Contacts of the helix formed by residues 289 - 298 (chain A) in PDB entry 6HBU
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 289 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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245A PRO 3.0 25.3 + - - +
246A ARG* 3.8 9.0 - - - +
247A TYR* 3.9 21.9 + - + -
250A PHE* 4.4 2.1 - - - +
287A TYR* 3.2 6.8 - - - +
288A ASN* 1.3 77.8 - - + +
290A PRO* 1.3 73.8 - - - +
291A ALA* 3.3 12.1 + - - +
292A ASP* 3.1 38.0 + - + +
293A PHE* 3.2 19.2 + - - +
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Residues in contact with PRO 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247A TYR* 3.6 26.2 - - + -
250A PHE* 3.6 28.5 - - + -
274A LEU* 4.3 25.6 - - + -
284A CYS* 5.2 3.8 - - - -
288A ASN 3.8 4.7 - - - +
289A ASN* 1.3 91.8 - - - +
291A ALA* 1.3 55.6 + - - +
293A PHE* 3.1 7.4 + - + +
294A PHE* 2.9 46.6 + - + -
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Residues in contact with ALA 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A LEU* 5.0 6.7 - - + +
245A PRO* 3.7 37.2 - - + +
250A PHE* 3.8 18.0 - - + -
289A ASN* 3.3 10.8 + - - +
290A PRO* 1.3 78.3 - - - +
292A ASP* 1.3 62.5 + - - +
294A PHE* 3.9 10.1 - - - -
295A LEU* 3.5 28.2 + - - +
218B SER* 4.2 3.7 + - - -
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Residues in contact with ASP 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A GLN* 5.2 1.2 - - - +
245A PRO 4.6 2.4 - - - +
287A TYR* 4.6 10.1 - - + -
289A ASN* 3.1 38.6 + - + +
290A PRO 3.2 0.6 - - - -
291A ALA* 1.3 77.5 - - - +
293A PHE* 1.3 59.9 + - - +
295A LEU 4.3 1.0 - - - -
296A ASP* 2.9 31.9 + - - +
218B SER* 2.8 25.9 + - - -
246B ARG* 3.5 41.8 + - - +
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Residues in contact with PHE 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274A LEU* 4.0 17.0 - - + -
277A PHE* 4.3 9.9 - - + -
282A TYR* 3.6 34.1 - + + -
283A HIS 3.2 27.1 - - - -
284A CYS* 4.1 14.8 - - - -
286A ALA* 6.5 0.2 - - + -
287A TYR* 3.5 35.2 - + + +
289A ASN 3.2 11.3 + - - +
290A PRO* 3.1 10.2 + - + +
292A ASP* 1.3 77.0 - - - +
294A PHE* 1.3 74.7 + + - +
295A LEU 3.3 1.0 + - - -
296A ASP* 3.5 7.7 + - + +
297A ILE* 3.3 36.1 + - + +
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Residues in contact with PHE 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A LEU* 6.2 1.3 - - + -
250A PHE* 3.5 30.5 - + - -
256A LEU* 3.7 24.2 - - + -
258A LEU* 4.3 13.9 - - + +
273A ALA* 3.6 6.7 - - + -
274A LEU* 3.6 48.9 - - + -
277A PHE* 3.7 29.5 - + - -
290A PRO* 2.9 22.9 + - + +
291A ALA* 3.8 2.9 + - - +
292A ASP 3.5 0.2 - - - -
293A PHE* 1.3 84.6 - + - +
295A LEU* 1.3 72.3 + - + +
296A ASP 3.4 0.2 - - - -
297A ILE* 3.7 5.5 + - - +
298A ILE* 3.4 30.0 + - - +
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Residues in contact with LEU 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A LEU* 3.7 37.7 - - + -
80A GLY 3.6 22.2 - - - +
81A PRO* 4.9 0.4 - - + -
243A HIS* 5.4 0.4 - - - +
244A GLN 6.1 0.7 - - - +
258A LEU* 4.2 4.0 - - + -
291A ALA* 3.5 21.3 + - - +
292A ASP 4.2 0.4 + - - +
293A PHE 3.3 0.2 - - - -
294A PHE* 1.3 87.3 - - + +
296A ASP* 1.3 62.4 + - - +
297A ILE 3.4 0.7 - - - -
298A ILE* 3.9 15.0 - - + -
299A ASN* 3.2 24.1 - - - +
217B ASP* 3.5 37.2 - - + +
218B SER* 4.4 13.5 - - - +
219B SER* 3.3 7.7 - - - -
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Residues in contact with ASP 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287A TYR* 3.1 40.3 + - + +
292A ASP 2.9 21.6 + - - +
293A PHE* 3.5 6.1 + - + +
294A PHE 3.4 0.4 - - - -
295A LEU* 1.3 77.4 - - - +
297A ILE* 1.3 64.5 + - + +
299A ASN* 4.2 1.3 - - - -
300A GLY* 3.8 15.6 + - - -
218B SER 4.9 0.2 - - - -
219B SER* 3.3 27.6 + - - -
246B ARG* 3.6 16.3 + - - -
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Residues in contact with ILE 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277A PHE* 3.8 26.7 - - + -
282A TYR* 3.7 47.6 - - + -
293A PHE* 3.3 50.2 + - + +
294A PHE* 3.9 7.2 - - - +
295A LEU 3.4 0.2 - - - -
296A ASP* 1.3 79.7 - - + +
298A ILE* 1.3 61.2 + - + +
299A ASN 3.2 4.8 + - - -
300A GLY* 3.5 2.3 + - - -
328A LEU* 3.3 25.5 - - - +
332A LEU* 3.8 17.9 - - + -
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Residues in contact with ILE 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A GLY* 4.2 3.6 - - - -
81A PRO* 3.8 23.3 - - + +
258A LEU* 4.1 21.5 - - + -
259A LEU 3.7 23.1 - - - +
260A ALA* 4.1 4.3 - - + +
265A MET* 3.8 31.6 - - + -
277A PHE* 4.8 10.3 - - + -
294A PHE 3.4 20.6 - - - +
295A LEU* 3.9 10.5 - - + -
297A ILE* 1.3 79.9 - - + +
299A ASN* 1.3 57.2 + - - +
300A GLY 3.7 0.4 - - - -
301A ASP* 4.3 2.1 - - - +
328A LEU* 5.0 1.3 - - - -
329A ILE* 3.8 20.2 - - - +
332A LEU* 3.9 18.2 - - + -
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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