SER* 1.3 72.9 + - - +
283C GLN* 1.3 67.0 + - - +
285C PRO* 2.8 20.9 - - + +
286C LEU* 2.9 18.4 + - + -
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Residues in contact with GLN 283 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271C GLY* 4.2 10.7 + - - -
274C VAL* 3.0 52.4 - - + +
275C ILE* 5.1 2.4 - - - +
279C ASP 3.8 2.8 + - - -
280C HIS* 3.8 11.9 + - - +
281C SER 3.2 0.6 + - - -
282C THR* 1.3 76.9 - - - +
284C LYS* 1.3 62.3 + - - +
286C LEU* 4.6 2.7 - - - -
287C ILE* 3.1 45.2 + - + +
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Residues in contact with LYS 284 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
859A GLN* 5.3 7.7 + - - +
860A THR* 2.8 33.1 + - - +
861A VAL* 4.1 7.5 + - - +
280C HIS 4.8 0.4 + - - -
281C SER 3.4 7.0 + - - +
282C THR 2.8 4.6 + - - -
283C GLN* 1.3 76.2 - - - +
285C PRO* 1.3 77.3 - - + +
287C ILE* 4.2 1.7 - - - +
288C ALA* 3.2 21.6 + - + +
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Residues in contact with PRO 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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228C LYS* 5.1 13.0 - - - +
232C GLU* 5.5 0.2 - - - +
236C LEU* 4.0 23.8 - - + -
281C SER* 3.3 12.1 - - - +
282C THR* 2.8 20.4 - - - +
284C LYS* 1.3 92.6 - - + +
286C LEU* 1.3 66.5 + - - +
288C ALA* 3.2 8.0 + - + +
289C CYS* 3.0 26.0 + - - -
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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
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204C ARG* 3.7 13.0 - - - +
235C PHE* 3.8 10.5 - - + -
236C LEU* 4.1 10.4 - - + +
239C THR* 3.7 17.5 - - + +
270C GLU* 3.1 56.3 - - + +
274C VAL* 4.3 7.9 - - + -
278C LEU* 4.1 22.2 - - + -
282C THR* 2.9 22.8 + - + +
283C GLN* 4.1 1.3 - - - +
285C PRO* 1.3 76.5 - - - +
287C ILE* 1.3 68.7 + - + +
289C CYS* 2.8 17.9 + - - +
290C VAL* 3.0 12.5 + - + +
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Residues in contact with ILE 287 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267C LEU* 4.6 22.7 - - + +
270C GLU* 5.0 12.6 - - + +
271C GLY* 4.9 5.6 - - - -
283C GLN* 3.1 37.5 + - + +
284C LYS* 4.3 1.8 - - - +
286C LEU* 1.3 84.3 - - + +
288C ALA* 1.3 63.9 + - - +
290C VAL* 3.3 6.4 + - - +
291C GLU* 2.8 46.8 + - + +
328C ARG* 4.8 12.1 - - - +
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Residues in contact with ALA 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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284C LYS* 3.2 13.8 + - + +
285C PRO* 3.2 11.1 + - + +
286C LEU 3.1 0.8 - - - -
287C ILE* 1.3 76.3 - - - +
289C CYS* 1.3 58.5 + - - +
291C GLU* 3.3 13.0 + - - +
292C LYS* 2.8 33.3 + - - +
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Residues in contact with CYS 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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236C LEU* 4.8 14.8 - - + -
239C THR* 5.3 5.8 - - + -
240C ASN* 2.7 48.2 - - - +
243C TYR* 6.0 0.2 - - - -
285C PRO* 3.0 29.7 + - - -
286C LEU* 2.8 11.3 + - - +
288C ALA* 1.3 75.5 - - - +
290C VAL* 1.3 64.9 + - - +
292C LYS* 2.9 24.8 + - - +
293C GLN* 3.4 7.1 + - - +
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Residues in contact with VAL 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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239C THR* 4.7 4.7 - - + +
243C TYR* 3.5 44.9 - - + -
263C VAL* 5.9 0.4 - - + -
266C ARG* 5.0 2.7 - - + -
267C LEU* 3.1 34.3 - - + -
270C GLU* 4.0 16.4 - - + -
286C LEU* 3.0 12.6 + - + +
287C ILE* 3.7 7.2 - - - +
289C CYS* 1.3 74.7 - - - +
291C GLU* 1.3 63.5 + - - +
293C GLN* 3.2 4.6 + - - +
294C LEU* 3.1 40.4 + - + +
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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
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263C VAL* 6.5 0.2 - - - -
267C LEU* 4.3 14.8 - - + -
287C ILE* 2.8 43.3 + - + +
288C ALA* 3.6 10.0 - - - +
290C VAL* 1.3 73.7 - - - +
292C LYS* 1.3 58.9 + - - +
293C GLN 2.9 6.2 + - - -
294C LEU* 5.2 0.4 - - - -
295C LEU* 3.0 30.8 + - + +
296C GLY* 3.0 7.6 + - - -
328C ARG* 3.1 52.8 + - + +
329C VAL* 5.4 10.9 - - + -
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Residues in contact with LYS 292 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240C ASN* 5.3 7.2 + - - +
288C ALA 2.8 21.2 + - - +
289C CYS* 2.9 5.4 + - - +
291C GLU* 1.3 71.0 - - + +
293C GLN* 1.3 92.2 + - - +
296C GLY* 3.6 13.2 - - - +
297C GLU* 3.7 26.0 + - + +
329C VAL* 5.9 1.1 - - - -
330C ARG* 3.1 45.5 - - - +
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Residues in contact with GLN 293 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240C ASN* 3.8 25.9 + - - +
243C TYR* 3.8 24.5 - - + +
244C ALA* 2.9 37.7 - - - +
247C GLY* 4.1 3.1 - - - -
289C CYS 3.5 12.8 - - - +
290C VAL 3.7 3.1 - - - +
291C GLU 2.9 1.2 + - - -
292C LYS* 1.3 103.9 + - - +
294C LEU* 1.3 71.6 + - - +
295C LEU 3.6 0.7 - - - -
296C GLY 3.4 8.6 + - - -
297C GLU* 4.3 12.3 + - - +
298C HIS* 4.1 14.0 + - - -
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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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243C TYR* 3.9 46.7 - - + +
246C GLU* 4.3 14.6 - - + +
247C GLY 4.4 1.8 - - - +
250C LEU* 6.2 0.4 - - + -
259C TYR* 3.3 31.8 + - + +
262C HIS* 4.9 2.2 - - + -
263C VAL* 3.8 32.8 - - + +
266C ARG* 4.2 15.9 - - + -
290C VAL* 3.1 27.7 + - + +
291C GLU* 5.2 0.2 - - - -
293C GLN* 1.3 91.4 - - - +
295C LEU* 1.3 70.3 + - + +
298C HIS* 4.2 4.4 - - - -
302C ILE* 4.1 3.5 - - - +
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Residues in contact with LEU 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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260C LEU* 4.7 9.6 - - + -
263C VAL* 3.7 24.2 - - + -
267C LEU* 5.5 2.9 - - + -
291C GLU* 3.0 16.1 + - + +
294C LEU* 1.3 102.9 - - + +
296C GLY* 1.3 68.5 + - - +
298C HIS 2.7 29.1 + - - +
299C LEU* 3.5 10.4 - - + +
302C ILE* 4.6 10.1 - - + -
325C LEU* 3.6 42.6 - - + +
326C PHE* 4.4 5.8 - - + +
328C ARG* 5.4 3.8 - - + -
329C VAL* 3.5 25.4 - - + -
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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