Contacts of the helix formed by residues 272 - 284 (chain D) in PDB entry 5JLH
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 GLY 272 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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177D LEU* 4.5 0.2 - - - -
260D LEU 3.3 14.1 - - - -
261D PHE* 4.2 7.8 + - - -
263D PRO* 3.7 16.9 - - - +
271D CYS* 1.3 77.1 - - - +
273D ILE* 1.3 65.8 + - - -
274D HIS 3.3 2.5 - - - -
275D GLU* 3.0 18.6 + - - +
276D THR* 3.0 19.3 + - - +
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Residues in contact with ILE 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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152D MET* 3.6 31.5 - - + +
159D THR* 4.7 3.4 - - + +
177D LEU* 3.7 18.8 - - + -
179D LEU* 4.3 4.5 - - + -
260D LEU* 3.1 41.0 + - + +
261D PHE* 3.7 24.5 - - + -
272D GLY* 1.3 70.2 - - - -
274D HIS* 1.3 60.5 + - - +
276D THR* 2.3 27.9 + - - -
277D THR* 2.9 17.6 + - - -
298D LEU* 6.4 0.4 - - + -
303D THR* 6.4 2.2 - - + -
308D ILE* 5.1 4.7 - - + -
312D MET* 3.4 27.1 - - + -
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Residues in contact with HIS 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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261D PHE* 3.5 29.0 - + + -
262D GLN* 5.5 2.5 - - - -
273D ILE* 1.3 81.6 + - - +
275D GLU* 1.3 102.6 + - - +
277D THR* 3.1 6.3 + - - -
278D PHE* 3.1 24.3 + - - +
311D ARG* 5.6 0.2 - - - -
312D MET* 3.9 19.1 - - - -
315D GLU* 2.9 57.3 + - + +
316D ILE* 4.1 11.7 - - + +
319D LEU* 4.0 16.1 - - + +
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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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261D PHE 4.8 1.9 - - - +
262D GLN* 5.9 0.3 + - - -
271D CYS* 3.7 22.8 - - + -
272D GLY* 3.0 19.6 - - - +
274D HIS* 1.3 119.0 + - + +
276D THR* 1.3 57.4 + - - +
278D PHE* 3.5 9.2 + - + +
279D ASN* 2.9 25.3 + - - +
319D LEU* 4.3 12.8 - - + +
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Residues in contact with THR 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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152D MET* 4.9 2.6 - - - +
159D THR* 5.7 0.3 - - - +
161D THR* 4.5 10.7 + - - -
175D LEU* 3.5 25.1 - - + +
177D LEU* 3.8 25.9 - - + +
271D CYS* 3.7 20.4 - - + +
272D GLY 3.0 12.7 + - - +
273D ILE* 2.3 31.2 + - - +
275D GLU* 1.3 72.4 - - - +
277D THR* 1.3 61.4 + - - +
279D ASN* 3.2 5.5 + - - +
280D SER* 2.9 30.4 + - - -
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Residues in contact with THR 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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150D ILE* 4.0 18.4 - - + -
152D MET* 4.3 14.0 - - + +
161D THR* 4.7 4.9 - - - +
273D ILE 2.9 14.0 + - - -
274D HIS 3.1 8.9 + - - -
276D THR* 1.3 76.5 + - - +
278D PHE* 1.3 58.0 + - - +
280D SER* 3.0 8.2 + - - -
281D ILE* 2.9 46.2 + - + +
296D THR* 4.9 6.9 - - + +
312D MET* 3.9 12.3 - - - +
316D ILE* 3.9 20.4 - - + -
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Residues in contact with PHE 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 HIS 3.1 12.2 + - - +
275D GLU* 3.5 11.2 - - + +
276D THR 3.3 0.2 - - - -
277D THR* 1.3 71.8 - - - +
279D ASN* 1.3 60.8 + - - +
281D ILE* 4.5 6.1 - - + +
282D MET* 2.8 57.6 + - + +
293D TYR* 3.9 19.5 - + - -
316D ILE* 3.9 22.0 - - + -
319D LEU* 3.3 39.9 - - + -
320D ALA* 3.3 38.6 - - + -
321D PRO* 5.4 1.6 - - + -
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Residues in contact with ASN 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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175D LEU* 3.5 27.2 - - + +
275D GLU 2.9 14.9 + - - +
276D THR* 3.2 11.4 + - - +
278D PHE* 1.3 75.6 - - - +
280D SER* 1.3 62.0 + - - +
282D MET* 3.7 4.8 + - - +
283D LYS* 3.3 44.4 + - - +
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Residues in contact with SER 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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150D ILE* 3.5 19.3 - - - -
161D THR* 3.3 17.1 - - - +
163D PRO* 4.6 4.3 - - - -
173D ALA* 3.4 25.1 + - - +
175D LEU* 3.5 11.1 - - - +
276D THR 2.9 14.9 + - - -
277D THR 3.0 7.4 + - - -
279D ASN* 1.3 75.5 - - - +
281D ILE* 1.3 66.1 + - - +
283D LYS* 3.1 16.0 + - - +
284D CYS* 3.1 14.5 - - - -
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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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150D ILE* 3.7 20.0 - - + -
277D THR* 2.9 36.8 + - + +
278D PHE* 4.0 5.4 - - + +
280D SER* 1.3 74.4 - - - +
282D MET* 1.3 59.1 + - + +
284D CYS* 3.0 24.2 + - - +
289D ARG* 2.9 43.4 + - + -
292D LEU* 4.1 26.7 - - + -
293D TYR* 3.7 43.3 - - + +
296D THR* 5.1 1.3 - - - +
316D ILE* 5.9 2.0 - - + -
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Residues in contact with MET 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 PHE* 2.8 40.5 + - + +
279D ASN* 4.1 5.6 - - - +
281D ILE* 1.3 78.0 - - + +
283D LYS* 1.3 59.3 + - + +
289D ARG* 2.7 52.4 + - - +
293D TYR* 3.2 26.7 - - - +
243E ASP* 4.6 4.7 - - - +
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Residues in contact with LYS 283 (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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186A ASP* 5.2 11.5 + - - +
172D HIS* 3.3 46.8 + - + +
173D ALA* 3.9 17.3 - - - +
174D ILE 5.7 0.9 - - - +
175D LEU* 5.5 8.3 - - + -
279D ASN* 3.3 38.4 + - - +
280D SER 3.1 10.6 + - - +
282D MET* 1.3 80.5 - - + +
284D CYS* 1.3 57.5 + - - +
285D ASP* 4.9 1.2 - - - +
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Residues in contact with CYS 284 (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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163D PRO* 4.0 4.9 - - - -
170D LEU* 3.7 30.5 - - + -
172D HIS* 4.7 1.6 - - - -
173D ALA* 4.0 7.4 - - - -
280D SER 3.1 18.4 - - - -
281D ILE* 3.0 19.1 + - - +
283D LYS* 1.3 80.2 - - - +
285D ASP* 1.3 69.1 + - - +
288D ILE* 4.1 8.7 - - + -
289D ARG* 2.8 27.6 + - + -
292D LEU* 3.8 17.5 - - + -
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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