Contacts of the helix formed by residues 265 - 281 (chain D) in PDB entry 3UYS
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 265 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254D PHE* 4.1 20.8 - - + -
263D LYS 3.8 1.8 + - - -
264D PRO* 1.3 70.1 - - - +
266D TYR* 1.3 64.6 + - - +
267D SER* 3.6 11.4 + - - -
268D TYR* 3.0 39.9 + - + +
269D LEU* 3.2 15.6 + - - +
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Residues in contact with TYR 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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113D ILE* 4.1 14.9 - - + +
117D GLU* 2.9 66.4 - - + +
120D HIS* 2.6 35.8 + - + +
192D ARG* 3.8 2.6 - - - -
196D LEU* 3.7 32.3 - - + -
263D LYS* 4.8 16.2 - - + -
264D PRO* 2.9 47.9 + - + +
265D ASP* 1.3 70.3 - - - +
267D SER* 1.3 63.5 - - - +
269D LEU* 3.1 9.0 + - - +
270D ARG* 2.9 33.9 + - - +
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Residues in contact with SER 267 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117D GLU* 5.0 1.9 + - - -
265D ASP* 3.1 10.9 + - - -
266D TYR* 1.3 79.1 - - - +
268D TYR* 1.3 60.8 + - - +
270D ARG* 3.5 5.5 + - - +
271D GLN* 3.1 23.4 + - - +
274D ARG* 4.6 0.3 + - - -
295D SO4 2.7 39.9 + - - -
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Residues in contact with TYR 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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250D THR* 3.6 20.8 - - + +
254D PHE* 3.7 41.7 - + + -
265D ASP* 3.0 29.2 + - + +
267D SER* 1.3 76.4 - - - +
269D LEU* 1.3 73.4 + - + +
271D GLN* 3.2 6.8 + - + +
272D LEU* 3.0 45.2 + - + +
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Residues in contact with LEU 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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113D ILE* 4.2 18.6 - - + -
196D LEU* 3.9 27.4 - - + -
251D TYR* 3.9 32.8 - - + +
254D PHE* 3.7 39.7 - - + -
255D CYS* 4.7 2.0 - - - -
264D PRO* 5.2 0.4 - - + -
265D ASP 3.2 12.3 + - - +
266D TYR* 3.1 12.7 + - - +
268D TYR* 1.3 81.6 - - + +
270D ARG* 1.3 60.1 + - - +
272D LEU* 3.0 34.5 + - + +
273D PHE* 3.4 12.3 + - - -
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Residues in contact with ARG 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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110D ASP* 3.7 27.1 - - - +
113D ILE* 3.8 27.0 - - + +
114D SER* 2.9 39.3 + - - +
117D GLU* 2.7 32.9 + - - -
266D TYR* 2.9 17.7 + - - +
267D SER* 3.7 8.6 + - - +
268D TYR 3.3 0.2 - - - -
269D LEU* 1.3 78.8 - - - +
271D GLN* 1.3 56.0 + - - +
273D PHE* 3.6 3.8 + - - +
274D ARG* 3.0 41.3 + - - +
295D SO4 2.7 44.6 + - - +
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Residues in contact with GLN 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 SER 3.1 16.1 + - - +
268D TYR* 3.2 6.9 + - + +
270D ARG* 1.3 74.6 - - - +
272D LEU* 1.3 67.7 + - - +
273D PHE 3.2 0.4 - - - -
274D ARG* 2.6 45.1 + - - +
275D ASN* 2.5 55.3 + - - +
278D HIS* 5.8 2.0 + - - -
295D SO4 4.9 1.0 + - - -
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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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247D GLU* 3.4 37.8 - - + +
250D THR* 3.7 37.0 - - + +
251D TYR* 4.3 12.8 - - + +
268D TYR* 3.0 40.2 + - + +
269D LEU* 3.0 26.7 - - + +
271D GLN* 1.3 79.3 - - - +
273D PHE* 1.3 67.3 + - + +
275D ASN* 4.0 3.5 - - - +
276D LEU 3.5 8.5 + - - -
279D ARG* 5.1 0.2 + - - -
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Residues in contact with PHE 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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106D LEU* 3.7 31.2 - - + +
109D ALA* 3.8 22.7 - - + -
110D ASP* 5.7 4.0 - - + +
113D ILE* 3.9 16.4 - - + -
203D LEU* 4.0 14.1 - - + -
247D GLU* 3.9 25.1 - - + -
248D PHE* 3.7 26.0 - + - -
251D TYR* 3.5 40.8 - + + -
269D LEU 3.4 14.6 + - - -
270D ARG* 3.6 5.1 + - - +
272D LEU* 1.3 81.4 - - + +
274D ARG* 1.3 54.3 + - - +
275D ASN 3.2 0.2 - - - -
276D LEU* 2.9 6.0 + - - +
277D PHE* 2.7 36.2 + - - +
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Residues in contact with ARG 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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110D ASP* 4.2 16.0 + - - +
270D ARG* 3.0 37.5 + - - +
271D GLN* 2.6 54.5 + - - +
273D PHE* 1.3 75.1 - - - +
275D ASN* 1.3 57.9 + - - +
277D PHE* 3.0 10.6 - - + +
278D HIS* 2.9 46.7 + - + +
284D TYR* 6.3 1.6 - - + -
295D SO4 2.7 50.0 + - - -
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Residues in contact with ASN 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 GLN* 2.5 56.3 + - - +
272D LEU* 4.0 4.2 - - - +
274D ARG* 1.3 73.9 - - - +
276D LEU* 1.3 59.3 + - - +
278D HIS* 4.0 5.7 + - - +
279D ARG* 3.0 42.5 + - - +
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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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102D LEU* 4.4 1.3 - - + -
106D LEU* 3.9 26.5 - - + -
245D PRO* 3.5 33.4 - - + -
247D GLU* 3.6 35.2 - - + +
248D PHE* 4.3 4.0 - - + -
272D LEU 3.5 3.0 + - - +
273D PHE 2.9 8.8 + - - +
275D ASN* 1.3 74.7 - - - +
277D PHE* 1.3 57.2 + - - +
279D ARG* 3.1 29.5 + - - +
280D GLN* 2.8 61.3 + - + +
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Residues in contact with PHE 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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103D LYS* 4.1 16.2 - - + -
106D LEU* 3.8 26.2 - - + +
107D LEU* 4.1 13.9 - - + -
273D PHE 2.7 12.4 + - - +
274D ARG* 3.0 15.0 - - + +
276D LEU* 1.3 75.4 - - - +
278D HIS* 1.3 78.1 + + - +
280D GLN* 2.9 20.8 + - - +
281D GLY 3.1 8.8 + - - -
282D PHE* 3.5 41.5 + + + -
283D SER 3.4 23.3 - - - -
284D TYR* 3.8 39.9 - + + -
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Residues in contact with HIS 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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271D GLN* 5.8 1.6 + - - -
274D ARG* 2.9 34.2 + - + +
275D ASN* 4.3 5.5 + - - +
277D PHE* 1.3 94.6 - + - +
279D ARG* 1.3 65.3 + - - +
281D GLY* 3.0 15.2 + - - +
282D PHE 4.5 7.9 - - - +
284D TYR* 5.4 6.8 + + - +
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Residues in contact with ARG 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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246D SER* 5.5 0.2 + - - -
247D GLU* 3.3 27.1 + - - -
272D LEU 5.1 0.6 + - - -
275D ASN* 3.0 40.5 + - - +
276D LEU* 3.1 28.7 + - + +
278D HIS* 1.3 77.4 - - - +
280D GLN* 1.3 67.5 + - + +
281D GLY* 3.4 0.7 + - - -
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Residues in contact with GLN 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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102D LEU* 3.6 20.5 - - + +
245D PRO* 5.6 2.2 - - - +
276D LEU* 2.8 33.2 + - + +
277D PHE 2.9 10.5 + - - +
279D ARG* 1.3 85.0 + - - +
281D GLY* 1.3 57.6 + - - +
282D PHE* 3.3 41.8 + - + -
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Residues in contact with GLY 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 PHE 3.1 1.2 + - - -
278D HIS* 3.0 17.4 + - - -
279D ARG 4.4 0.7 - - - -
280D GLN* 1.3 78.9 - - - +
282D PHE* 1.3 69.7 + - - +
283D SER* 4.6 3.1 + - - -
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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