Contacts of the helix formed by residues 267 - 281 (chain D) in PDB entry 6UZA
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 PHE 267 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336C CYS 3.7 20.0 - - - -
337C ARG 3.3 21.1 - - - -
338C ASN 3.5 15.9 - - - +
339C THR* 4.5 6.1 - - - -
342C VAL* 4.1 10.5 - - + -
382C ASN* 3.3 36.1 - - - -
385C GLN* 4.1 32.3 - - + -
265D ASP* 3.3 12.6 + - - +
266D SER* 1.3 76.7 + - - +
268D SER* 1.3 60.3 + - - +
269D HIS 3.2 1.3 + - - -
270D SER* 3.3 5.7 + - - -
271D ARG* 3.0 41.0 + - + +
314D PHE* 5.4 12.0 - + - -
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Residues in contact with SER 268 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337C ARG 3.8 17.9 + - - -
338C ASN* 4.6 7.1 + - - -
218D HIS* 4.3 23.2 + - - -
265D ASP* 3.4 27.5 + - - +
267D PHE* 1.3 76.1 - - - +
269D HIS* 1.3 60.3 + - - +
271D ARG* 3.8 8.0 - - - +
272D SER* 2.9 30.5 + - - -
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Residues in contact with HIS 269 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258D CYS* 4.3 16.8 + - + +
261D LYS* 3.8 40.0 - - + +
262D GLN* 4.5 21.9 + - + -
265D ASP 3.5 16.7 + - - +
266D SER* 4.4 7.4 - - - -
267D PHE 3.2 0.6 - - - -
268D SER* 1.3 79.3 + - - +
270D SER* 1.3 63.6 + - - +
272D SER* 2.6 24.4 + - - -
273D ARG* 3.0 35.7 + - + +
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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
----------------------------------------------------------
251D TYR* 5.9 1.4 - - - -
266D SER 3.3 15.1 + - - -
267D PHE* 3.3 8.5 + - - -
269D HIS* 1.3 78.5 - - - +
271D ARG* 1.3 60.7 + - - +
273D ARG* 3.4 10.7 + - - +
274D ILE* 3.0 30.0 + - - +
311D GLU* 4.1 13.4 + - - +
314D PHE* 3.8 30.7 - - - -
318D TYR* 5.2 0.3 + - - -
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Residues in contact with ARG 271 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334C ASP* 4.0 14.3 + - - -
335C LEU 5.1 0.8 + - - -
336C CYS 3.0 26.1 + - - -
337C ARG* 4.1 37.7 - - - +
382C ASN* 5.2 3.0 + - - +
217D SER* 4.9 8.1 + - - -
219D ASP* 4.4 0.4 - - - -
267D PHE* 3.0 31.3 + - + +
268D SER* 3.8 7.4 - - - +
270D SER* 1.3 77.9 - - - +
272D SER* 1.3 56.7 + - - +
274D ILE* 3.3 11.2 - - + +
275D ASN* 2.9 49.6 + - - +
314D PHE* 4.9 7.3 - - + -
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Residues in contact with SER 272 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218D HIS* 5.6 5.2 - - - -
219D ASP* 3.2 33.5 - - - +
261D LYS* 5.9 1.4 - - - +
268D SER 2.9 16.4 + - - -
269D HIS* 2.6 29.6 + - - -
271D ARG* 1.3 73.6 - - - +
273D ARG* 1.3 59.8 + - - +
275D ASN* 3.3 1.9 + - - +
276D ALA* 3.0 30.1 + - - +
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Residues in contact with ARG 273 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248D PRO* 4.2 16.8 - - + +
249D HIS* 3.1 34.1 + - - +
250D ASP 3.3 16.4 + - - -
251D TYR* 3.9 19.1 - - - +
269D HIS* 3.0 36.6 + - + +
270D SER* 3.7 8.1 - - - +
271D ARG 3.4 0.2 - - - -
272D SER* 1.3 77.3 + - - +
274D ILE* 1.3 57.2 + - - +
276D ALA* 3.4 2.6 + - - +
277D TYR* 3.0 41.4 + - + -
307D LEU* 3.7 22.4 - - - +
311D GLU* 3.7 19.0 + - - -
318D TYR* 3.4 22.2 - - - +
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Residues in contact with ILE 274 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270D SER 3.0 16.2 + - - +
271D ARG* 3.3 18.8 - - + +
273D ARG* 1.3 76.6 - - - +
275D ASN* 1.3 69.7 + - - +
277D TYR* 3.8 2.4 - - - +
278D LYS* 2.9 40.2 + - - +
314D PHE* 3.7 35.9 - - + +
317D ASP* 3.7 31.6 - - + +
318D TYR* 4.1 23.6 - - + +
321D LEU* 4.6 8.7 - - + -
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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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217D SER* 3.3 19.4 + - - -
219D ASP* 2.9 29.9 + - - +
220D VAL* 4.2 4.9 - - + +
224D ILE* 3.8 10.0 - - + +
228D HIS* 3.0 23.5 + - + -
271D ARG* 2.9 29.2 + - - +
272D SER 3.8 0.4 - - - +
273D ARG 3.3 0.4 - - - -
274D ILE* 1.3 78.7 - - - +
276D ALA* 1.3 59.1 + - - +
278D LYS* 3.3 22.4 + - - -
279D GLY 3.0 23.2 + - - -
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Residues in contact with ALA 276 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224D ILE* 4.5 16.1 - - + +
245D ILE* 4.0 6.0 - - + +
246D GLU 4.4 9.6 - - - +
248D PRO* 3.7 26.0 - - + -
272D SER 3.0 17.2 + - - +
273D ARG 3.8 0.2 - - - +
275D ASN* 1.3 77.5 - - - +
277D TYR* 1.3 57.3 + - - +
279D GLY* 3.3 1.7 + - - -
280D LEU* 2.9 32.8 + - - +
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Residues in contact with TYR 277 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247D ARG* 4.4 5.2 - - - +
248D PRO* 3.9 30.3 + - + +
249D HIS 4.7 1.9 + - - -
273D ARG* 3.0 40.1 + - + +
274D ILE 4.0 2.9 - - - +
276D ALA* 1.3 75.0 - - - +
278D LYS* 1.3 60.3 + - - +
280D LEU* 3.8 10.8 - - + +
281D ALA* 2.9 34.1 + - - +
300D LEU* 4.3 14.4 - - + -
303D GLU* 2.6 37.2 + - + +
304D LEU* 3.8 27.1 - - + -
307D LEU* 3.7 26.5 - - + +
318D TYR* 4.1 15.9 - + + -
321D LEU* 4.1 7.9 - - + -
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Residues in contact with LYS 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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227D ALA 4.9 0.2 - - - +
228D HIS* 3.6 31.2 - - + +
274D ILE* 2.9 31.5 + - - +
275D ASN* 3.6 16.9 + - - +
276D ALA 3.3 0.2 - - - -
277D TYR* 1.3 76.7 - - - +
279D GLY* 1.3 61.1 + - - +
281D ALA 3.9 5.9 + - - -
282D SER* 4.1 12.1 + - - -
317D ASP* 6.3 3.4 - - - -
321D LEU* 3.9 27.0 - - + +
324D GLN* 4.6 4.1 + - - +
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Residues in contact with GLY 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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224D ILE* 4.6 2.5 - - - -
227D ALA* 3.6 8.5 - - - +
228D HIS* 3.3 17.4 + - - -
245D ILE* 3.5 25.4 - - - +
275D ASN 3.0 12.9 + - - -
276D ALA 3.8 2.7 - - - -
277D TYR 3.2 0.2 - - - -
278D LYS* 1.3 76.6 - - - +
280D LEU* 1.3 61.4 + - - +
282D SER* 3.5 16.1 + - - -
285D TYR* 3.8 4.3 - - - +
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Residues in contact with LEU 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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245D ILE* 3.9 23.8 - - + +
247D ARG* 3.9 54.1 - - + +
248D PRO* 4.1 9.6 - - + -
276D ALA 2.9 19.9 + - - +
277D TYR* 3.3 15.0 + - + +
279D GLY* 1.3 77.1 - - - +
281D ALA* 1.3 56.4 + - - +
282D SER 3.3 5.0 + - - -
285D TYR* 3.7 33.3 - - + -
286D LEU* 3.8 13.5 - - - +
300D LEU* 3.4 19.6 - - + +
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Residues in contact with ALA 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 TYR 2.9 17.7 + - - +
278D LYS 3.9 1.8 + - - +
279D GLY 3.3 0.6 - - - -
280D LEU* 1.3 76.0 - - - +
282D SER* 1.3 52.9 + - - +
283D PRO* 4.4 0.5 - - - +
286D LEU* 4.5 6.1 - - - +
300D LEU* 3.8 8.3 - - + -
304D LEU* 4.0 15.5 - - + -
321D LEU* 4.2 9.9 - - + +
324D GLN* 2.4 43.1 + - - +
325D CYS* 3.6 22.1 + - - -
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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