Contacts of the helix formed by residues 264 - 275 (chain D) in PDB entry 5UQ9
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 264 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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188D ASN* 4.6 2.2 - - - -
189D GLY* 4.2 9.8 - - - -
192D TYR* 3.4 27.2 + - - -
263D THR* 1.3 79.4 - - - +
265D LYS* 1.3 62.9 + - - +
266D TRP 3.3 1.6 - - - -
267D THR* 3.3 26.4 + - - -
268D ALA 3.7 1.9 + - - -
281D ILE* 4.3 0.5 - - - +
285D VAL* 3.5 16.1 - - - +
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Residues in contact with LYS 265 (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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272C LEU* 3.2 29.4 + - + +
273C GLU* 3.2 27.6 + - - +
275C GLY* 5.3 1.0 - - - +
192D TYR* 5.0 0.6 - - - -
260D GLN* 5.4 3.0 + - - -
261D LYS 3.8 13.0 + - - -
262D GLY* 3.4 30.7 - - - +
263D THR 4.3 0.6 - - - +
264D GLY* 1.3 73.0 - - - +
266D TRP* 1.3 78.6 + - + +
267D THR 3.0 4.9 - - - -
268D ALA* 2.8 6.6 + - - +
269D ILE* 2.6 45.6 + - + +
285D VAL* 3.9 28.2 - - + +
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Residues in contact with TRP 266 (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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273C GLU* 5.2 12.6 - - + -
105D GLU* 4.5 26.0 - - - +
107D ARG* 6.2 1.3 - - - -
185D MET* 3.2 19.5 - - + +
262D GLY 4.7 0.8 + - - -
263D THR* 3.4 34.6 + - - +
264D GLY 3.3 0.8 - - - -
265D LYS* 1.3 100.7 - - + +
267D THR* 1.3 56.7 + - - +
269D ILE* 3.8 33.8 - - + +
270D SER* 3.0 27.5 + - - -
273D GLU* 5.9 0.4 - - - -
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Residues in contact with THR 267 (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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185D MET* 2.4 37.3 + - - +
186D VAL* 3.9 17.0 - - + -
189D GLY* 3.3 13.7 + - - -
263D THR 4.8 0.4 + - - -
264D GLY* 3.3 12.8 + - - -
265D LYS 3.0 0.6 - - - -
266D TRP* 1.3 78.5 - - - +
268D ALA* 1.3 62.3 + - - +
270D SER* 3.5 3.7 + - - -
271D ALA* 3.1 18.0 + - - +
278D VAL* 5.1 1.9 - - + +
281D ILE* 3.8 29.2 - - + -
341D LEU* 3.7 18.7 - - + +
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Residues in contact with ALA 268 (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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272C LEU* 3.7 22.7 - - + -
286C PHE* 4.3 5.8 - - + -
264D GLY 3.7 2.4 + - - +
265D LYS* 2.8 11.1 + - - +
267D THR* 1.3 75.5 - - - +
269D ILE* 1.3 66.9 + - - +
271D ALA* 3.2 9.2 + - - +
272D LEU* 3.1 25.1 + - - +
278D VAL* 5.4 1.3 - - - -
281D ILE* 4.5 5.6 - - + +
282D GLY* 4.0 28.7 - - - +
285D VAL* 4.8 1.6 - - + -
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Residues in contact with ILE 269 (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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269C ILE* 3.9 20.2 - - + +
272C LEU* 3.6 34.1 - - + -
273C GLU* 4.0 20.9 - - + +
265D LYS* 2.6 30.9 + - + +
266D TRP* 3.8 37.9 - - + -
268D ALA* 1.3 72.2 - - - +
270D SER* 1.3 58.5 + - - +
272D LEU* 3.2 6.2 + - - +
273D GLU* 2.8 49.6 + - - +
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Residues in contact with SER 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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106D TYR* 4.4 2.9 + - - -
107D ARG* 5.8 0.2 - - - -
182D PHE* 3.7 14.7 - - - -
185D MET* 3.9 13.8 - - - +
266D TRP 3.0 22.9 + - - -
267D THR 3.7 5.2 - - - -
268D ALA 3.3 0.2 - - - -
269D ILE* 1.3 76.2 - - - +
271D ALA* 1.3 58.5 + - - +
273D GLU* 3.4 12.2 + - - +
274D TYR* 3.0 53.9 + - - +
341D LEU* 4.0 5.5 - - - +
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Residues in contact with ALA 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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286C PHE* 3.9 6.5 - - + -
267D THR 3.1 12.2 + - - +
268D ALA 3.2 10.1 + - - +
270D SER* 1.3 76.5 - - - +
272D LEU* 1.3 51.7 + - - +
274D TYR 3.3 0.5 + - - -
275D GLY 2.6 32.2 + - - -
276D VAL 2.9 29.4 + - - +
278D VAL* 3.6 28.5 - - + -
341D LEU* 3.8 12.3 - - + +
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Residues in contact with LEU 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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265C LYS* 2.2 40.6 + - + +
268C ALA* 3.6 29.2 - - + -
269C ILE* 3.7 26.9 - - + +
272C LEU* 3.7 28.3 - - + -
282C GLY* 4.6 1.6 - - - +
285C VAL* 3.8 31.2 - - + -
286C PHE* 3.5 31.2 - - + -
268D ALA 3.1 8.9 + - - +
269D ILE* 3.7 2.2 - - - +
271D ALA* 1.3 75.3 - - - +
273D GLU* 1.3 56.4 + - - +
274D TYR 3.4 0.3 + - - -
275D GLY* 3.5 4.5 + - - -
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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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265C LYS* 4.2 12.3 + - - +
266C TRP* 5.0 11.9 - - + -
269C ILE* 3.8 19.6 - - + +
106D TYR* 4.6 0.2 + - - -
107D ARG* 2.6 32.9 + - - -
266D TRP* 5.9 0.7 - - - -
269D ILE* 2.8 36.3 + - - +
270D SER* 3.8 10.6 - - - +
271D ALA 3.3 0.2 - - - -
272D LEU* 1.3 76.8 - - - +
274D TYR* 1.3 71.7 + - + +
275D GLY 3.9 0.2 + - - -
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Residues in contact with TYR 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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106D TYR* 2.5 26.4 + - - -
107D ARG* 4.1 8.4 + - - -
182D PHE* 4.1 12.8 - + - -
270D SER* 3.0 41.1 + - - +
271D ALA 3.4 1.3 - - - +
273D GLU* 1.3 86.5 - - + +
275D GLY* 1.3 63.5 + - - +
276D VAL* 3.6 9.3 + - + +
341D LEU* 4.3 8.5 - - + -
344D GLN* 4.0 29.3 + - + +
345D ALA* 4.8 8.3 - - + -
348D GLU* 4.0 31.9 - - + -
349D PHE* 3.2 27.5 - + - -
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Residues in contact with GLY 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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261C LYS* 4.6 12.1 + - - -
265C LYS* 4.5 4.2 - - - +
289C CYS* 3.5 35.6 - - - +
292C SER* 5.4 0.5 + - - -
293C LEU* 5.3 4.7 - - - +
271D ALA 2.6 13.4 + - - -
272D LEU 3.5 6.0 + - - -
273D GLU 3.5 2.6 - - - -
274D TYR* 1.3 76.3 - - - +
276D VAL* 1.3 57.6 + - - +
277D PRO* 4.1 2.1 - - - +
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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