Contacts of the helix formed by residues 275 - 287 (chain A) in PDB entry 4BHT
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 275 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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252A MET* 3.4 8.9 - - - +
272A SER 5.9 0.2 - - - +
273A GLY 3.6 8.7 + - - +
274A PHE* 1.3 80.1 - - - +
276A LYS* 1.3 55.0 + - - +
277A GLU* 2.6 27.4 + - - +
278A LYS* 3.1 33.1 + - + +
279A LEU* 2.9 29.8 + - - +
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Residues in contact with LYS 276 (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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252A MET* 3.8 19.0 - - + -
275A THR* 1.3 71.0 - - - +
277A GLU* 1.3 69.2 + - + +
279A LEU* 3.9 1.8 - - - +
280A ALA* 3.0 31.9 + - - +
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Residues in contact with GLU 277 (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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275A THR* 2.6 32.6 + - - +
276A LYS* 1.3 80.9 + - - +
278A LYS* 1.3 64.1 + - + +
280A ALA* 3.6 6.0 + - - +
281A ARG* 3.4 17.5 + - - +
300A PHE* 4.4 7.1 - - + -
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Residues in contact with LYS 278 (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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270A ASP* 2.7 31.5 + - - +
272A SER* 3.4 19.2 + - - -
273A GLY 3.6 6.0 + - - +
274A PHE* 4.3 2.5 - - + -
275A THR* 3.1 34.1 + - - +
277A GLU* 1.3 83.4 - - + +
279A LEU* 1.3 63.1 + - - +
281A ARG* 3.1 12.1 + - - +
282A LEU 3.1 9.9 + - - -
296A TYR* 3.4 27.8 - - - +
300A PHE* 3.7 42.6 - - + -
302A LEU* 4.5 5.4 - - + +
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Residues in contact with LEU 279 (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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245A GLN* 3.6 33.7 - - + +
246A TYR* 5.5 0.2 - - + -
248A ILE* 4.2 11.9 - - + -
249A GLU* 3.6 37.5 - - + +
252A MET* 3.9 11.0 - - + -
274A PHE* 4.0 19.9 - - + -
275A THR 2.9 18.5 + - - +
276A LYS* 4.0 2.9 - - - +
278A LYS* 1.3 76.2 - - - +
280A ALA* 1.3 64.1 + - - +
282A LEU* 3.2 11.1 + - + +
283A ILE* 3.0 40.8 + - + +
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Residues in contact with ALA 280 (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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276A LYS 3.0 19.4 + - - +
277A GLU* 3.7 7.4 - - - +
279A LEU* 1.3 77.4 - - - +
281A ARG* 1.3 56.5 + - - +
283A ILE* 3.2 13.0 + - - +
284A GLU* 3.0 35.6 + - - +
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Residues in contact with ARG 281 (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 GLU 3.4 7.5 + - - +
278A LYS 3.1 9.0 + - - +
280A ALA* 1.3 76.4 - - - +
282A LEU* 1.3 64.2 + - - +
284A GLU* 3.0 40.3 + - - +
285A ILE* 3.0 51.7 + - + +
296A TYR* 4.9 0.2 - - + -
299A GLU* 2.8 43.2 + - - +
300A PHE* 3.9 17.7 - - + -
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Residues in contact with LEU 282 (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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240A SER* 4.6 10.8 - - - +
245A GLN* 5.2 4.7 - - + -
248A ILE* 4.8 3.1 - - + -
261A ALA* 4.0 15.5 - - + -
274A PHE* 3.8 28.0 - - + -
278A LYS 3.1 8.9 + - - +
279A LEU* 3.7 18.4 - - + +
281A ARG* 1.3 75.0 - - - +
283A ILE* 1.3 57.6 + - - +
285A ILE* 3.2 5.4 + - + +
286A LYS* 2.8 53.8 + - + +
293A VAL* 4.6 14.8 - - + -
296A TYR* 3.9 41.3 - - + -
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Residues in contact with ILE 283 (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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245A GLN* 3.6 34.6 + - + +
246A TYR* 3.9 35.9 - - + +
249A GLU* 5.1 2.5 - - - +
279A LEU* 3.0 39.1 + - + +
280A ALA* 3.2 12.5 + - - +
282A LEU* 1.3 76.0 - - - +
284A GLU* 1.3 58.6 + - + +
286A LYS* 3.3 1.2 + - - +
287A ALA* 2.8 33.7 + - + +
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Residues in contact with GLU 284 (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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280A ALA* 3.0 21.2 + - - +
281A ARG* 3.0 39.7 + - - +
283A ILE* 1.3 77.4 - - + +
285A ILE* 1.3 63.5 + - - +
287A ALA* 3.2 20.1 + - - +
288A SER* 4.1 1.7 + - - -
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Residues in contact with ILE 285 (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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281A ARG* 3.0 60.3 + - + +
282A LEU* 3.6 5.8 - - + +
284A GLU* 1.3 75.7 - - - +
286A LYS* 1.3 63.5 + - + +
287A ALA 3.3 0.3 + - - -
288A SER* 3.5 9.7 + - - -
291A GLY* 3.5 16.2 - - - -
292A ARG 3.6 36.3 - - - +
295A ASP* 4.6 7.0 - - + -
296A TYR* 3.8 33.2 - - + +
299A GLU* 4.2 4.9 - - - +
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Residues in contact with LYS 286 (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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240A SER* 3.4 36.6 + - - +
241A GLY* 5.5 0.9 - - - -
245A GLN* 3.6 21.6 + - - +
263A ASP* 3.2 27.4 + - - +
282A LEU* 2.8 30.8 + - + +
283A ILE 3.5 1.6 - - - +
285A ILE* 1.3 73.3 - - + +
287A ALA* 1.3 59.9 + - - +
288A SER 2.8 18.2 - - - +
289A ARG 5.9 0.6 + - - -
291A GLY 2.9 30.0 + - - +
292A ARG* 4.0 5.7 - - - +
293A VAL* 3.9 11.0 - - - +
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Residues in contact with ALA 287 (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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283A ILE* 2.8 18.6 + - + +
284A GLU* 3.2 14.4 + - - +
286A LYS* 1.3 77.8 - - - +
288A SER* 1.3 57.5 + - - +
289A ARG* 5.6 0.9 - - - +
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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