Contacts of the helix formed by residues 269 - 282 (chain D) in PDB entry 5UHE
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 ASP 269 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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267D ASN 3.8 3.8 + - - +
268D PHE* 1.3 72.9 - - - +
270D ILE* 1.3 59.5 + - - +
271D ASP* 3.4 11.3 + - - +
272D ALA* 3.3 32.9 + - + +
273D GLU* 3.0 33.3 + - + +
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Residues in contact with ILE 270 (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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268D PHE* 3.4 28.2 + - + +
269D ASP* 1.3 73.6 + - - +
271D ASP* 1.3 65.9 + - - +
273D GLU 3.5 0.9 + - - -
274D ALA* 3.0 25.5 + - - +
299D VAL* 3.6 33.9 - - + +
302D PHE* 4.5 14.4 - - + +
303D GLN* 3.8 20.2 - - + +
309D PRO* 4.0 29.2 - - + -
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Residues in contact with ASP 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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269D ASP* 3.3 8.1 + - - +
270D ILE* 1.3 79.7 - - - +
272D ALA* 1.3 62.0 + - - +
274D ALA* 3.3 15.4 + - - +
275D GLU* 3.3 21.6 + - + +
303D GLN* 3.5 29.1 + - - +
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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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269D ASP* 3.3 31.8 + - + +
270D ILE 3.3 0.4 - - - -
271D ASP* 1.3 80.1 - - - +
273D GLU* 1.3 54.6 + - + +
274D ALA 3.1 0.2 - - - -
275D GLU* 3.5 5.1 + - - +
276D SER* 2.4 38.2 + - - +
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Residues in contact with GLU 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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119D ASP* 5.5 0.3 - - - +
232D LYS* 3.1 26.4 + - - -
268D PHE* 3.5 33.5 - - + -
269D ASP* 3.0 23.8 + - + +
270D ILE 3.8 2.0 - - - +
272D ALA* 1.3 76.3 - - + +
274D ALA* 1.3 58.8 + - - +
275D GLU 3.5 0.2 - - - -
276D SER* 4.0 9.1 - - - -
277D LEU* 3.2 33.5 + - + +
295D ARG* 3.4 23.1 + - - +
299D VAL* 4.6 4.0 - - + -
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Residues in contact with ALA 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 ILE 3.0 18.2 + - - +
271D ASP 3.3 7.4 - - - +
272D ALA 3.1 0.6 - - - -
273D GLU* 1.3 77.3 - - - +
275D GLU* 1.3 62.4 + - - +
277D LEU* 3.4 5.2 + - - +
278D ARG* 3.1 42.2 + - - +
296D LEU* 3.9 12.5 - - + +
299D VAL* 4.7 7.4 - - + -
303D GLN* 3.2 26.7 - - - +
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Residues in contact with GLU 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 ASP* 3.3 16.4 + - + +
272D ALA* 4.1 4.3 - - - +
274D ALA* 1.3 72.1 - - - +
276D SER* 1.3 61.0 + - - +
277D LEU 3.1 1.6 - - - -
278D ARG* 2.9 52.9 + - - +
279D ASP* 2.9 19.4 + - - +
303D GLN* 4.6 6.8 + - - -
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Residues in contact with SER 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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272D ALA* 2.4 26.1 + - - +
273D GLU* 4.0 10.9 - - - -
275D GLU* 1.3 76.9 - - - +
277D LEU* 1.3 59.2 + - - +
279D ASP* 3.8 8.3 + - - +
280D VAL* 3.2 25.8 + - - +
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Residues in contact with LEU 277 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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273D GLU* 3.2 24.4 + - - +
274D ALA 3.4 6.0 + - - +
275D GLU 3.1 0.4 - - - -
276D SER* 1.3 77.8 - - - +
278D ARG* 1.3 60.0 + - - +
279D ASP 3.1 1.6 - - - -
280D VAL* 3.1 10.1 + - + +
281D ILE* 3.0 30.9 + - - +
292D ALA* 4.0 28.0 - - + +
295D ARG* 3.9 50.9 - - + +
296D LEU* 4.0 21.8 - - + +
299D VAL* 4.0 17.5 - - + -
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Residues in contact with ARG 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 ALA* 3.1 36.7 + - - +
275D GLU* 2.9 43.5 + - - +
277D LEU* 1.3 78.0 - - - +
279D ASP* 1.3 58.6 + - - +
281D ILE* 3.3 12.3 + - + +
282D ARG* 2.9 36.9 + - + +
296D LEU* 4.2 29.8 - - + +
300D ALA* 4.4 9.5 - - - +
303D GLN* 3.8 16.3 + - - +
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Residues in contact with ASP 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 GLU* 2.9 15.9 + - - +
276D SER* 3.8 9.6 - - - +
278D ARG* 1.3 77.6 - - - +
280D VAL* 1.3 64.2 + - + +
281D ILE 3.2 0.4 - - - -
282D ARG* 3.4 13.9 + - - +
283D ASN* 3.4 27.3 + - - +
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Residues in contact with VAL 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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276D SER 3.2 18.4 - - - +
277D LEU* 3.1 11.3 + - + +
279D ASP* 1.3 76.6 - - + +
281D ILE* 1.3 62.5 + - - +
283D ASN* 3.5 25.2 + - + +
285D LYS 5.1 0.5 - - - +
288D LYS* 3.6 34.5 - - + +
289D LYS* 4.0 8.5 - - - +
292D ALA* 3.9 11.4 - - + -
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Residues in contact with ILE 281 (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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277D LEU 3.0 17.1 + - - +
278D ARG* 3.4 14.8 - - + +
279D ASP 3.2 0.4 - - - -
280D VAL* 1.3 76.2 - - - +
282D ARG* 1.3 67.7 + - - +
283D ASN 3.1 13.5 - - - +
289D LYS* 3.3 19.7 - - + +
292D ALA* 4.3 18.6 - - + +
293D LEU* 3.6 28.0 - - + -
296D LEU* 3.9 27.6 - - + -
1177D PRO* 4.0 24.2 - - + -
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Residues in contact with ARG 282 (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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278D ARG* 2.9 29.2 + - + +
279D ASP* 3.7 15.7 - - - +
280D VAL 3.4 0.2 - - - -
281D ILE* 1.3 85.3 - - - +
283D ASN* 1.3 63.6 + - - +
284D GLY 4.1 0.3 + - - -
1169D ASP* 4.6 13.1 + - - -
1170D SER* 4.9 10.8 + - - -
1171D GLY* 4.5 15.8 + - - +
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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