Contacts of the helix formed by residues 289 - 298 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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245B PRO 3.0 24.9 + - - +
246B ARG* 3.8 8.6 - - - +
247B TYR* 3.9 22.3 + - + +
250B PHE* 4.4 1.9 - - - +
284B CYS* 5.7 0.2 - - - -
287B TYR* 3.2 6.7 - - - +
288B ASN* 1.3 79.1 - - + +
290B PRO* 1.3 74.2 - - - +
291B ALA* 3.3 12.0 + - - +
292B ASP* 3.1 37.0 + - + +
293B PHE* 3.2 19.1 + - - +
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Residues in contact with PRO 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247B TYR* 3.6 25.4 - - + -
250B PHE* 3.6 28.3 - - + -
274B LEU* 4.3 25.4 - - + -
284B CYS* 5.2 4.7 - - - -
288B ASN 3.8 4.5 - - - +
289B ASN* 1.3 91.7 - - - +
291B ALA* 1.3 57.2 + - - +
293B PHE* 3.1 7.9 + - + +
294B PHE* 2.9 46.2 + - + -
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Residues in contact with ALA 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218A SER* 4.3 3.5 + - - -
79B LEU* 5.0 7.7 - - + +
245B PRO* 3.7 37.0 - - + +
250B PHE* 3.8 18.2 - - + -
289B ASN* 3.3 10.2 + - - +
290B PRO* 1.3 78.7 - - - +
292B ASP* 1.3 62.8 + - - +
293B PHE 3.3 0.4 + - - -
294B PHE* 4.3 9.4 - - - -
295B LEU* 3.5 27.7 + - - +
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Residues in contact with ASP 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218A SER* 3.0 24.7 + - - -
246A ARG* 3.6 42.8 + - - +
244B GLN* 5.2 1.4 - - - +
245B PRO* 4.6 2.6 - - - +
287B TYR* 4.6 11.2 - - + -
289B ASN* 3.1 38.2 + - + +
290B PRO 3.2 0.6 - - - -
291B ALA* 1.3 76.9 - - - +
293B PHE* 1.3 59.0 + - - +
295B LEU* 4.3 1.6 - - - +
296B ASP* 2.9 32.6 + - - +
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Residues in contact with PHE 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274B LEU* 4.0 17.5 - - + -
277B PHE* 4.3 9.2 - - + -
282B TYR* 3.6 34.5 - + + -
283B HIS 3.2 26.5 - - - -
284B CYS* 4.1 15.3 - - + -
287B TYR* 3.5 34.8 - + + -
289B ASN 3.2 11.3 + - - +
290B PRO* 3.1 9.5 + - + +
292B ASP* 1.3 78.4 - - - +
294B PHE* 1.3 75.7 + + - +
295B LEU 3.3 1.2 + - - -
296B ASP* 3.5 7.1 + - + +
297B ILE* 3.3 35.8 + - + +
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Residues in contact with PHE 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79B LEU* 6.2 1.1 - - + -
250B PHE* 3.5 30.1 - + - -
256B LEU* 3.7 25.8 - - + -
258B LEU* 4.3 13.2 - - + +
273B ALA* 3.6 7.2 - - + -
274B LEU* 3.6 47.6 - - + -
277B PHE* 3.7 30.3 - + - -
290B PRO* 2.9 23.0 + - + +
291B ALA* 3.8 2.9 + - + +
292B ASP 3.5 0.6 - - - -
293B PHE* 1.3 84.8 - + - +
295B LEU* 1.3 72.3 + - + +
297B ILE* 3.7 6.1 + - - +
298B ILE* 3.4 30.3 + - - +
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Residues in contact with LEU 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217A ASP* 3.6 27.1 - - + +
218A SER* 4.4 16.6 - - - +
219A SER* 3.4 7.8 - - - -
79B LEU* 3.7 37.0 - - + -
80B GLY 3.6 32.5 - - - +
81B PRO* 4.9 0.4 - - + -
243B HIS* 5.4 0.2 - - - +
244B GLN 6.1 0.7 - - - +
258B LEU* 4.2 4.5 - - + -
291B ALA 3.5 20.2 + - - +
292B ASP 4.2 0.9 + - - +
293B PHE 3.3 0.2 - - - -
294B PHE* 1.3 86.9 - - + +
296B ASP* 1.3 62.7 + - - +
297B ILE 3.4 0.4 - - - -
298B ILE* 3.9 15.0 - - + -
299B ASN* 3.2 23.8 - - + +
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Residues in contact with ASP 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218A SER* 5.6 0.2 - - - -
219A SER* 3.5 26.0 + - - -
246A ARG* 3.7 16.6 + - - -
287B TYR* 3.1 39.3 + - + +
292B ASP 2.9 20.6 + - - +
293B PHE* 3.5 5.9 + - + +
294B PHE 3.4 0.4 - - - -
295B LEU* 1.3 77.4 - - - +
297B ILE* 1.3 64.8 + - + +
299B ASN* 4.2 1.7 - - - -
300B GLY* 3.8 15.8 + - - -
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Residues in contact with ILE 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277B PHE* 3.8 26.7 - - + -
282B TYR* 3.7 48.7 - - + -
293B PHE* 3.3 49.5 + - + +
294B PHE* 3.9 7.2 - - - +
295B LEU 3.4 0.2 - - - -
296B ASP* 1.3 79.3 - - + +
298B ILE* 1.3 60.7 + - + +
299B ASN 3.2 5.5 + - - -
300B GLY* 3.5 2.1 + - - -
328B LEU* 3.3 24.3 - - - +
332B LEU* 3.8 17.4 - - + +
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Residues in contact with ILE 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80B GLY* 4.2 3.6 - - - -
81B PRO* 3.8 22.2 - - + +
258B LEU* 4.1 22.2 - - + -
259B LEU 3.7 22.2 - - - +
260B ALA* 4.1 5.4 - - + +
265B MET* 3.8 30.3 - - + -
277B PHE* 4.8 10.1 - - + -
294B PHE 3.4 19.7 - - - +
295B LEU* 3.9 10.8 - - + -
296B ASP 3.6 0.2 - - - -
297B ILE* 1.3 79.4 - - + +
299B ASN* 1.3 57.7 + - - +
300B GLY 3.7 0.4 - - - -
301B ASP* 4.3 2.9 - - - +
328B LEU* 5.0 1.1 - - - -
329B ILE* 3.8 19.8 - - - +
332B LEU* 3.9 18.4 - - + -
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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