Contacts of the helix formed by residues 270 - 284 (chain A) in PDB entry 4H3K
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 PHE 270 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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191A ILE* 3.9 16.2 - - + -
195A SER* 3.7 24.9 - - - -
229A TRP* 3.8 35.2 - + - -
232A GLY 5.4 1.8 - - - -
233A LYS* 4.8 14.4 - - + -
236A LEU* 3.5 29.8 - - + -
263A ILE* 3.7 27.8 - - + -
264A ALA* 5.0 0.7 - - - -
267A ARG* 3.0 22.5 + - + +
269A MET* 1.3 84.5 - - + +
271A MET* 1.3 66.4 + - - +
272A SER 3.1 4.2 + - - -
273A GLU* 3.2 21.4 + - - +
274A VAL* 3.0 23.9 + - + +
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Residues in contact with MET 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A ALA* 3.4 39.3 - - + +
265A ARG* 4.6 0.9 - - + +
267A ARG 4.2 0.8 + - - -
268A PRO* 2.9 20.0 + - + +
269A MET 3.3 0.4 - - - -
270A PHE* 1.3 78.0 - - - +
272A SER* 1.3 57.4 + - - +
274A VAL* 3.2 1.4 + - - +
275A ILE* 2.9 36.9 + - + +
308A VAL* 3.9 29.2 - - + -
311A HIS* 3.6 33.4 - - + +
313A ALA* 3.6 30.7 - - + +
314A SER* 3.7 10.1 - - - -
317A PHE* 3.9 18.4 - - + -
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Residues in contact with SER 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269A MET 4.8 3.1 + - - -
270A PHE 3.1 0.6 - - - -
271A MET* 1.3 79.2 - - - +
273A GLU* 1.3 65.8 + - - +
275A ILE* 3.4 2.1 + - - +
276A GLN* 2.9 30.0 + - - +
317A PHE* 3.7 30.7 - - - -
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Residues in contact with GLU 273 (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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236A LEU* 4.6 12.3 - - + +
240A LEU* 4.3 26.0 - - + +
269A MET 3.6 6.8 - - - +
270A PHE* 3.2 40.2 + - - +
272A SER* 1.3 83.3 - - - +
274A VAL* 1.3 62.8 + - + +
276A GLN* 3.5 7.1 + - - +
277A ALA* 3.0 23.6 + - - +
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Residues in contact with VAL 274 (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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236A LEU* 5.8 2.0 - - + -
240A LEU* 5.5 0.4 - - + -
260A LEU* 3.3 49.8 - - + +
261A ALA 4.6 0.2 - - - +
263A ILE* 4.8 6.7 - - + -
264A ALA* 3.9 19.7 - - + +
270A PHE* 3.0 18.1 + - + +
271A MET 3.2 7.4 + - - +
273A GLU* 1.3 76.1 - - + +
275A ILE* 1.3 70.1 + - + +
277A ALA* 3.1 8.9 + - - +
278A TYR* 3.0 49.9 + - + +
308A VAL* 4.8 1.6 - - + -
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Residues in contact with ILE 275 (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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271A MET* 2.9 23.7 + - + +
272A SER 3.9 3.8 - - - +
274A VAL* 1.3 76.6 - - + +
276A GLN* 1.3 63.3 + - - +
278A TYR* 3.1 21.6 + - + +
279A GLU* 2.9 30.1 + - + +
305A LEU* 4.4 3.6 - - + -
308A VAL* 3.9 16.8 - - + -
317A PHE* 4.3 17.5 - - + -
320A GLN* 3.9 33.2 - - + +
321A ILE* 3.8 35.7 - - + +
324A LEU* 5.3 4.9 - - + -
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Residues in contact with GLN 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A SER* 2.9 18.6 + - - +
273A GLU* 3.6 8.7 - - - +
275A ILE* 1.3 78.2 - - - +
277A ALA* 1.3 57.3 + - - +
279A GLU* 3.3 25.6 + - - +
280A THR* 2.9 46.6 + - - +
320A GLN* 5.8 0.4 - - - +
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Residues in contact with ALA 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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240A LEU* 3.8 14.1 - - + -
243A MET* 4.8 8.7 - - + +
244A VAL* 6.1 0.3 - - - +
257A LEU* 6.1 0.2 - - - -
260A LEU* 3.7 24.9 - - + -
273A GLU 3.0 14.6 + - - +
274A VAL 3.1 8.5 + - - +
276A GLN* 1.3 74.0 - - - +
278A TYR* 1.3 62.1 + - - +
280A THR* 3.5 7.1 + - - -
281A LEU* 3.0 30.1 + - - +
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Residues in contact with TYR 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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257A LEU* 2.8 56.3 + - + -
260A LEU* 4.3 12.8 - - + -
261A ALA* 3.3 21.5 + - - +
274A VAL* 3.0 29.8 + - + -
275A ILE* 3.1 13.9 + - + +
277A ALA* 1.3 79.0 - - - +
279A GLU* 1.3 57.5 + - - +
281A LEU* 3.5 3.0 + - - +
282A HIS* 2.9 30.8 + - - +
301A LEU* 3.8 18.4 - - + +
304A HIS* 3.5 23.9 - - + +
305A LEU* 3.4 33.0 - - + -
308A VAL* 4.4 6.7 - - + -
324A LEU* 4.1 3.6 - - + -
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Residues in contact with GLU 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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275A ILE* 2.9 21.2 + - + +
276A GLN* 3.4 31.3 + - - +
278A TYR* 1.3 75.9 - - - +
280A THR* 1.3 62.4 + - - +
282A HIS* 3.3 3.5 + - - +
283A ALA* 3.0 25.0 + - - +
320A GLN* 3.0 41.0 + - - +
324A LEU* 3.9 32.4 - - + +
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Residues in contact with THR 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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244A VAL* 4.0 26.7 - - + -
276A GLN* 2.9 32.6 + - - +
277A ALA* 3.6 7.1 - - - -
279A GLU* 1.3 72.5 - - - +
281A LEU* 1.3 66.1 + - - +
283A ALA* 3.3 1.9 + - - -
284A ASN* 2.8 47.4 + - + +
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Residues in contact with LEU 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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243A MET* 5.3 6.7 - - + +
244A VAL* 5.8 2.4 - - + +
253A LEU* 3.8 24.2 - - + -
257A LEU* 3.7 39.0 - - + -
277A ALA 3.0 17.5 + - - +
278A TYR* 3.8 4.0 - - - +
280A THR* 1.3 75.4 - - - +
282A HIS* 1.3 66.0 + - - +
284A ASN 2.9 14.7 + - - +
285A LEU* 3.1 18.3 + - + +
286A PRO* 3.6 31.0 - - + -
297A VAL* 4.3 8.3 - - + -
301A LEU* 4.4 14.4 - - + -
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Residues in contact with HIS 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A TYR 2.9 17.8 + - - +
279A GLU* 3.3 7.5 + - - +
281A LEU* 1.3 77.2 - - - +
283A ALA* 1.3 61.6 + - - +
284A ASN 3.6 0.2 + - - -
285A LEU* 4.4 10.9 - - - +
298A ARG* 5.8 4.4 + - + -
301A LEU* 3.8 14.4 - - + -
324A LEU* 4.2 21.7 - - + +
327A ASP* 3.1 46.8 + - + +
328A LEU* 3.6 32.6 - - + +
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Residues in contact with ALA 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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279A GLU 3.0 16.6 + - - +
280A THR* 4.8 0.9 - - - -
282A HIS* 1.3 79.0 + - - +
284A ASN* 1.3 75.9 + - - +
285A LEU* 4.0 6.2 + - - +
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Residues in contact with ASN 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 THR* 2.8 39.0 + - + +
281A LEU* 2.9 11.6 + - - +
283A ALA* 1.3 91.3 - - - +
285A LEU* 1.3 68.1 + - - +
286A PRO* 3.2 7.4 - - - +
332D GLN* 5.7 5.5 - - - +
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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