Contacts of the helix formed by residues 270 - 280 (chain D) in PDB entry 4XH9
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 GLN 270 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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266D TYR* 4.0 16.1 - - + +
267D CYS* 3.5 22.9 - - - +
268D SER 3.4 2.0 - - - -
269D ASN* 1.3 77.7 - - - +
271D LEU* 1.3 62.7 + - - +
272D ALA 3.3 1.1 - - - -
273D ALA* 3.3 6.1 + - + +
274D LYS* 2.9 30.7 + - - +
305D TRP* 3.4 39.7 - - + -
308D LEU* 4.0 12.9 + - + +
309D ASP* 2.7 38.2 + - - +
312D ARG* 3.9 15.1 + - - +
72E LEU* 4.0 18.1 - - + +
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Residues in contact with LEU 271 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267D CYS 4.8 1.2 + - - -
268D SER 4.7 6.5 + - - +
270D GLN* 1.3 79.5 - - - +
272D ALA* 1.3 57.5 + - - +
274D LYS* 3.3 10.9 + - + +
275D ALA* 3.0 24.8 + - + +
357D LYS* 4.8 14.6 - - + +
361D GLU* 4.6 26.5 - - + +
364D TYR* 3.8 39.0 - - + +
365D TYR* 4.5 13.5 - - + +
72E LEU* 4.2 19.8 - - + +
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Residues in contact with ALA 272 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217D HIS* 3.5 31.9 + - + +
268D SER 5.3 0.6 + - - +
269D ASN* 3.9 15.4 - - - +
270D GLN 3.3 1.6 - - - +
271D LEU* 1.3 77.2 - - - +
273D ALA* 1.3 66.1 + - - +
275D ALA* 3.2 4.2 + - - +
276D LEU* 3.1 17.8 + - - +
364D TYR* 4.1 28.9 - - + -
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Residues in contact with ALA 273 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217D HIS* 4.0 11.6 + - - +
218D ILE* 3.7 38.7 - - + +
266D TYR* 6.4 0.2 - - + -
269D ASN* 3.8 16.3 + - - +
270D GLN* 3.3 12.4 + - + +
272D ALA* 1.3 79.2 - - - +
274D LYS* 1.3 57.0 + - - +
276D LEU* 3.3 4.7 + - - +
277D LEU* 3.0 32.8 + - - +
305D TRP* 5.0 5.4 - - + -
308D LEU* 5.3 1.6 - - + -
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Residues in contact with LYS 274 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270D GLN 2.9 17.3 + - - +
271D LEU* 3.6 10.5 - - + +
272D ALA 3.3 0.2 - - - -
273D ALA* 1.3 73.9 - - - +
275D ALA* 1.3 61.3 + - - +
277D LEU* 3.3 9.6 + - + +
278D ASP* 2.9 58.1 + - - +
281D LYS* 5.4 1.4 - - - +
303D ASP* 5.7 0.6 + - - -
305D TRP* 3.6 58.5 - - + +
72E LEU* 5.7 1.6 - - + -
75E PRO* 3.8 25.5 - - + +
76E ASP* 2.5 30.7 + - - -
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Residues in contact with ALA 275 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271D LEU* 3.0 14.2 + - + +
272D ALA 3.4 10.1 - - - +
273D ALA 3.2 0.2 - - - -
274D LYS* 1.3 77.0 - - - +
276D LEU* 1.3 62.3 + - - +
278D ASP* 3.2 9.8 + - - +
279D GLN* 3.0 32.6 + - - +
364D TYR* 3.4 26.5 - - + +
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Residues in contact with LEU 276 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214D GLU* 3.7 40.4 - - + +
217D HIS* 3.7 25.1 - - + -
218D ILE* 3.8 14.1 - - + -
272D ALA 3.1 12.0 + - - +
273D ALA 3.3 6.9 + - - +
275D ALA* 1.3 73.0 - - - +
277D LEU* 1.3 65.9 + - - +
279D GLN* 3.1 31.8 + - - +
280D LYS* 3.1 44.4 + - + +
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Residues in contact with LEU 277 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210D MET* 4.9 7.6 - - + -
218D ILE* 4.0 21.1 - - + -
273D ALA 3.0 16.3 + - - +
274D LYS* 3.5 12.8 - - + +
276D LEU* 1.3 76.9 - - - +
278D ASP* 1.3 64.5 + - - +
280D LYS* 3.1 19.9 + - + +
281D LYS* 3.4 13.4 + - - +
286D VAL* 5.6 2.2 - - + -
287D GLN* 4.8 1.4 - - - +
290D LEU* 5.2 11.4 - - + -
304D LEU* 4.1 23.6 - - + -
305D TRP* 4.1 21.5 - - + +
308D LEU* 3.6 29.6 - - + -
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Residues in contact with ASP 278 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274D LYS* 2.9 49.3 + - - +
275D ALA* 3.5 8.9 - - - +
276D LEU 3.2 0.2 - - - -
277D LEU* 1.3 74.4 - - - +
279D GLN* 1.3 65.3 + - - +
281D LYS* 3.3 43.0 + - + +
282D GLN* 5.4 1.9 + - - +
75E PRO* 5.8 0.7 - - - +
76E ASP* 4.5 2.6 - - - +
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Residues in contact with GLN 279 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275D ALA* 3.0 23.2 + - - +
276D LEU* 3.1 31.7 + - + +
278D ASP* 1.3 76.6 - - - +
280D LYS* 1.3 60.2 + - + +
281D LYS 3.1 4.6 + - - -
282D GLN* 3.3 29.8 + - - +
283D ASP 4.6 0.2 + - - -
420D GLU* 3.6 32.9 - - + +
421D ARG* 5.1 10.9 - - - +
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Residues in contact with LYS 280 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209D ILE 5.5 0.8 + - - -
210D MET* 3.9 22.0 - - - +
214D GLU* 2.8 39.6 + - - -
276D LEU* 3.3 26.2 - - + +
277D LEU* 3.1 13.1 + - + +
279D GLN* 1.3 75.7 - - - +
281D LYS* 1.3 55.7 + - - +
282D GLN 3.0 5.6 - - - -
283D ASP* 3.0 37.3 + - + +
286D VAL* 3.9 29.0 - - + +
287D GLN* 2.8 13.6 - - - +
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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